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Gentoo's Bugzilla – Attachment 863516 Details for
Bug 908020
sci-chemistry/votca-2022.1 fails tests (MUSL-SYSTEM)
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1-LastTest.log
1-LastTest.log (text/plain), 235.28 KB, created by
Agostino Sarubbo
on 2023-06-07 14:46:31 UTC
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Description:
1-LastTest.log
Filename:
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Creator:
Agostino Sarubbo
Created:
2023-06-07 14:46:31 UTC
Size:
235.28 KB
patch
obsolete
>Start testing: Jun 07 13:12 UTC >---------------------------------------------------------- >55/157 Testing: integration_Run_gmx_grompp_re >55/157 Test: integration_Run_gmx_grompp_re >Command: "/usr/bin/gmx" "grompp" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx >"integration_Run_gmx_grompp_re" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- > :-) GROMACS - gmx grompp, 2023.1 (-: > >Executable: /usr/bin/gmx >Data prefix: /usr >Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx >Command line: > gmx grompp > >Ignoring obsolete mdp entry 'title' > >NOTE 1 [file grompp.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > >NOTE 2 [file grompp.mdp]: > You have set rlist larger than the interaction cut-off, but you also have > verlet-buffer-tolerance > 0. Will set rlist using > verlet-buffer-tolerance. > >Setting the LD random seed to 2079299067 >Number of degrees of freedom in T-Coupling group System is 645.00 > >There were 2 NOTEs > >GROMACS reminds you: "You're Insignificant" (Tricky) > > >Generated 1 of the 1 non-bonded parameter combinations > >Excluding 1 bonded neighbours molecule type 'SOL' >Analysing residue names: >There are: 216 Water residues > >Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > >Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm > >Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm > >Note that mdrun will redetermine rlist based on the actual pair-list setup > >This run will generate roughly 0 Mb of data ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_gmx_grompp_re" end time: Jun 07 13:12 UTC >"integration_Run_gmx_grompp_re" time elapsed: 00:00:00 >---------------------------------------------------------- > >123/157 Testing: integration_Run_gmx_grompp_ppy >123/157 Test: integration_Run_gmx_grompp_ppy >Command: "/usr/bin/gmx" "grompp" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy >"integration_Run_gmx_grompp_ppy" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- > :-) GROMACS - gmx grompp, 2023.1 (-: > >Executable: /usr/bin/gmx >Data prefix: /usr >Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy >Command line: > gmx grompp > > >NOTE 1 [file grompp.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > >NOTE 2 [file grompp.mdp]: > You have set rlist larger than the interaction cut-off, but you also have > verlet-buffer-tolerance > 0. Will set rlist using > verlet-buffer-tolerance. > >Setting the LD random seed to -639238274 >Generating 1-4 interactions: fudge = 0.5 > >NOTE 3 [file topol.top, line 484]: > The bond in molecule-type Protein between atoms 1 N and 2 HN has an > estimated oscillational period of 1.0e-02 ps, which is less than 10 times > the time step of 2.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > >Number of degrees of freedom in T-Coupling group System is 243.00 > >There were 3 NOTEs > >GROMACS reminds you: "You're Insignificant" (Tricky) > > >Generated 28 of the 28 non-bonded parameter combinations > >Generated 28 of the 28 1-4 parameter combinations > >Excluding 3 bonded neighbours molecule type 'Protein' >Analysing residue names: >There are: 10 Other residues >Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... > >Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > >Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm > >Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm > >Note that mdrun will redetermine rlist based on the actual pair-list setup > >This run will generate roughly 0 Mb of data ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_gmx_grompp_ppy" end time: Jun 07 13:12 UTC >"integration_Run_gmx_grompp_ppy" time elapsed: 00:00:00 >---------------------------------------------------------- > >126/157 Testing: integration_Run_gmx_grompp_mma >126/157 Test: integration_Run_gmx_grompp_mma >Command: "/usr/bin/gmx" "grompp" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma >"integration_Run_gmx_grompp_mma" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- > :-) GROMACS - gmx grompp, 2023.1 (-: > >Executable: /usr/bin/gmx >Data prefix: /usr >Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma >Command line: > gmx grompp > >Ignoring obsolete mdp entry 'andersen_seed' >Ignoring obsolete mdp entry 'optimize_fft' >Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' >Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision' >Setting the LD random seed to 1591865191 >Generating 1-4 interactions: fudge = 0.5 > >NOTE 1 [file topol.top, line 522]: > The bond in molecule-type 3-MMA between atoms 17 C2 and 18 H4 has an > estimated oscillational period of 1.2e-02 ps, which is less than 10 times > the time step of 2.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > >Number of degrees of freedom in T-Coupling group System is 156.00 > >NOTE 2 [file grompp.mdp]: > You are using a plain Coulomb cut-off, which might produce artifacts. > You might want to consider using PME electrostatics. > > > >NOTE 3 [file grompp.mdp]: > This run will generate roughly 2997 Mb of data > > >NOTE 4 [file grompp.mdp]: > COM removal frequency is set to (705032704). > Other settings require a global communication frequency of 100. > Note that this will require additional global communication steps, > which will reduce performance when using multiple ranks. > Consider setting nstcomm to a multiple of 100. > > >There were 4 NOTEs > >GROMACS reminds you: "You're Insignificant" (Tricky) > > >Generated 21 of the 21 non-bonded parameter combinations > >Generated 21 of the 21 1-4 parameter combinations > >Excluding 3 bonded neighbours molecule type '3-MMA' > >Setting gen_seed to -1075970059 > >Velocities were taken from a Maxwell distribution at 600 K >Analysing residue names: >There are: 3 Other residues >Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... > >Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 600 K > >Calculated rlist for 1x1 atom pair-list as 1.052 nm, buffer size 0.152 nm > >Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.116 nm > >Note that mdrun will redetermine rlist based on the actual pair-list setup ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_gmx_grompp_mma" end time: Jun 07 13:12 UTC >"integration_Run_gmx_grompp_mma" time elapsed: 00:00:00 >---------------------------------------------------------- > >50/157 Testing: integration_Run_csg_reupdate >50/157 Test: integration_Run_csg_reupdate >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--gentable" "true" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate >"integration_Run_csg_reupdate" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Writing CG parameters and potential(s) >Writing file: CG-CG.pot.new >CG-CG potential's extrapolated core is attractive! >Artifically enforcing repulsive core. > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_reupdate" end time: Jun 07 13:12 UTC >"integration_Run_csg_reupdate" time elapsed: 00:00:00 >---------------------------------------------------------- > >52/157 Testing: integration_Run_csg_reupdate2 >52/157 Test: integration_Run_csg_reupdate2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol_cg.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame_cg.dump" "--hessian-check" "no" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 >"integration_Run_csg_reupdate2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >I have 216 beads in 216 molecules >Reading frame, timestep 0 >We have CG-CG CG potential > Between beads CG-CG > With Function form cbspl > And 4 parameters to optimize >Potential range: > rmin = 0.26 [nm] > rcutoff = 0.3 [nm] >Total number of parameters to optimize: 4 >Updating parameters >****************** WARNING ***************** >Hessian H NOT a positive definite! >This can be a result of poor initial guess or ill-suited CG potential settings or poor CG sampling. >******************************************** > >However, you want to proceed despite non-positive definite H. >Non-positive H does not gurantee relative entropy iterations to converge to minimum. >You can turn on Hessian check by setting command line option --hessian-check=true. >In this case, alternative update option is steepest descent. >AA Ensemble Avg Energy :: 0.328298 >CG Ensemble Avg Energy :: 5.32913 >Writing CG parameters and potential(s) >Writing file: CG-CG.pot.new >CG-CG potential's extrapolated core is attractive! >Artifically enforcing repulsive core. > >Writing file: CG-CG.param.new >CG-CG potential's extrapolated core is attractive! >Artifically enforcing repulsive core. > >Finished RE update! ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_reupdate2" end time: Jun 07 13:12 UTC >"integration_Run_csg_reupdate2" time elapsed: 00:00:00 >---------------------------------------------------------- > >65/157 Testing: integration_Run_csg_map >65/157 Test: integration_Run_csg_map >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--out" "frame.dump" "--no-map" "--force" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map >"integration_Run_csg_map" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >I have 648 beads in 216 molecules >Reading frame, timestep 0 >writing coarse-grained trajectory to frame.dump ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_map" end time: Jun 07 13:12 UTC >"integration_Run_csg_map" time elapsed: 00:00:00 >---------------------------------------------------------- > >59/157 Testing: integration_Run_csg_fmatch >59/157 Test: integration_Run_csg_fmatch >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_fmatch.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch >"integration_Run_csg_fmatch" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 >a: 0.37 ,sigma: 1 ,gamma: 0.12 >Number of spline functions for the interaction CG-CG:13 > >You are using VOTCA! > >hey, somebody wants to forcematch! > >Using constrained Least Squares! > >This should be a number: -19.5494 > >Block No1 done! >Updating file: CG-CG.force > >We are done, thank you very much! ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_fmatch" end time: Jun 07 13:12 UTC >"integration_Run_csg_fmatch" time elapsed: 00:00:00 >---------------------------------------------------------- > >67/157 Testing: integration_Run_csg_map_gro >67/157 Test: integration_Run_csg_map_gro >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" "--out" "conf_cg.gro" "--nframes" "1" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map_gro >"integration_Run_csg_map_gro" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 >writing coarse-grained trajectory to conf_cg.gro ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_map_gro" end time: Jun 07 13:12 UTC >"integration_Run_csg_map_gro" time elapsed: 00:00:00 >---------------------------------------------------------- > >79/157 Testing: integration_Run_csg_imc_solve >79/157 Test: integration_Run_csg_imc_solve >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "-i" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.imc" "-g" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.gmc" "-n" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.idx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve >"integration_Run_csg_imc_solve" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_imc_solve" end time: Jun 07 13:12 UTC >"integration_Run_csg_imc_solve" time elapsed: 00:00:00 >---------------------------------------------------------- > >89/157 Testing: integration_Run_csg_resample_akima >89/157 Test: integration_Run_csg_resample_akima >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_akima" "--type" "akima" "--grid" "0:0.1:3" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Run_csg_resample_akima" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_resample_akima" end time: Jun 07 13:12 UTC >"integration_Run_csg_resample_akima" time elapsed: 00:00:00 >---------------------------------------------------------- > >74/157 Testing: integration_Run_csg_stat-imc >74/157 Test: integration_Run_csg_stat-imc >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--do-imc" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_imc.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc >"integration_Run_csg_stat-imc" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >begin to calculate inverse monte carlo parameters ># of bonded interactions: 0 ># of non-bonded interactions: 1 >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 > >written CG-CG.dist.new >written CG-CG.imc >written CG-CG.gmc >written CG-CG.idx ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_stat-imc" end time: Jun 07 13:12 UTC >"integration_Run_csg_stat-imc" time elapsed: 00:00:00 >---------------------------------------------------------- > >56/157 Testing: integration_Run_csg_reupdate_gmx >56/157 Test: integration_Run_csg_reupdate_gmx >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_re.xml" "--top" "topol.tpr" "--trj" "conf.gro" "--hessian-check" "no" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx >"integration_Run_csg_reupdate_gmx" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) >I have 216 beads in 216 molecules >We have CG-CG CG potential > Between beads CG-CG > With Function form cbspl > And 4 parameters to optimize >Potential range: > rmin = 0.26 [nm] > rcutoff = 0.3 [nm] >Total number of parameters to optimize: 4 >Updating parameters >****************** WARNING ***************** >Hessian H NOT a positive definite! >This can be a result of poor initial guess or ill-suited CG potential settings or poor CG sampling. >******************************************** > >However, you want to proceed despite non-positive definite H. >Non-positive H does not gurantee relative entropy iterations to converge to minimum. >You can turn on Hessian check by setting command line option --hessian-check=true. >In this case, alternative update option is steepest descent. >AA Ensemble Avg Energy :: 0.328298 >CG Ensemble Avg Energy :: 5.31427 >Writing CG parameters and potential(s) >Writing file: CG-CG.pot.new >CG-CG potential's extrapolated core is attractive! >Artifically enforcing repulsive core. > >Writing file: CG-CG.param.new >CG-CG potential's extrapolated core is attractive! >Artifically enforcing repulsive core. > >Finished RE update! ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_reupdate_gmx" end time: Jun 07 13:12 UTC >"integration_Run_csg_reupdate_gmx" time elapsed: 00:00:00 >---------------------------------------------------------- > >91/157 Testing: integration_Run_csg_resample_cubic >91/157 Test: integration_Run_csg_resample_cubic >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_cubic" "--type" "cubic" "--grid" "0:0.1:3" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Run_csg_resample_cubic" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_resample_cubic" end time: Jun 07 13:12 UTC >"integration_Run_csg_resample_cubic" time elapsed: 00:00:00 >---------------------------------------------------------- > >93/157 Testing: integration_Run_csg_resample_linear >93/157 Test: integration_Run_csg_resample_linear >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_linear" "--type" "linear" "--grid" "0:0.1:3" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Run_csg_resample_linear" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_resample_linear" end time: Jun 07 13:12 UTC >"integration_Run_csg_resample_linear" time elapsed: 00:00:00 >---------------------------------------------------------- > >95/157 Testing: integration_Run_csg_resample_cubicfit >95/157 Test: integration_Run_csg_resample_cubicfit >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--in" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_in" "--out" "table_cubicfit" "--type" "cubic" "--grid" "0:1:9" "--fitgrid" "0:2:9" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Run_csg_resample_cubicfit" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >doing cubic fit 0:2:9 ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_resample_cubicfit" end time: Jun 07 13:12 UTC >"integration_Run_csg_resample_cubicfit" time elapsed: 00:00:00 >---------------------------------------------------------- > >69/157 Testing: integration_Run_csg_stat >69/157 Test: integration_Run_csg_stat >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_rdf.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat >"integration_Run_csg_stat" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >begin to calculate distribution functions ># of bonded interactions: 0 ># of non-bonded interactions: 1 >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 > >written CG-CG.dist.new >written CG-CG.force.new ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_stat" end time: Jun 07 13:12 UTC >"integration_Run_csg_stat" time elapsed: 00:00:00 >---------------------------------------------------------- > >97/157 Testing: integration_Run_csg_dump >97/157 Test: integration_Run_csg_dump >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/methanol-water//topol_cg.xml > csg_dump.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump >"integration_Run_csg_dump" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump" time elapsed: 00:00:00 >---------------------------------------------------------- > >99/157 Testing: integration_Run_csg_dump_gro >99/157 Test: integration_Run_csg_dump_gro >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro > csg_dump_gro.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_gro >"integration_Run_csg_dump_gro" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump_gro" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump_gro" time elapsed: 00:00:00 >---------------------------------------------------------- > >101/157 Testing: integration_Run_csg_dump_data >101/157 Test: integration_Run_csg_dump_data >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols_cg/spce.data > csg_dump_data.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_data >"integration_Run_csg_dump_data" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump_data" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump_data" time elapsed: 00:00:00 >---------------------------------------------------------- > >115/157 Testing: integration_Run_csg_property >115/157 Test: integration_Run_csg_property >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_defaults.xml --print . --short --path cg.inverse.gromacs.DESC > csg_property.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Run_csg_property" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_property" end time: Jun 07 13:12 UTC >"integration_Run_csg_property" time elapsed: 00:00:00 >---------------------------------------------------------- > >117/157 Testing: integration_Run_csg_property2 >117/157 Test: integration_Run_csg_property2 >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_defaults.xml --print . --path cg.inverse.gromacs.DESC > csg_property.out2" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Run_csg_property2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_property2" end time: Jun 07 13:12 UTC >"integration_Run_csg_property2" time elapsed: 00:00:00 >---------------------------------------------------------- > >121/157 Testing: integration_Run_csg_property4 >121/157 Test: integration_Run_csg_property4 >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/test.xml --path A.B --print C > csg_property.out4" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Run_csg_property4" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_property4" end time: Jun 07 13:12 UTC >"integration_Run_csg_property4" time elapsed: 00:00:00 >---------------------------------------------------------- > >1/157 Testing: integration_votca_propertyHelp >1/157 Test: integration_votca_propertyHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tools/votca_property" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tools >"integration_votca_propertyHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/tools/issues > >votca_property >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) > >Helper for parsing XML files > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --file arg xml file to parse > --format arg output format [XML TXT] > --level arg output from this level > ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_votca_propertyHelp" end time: Jun 07 13:12 UTC >"integration_votca_propertyHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >124/157 Testing: integration_Run_csg_boltzmann_ppy >124/157 Test: integration_Run_csg_boltzmann_ppy >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csg_boltzmann/csg_boltzmann" "--top" "topol.tpr" "--cg" "ppy10.xml" "--excl" "excl.txt" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy >"integration_Run_csg_boltzmann_ppy" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) >I have 82 beads in 1 molecules >I have 10 beads in 1 molecules for the coarsegraining >Writing exclusion list for atomistic molecule Protein in coarse grained representation Protein ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_boltzmann_ppy" end time: Jun 07 13:12 UTC >"integration_Run_csg_boltzmann_ppy" time elapsed: 00:00:00 >---------------------------------------------------------- > >72/157 Testing: integration_Run_csg_stat_angular >72/157 Test: integration_Run_csg_stat_angular >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_angular.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_angular >"integration_Run_csg_stat_angular" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >begin to calculate distribution functions ># of bonded interactions: 0 ># of non-bonded interactions: 1 >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 > >written CG-CG-CG.dist.new ><end of output> >Test time = 0.12 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_stat_angular" end time: Jun 07 13:12 UTC >"integration_Run_csg_stat_angular" time elapsed: 00:00:00 >---------------------------------------------------------- > >127/157 Testing: integration_Run_csg_boltzmann_mma >127/157 Test: integration_Run_csg_boltzmann_mma >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csg_boltzmann/csg_boltzmann" "--top" "topol.tpr" "--cg" "mapping.xml" "--excl" "excl.txt" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma >"integration_Run_csg_boltzmann_mma" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) >I have 53 beads in 1 molecules >I have 11 beads in 1 molecules for the coarsegraining >Writing exclusion list for atomistic molecule 3-MMA in coarse grained representation 3-MMA ><end of output> >Test time = 0.10 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_boltzmann_mma" end time: Jun 07 13:12 UTC >"integration_Run_csg_boltzmann_mma" time elapsed: 00:00:00 >---------------------------------------------------------- > >85/157 Testing: integration_Run_csg_stat_imc_multi >85/157 Test: integration_Run_csg_stat_imc_multi >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/traj.gro" "--do-imc" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/settings_imc.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi >"integration_Run_csg_stat_imc_multi" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >begin to calculate inverse monte carlo parameters ># of bonded interactions: 0 ># of non-bonded interactions: 3 >I have 200 beads in 200 molecules > >written LJ1-LJ1.dist.new >written LJ1-LJ2.dist.new >written LJ2-LJ2.dist.new >written all.imc >written all.gmc >written all.idx ><end of output> >Test time = 0.14 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_stat_imc_multi" end time: Jun 07 13:12 UTC >"integration_Run_csg_stat_imc_multi" time elapsed: 00:00:00 >---------------------------------------------------------- > >119/157 Testing: integration_Run_csg_property3 >119/157 Test: integration_Run_csg_property3 >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property --file /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/test.xml --path A.B.C --print . > csg_property.out3" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Run_csg_property3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.12 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_property3" end time: Jun 07 13:12 UTC >"integration_Run_csg_property3" time elapsed: 00:00:00 >---------------------------------------------------------- > >2/157 Testing: unit_test_calculator >2/157 Test: unit_test_calculator >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_calculator" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_calculator" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.10 sec >---------------------------------------------------------- >Test Passed. >"unit_test_calculator" end time: Jun 07 13:12 UTC >"unit_test_calculator" time elapsed: 00:00:00 >---------------------------------------------------------- > >3/157 Testing: unit_test_constants >3/157 Test: unit_test_constants >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_constants" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_constants" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.10 sec >---------------------------------------------------------- >Test Passed. >"unit_test_constants" end time: Jun 07 13:12 UTC >"unit_test_constants" time elapsed: 00:00:00 >---------------------------------------------------------- > >4/157 Testing: unit_test_correlate >4/157 Test: unit_test_correlate >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_correlate" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_correlate" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.09 sec >---------------------------------------------------------- >Test Passed. >"unit_test_correlate" end time: Jun 07 13:12 UTC >"unit_test_correlate" time elapsed: 00:00:00 >---------------------------------------------------------- > >5/157 Testing: unit_test_crosscorrelate >5/157 Test: unit_test_crosscorrelate >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_crosscorrelate" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_crosscorrelate" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.08 sec >---------------------------------------------------------- >Test Passed. >"unit_test_crosscorrelate" end time: Jun 07 13:12 UTC >"unit_test_crosscorrelate" time elapsed: 00:00:00 >---------------------------------------------------------- > >7/157 Testing: unit_test_datacollection >7/157 Test: unit_test_datacollection >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_datacollection" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_datacollection" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 6 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"unit_test_datacollection" end time: Jun 07 13:12 UTC >"unit_test_datacollection" time elapsed: 00:00:00 >---------------------------------------------------------- > >8/157 Testing: unit_test_edge_base >8/157 Test: unit_test_edge_base >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_edge_base" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_edge_base" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 8 test cases... >Vertices >2 3 > > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"unit_test_edge_base" end time: Jun 07 13:12 UTC >"unit_test_edge_base" time elapsed: 00:00:00 >---------------------------------------------------------- > >6/157 Testing: unit_test_cubicspline >6/157 Test: unit_test_cubicspline >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_cubicspline" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_cubicspline" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 5 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.08 sec >---------------------------------------------------------- >Test Passed. >"unit_test_cubicspline" end time: Jun 07 13:12 UTC >"unit_test_cubicspline" time elapsed: 00:00:00 >---------------------------------------------------------- > >9/157 Testing: unit_test_edgecontainer >9/157 Test: unit_test_edgecontainer >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_edgecontainer" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_edgecontainer" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 10 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"unit_test_edgecontainer" end time: Jun 07 13:12 UTC >"unit_test_edgecontainer" time elapsed: 00:00:00 >---------------------------------------------------------- > >81/157 Testing: integration_Run_csg_imc_solve_reg >81/157 Test: integration_Run_csg_imc_solve_reg >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "-r" "1000" "-i" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.imc" "-g" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.gmc" "-n" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/group_1.idx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg >"integration_Run_csg_imc_solve_reg" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.17 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_imc_solve_reg" end time: Jun 07 13:12 UTC >"integration_Run_csg_imc_solve_reg" time elapsed: 00:00:00 >---------------------------------------------------------- > >10/157 Testing: unit_test_elements >10/157 Test: unit_test_elements >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_elements" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_elements" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"unit_test_elements" end time: Jun 07 13:12 UTC >"unit_test_elements" time elapsed: 00:00:00 >---------------------------------------------------------- > >11/157 Testing: unit_test_filesystem >11/157 Test: unit_test_filesystem >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_filesystem" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_filesystem" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"unit_test_filesystem" end time: Jun 07 13:12 UTC >"unit_test_filesystem" time elapsed: 00:00:00 >---------------------------------------------------------- > >12/157 Testing: unit_test_floatingpointcomparison >12/157 Test: unit_test_floatingpointcomparison >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_floatingpointcomparison" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_floatingpointcomparison" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_floatingpointcomparison" end time: Jun 07 13:12 UTC >"unit_test_floatingpointcomparison" time elapsed: 00:00:00 >---------------------------------------------------------- > >13/157 Testing: unit_test_graphalgorithm >13/157 Test: unit_test_graphalgorithm >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphalgorithm" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graphalgorithm" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 5 test cases... >is single network 1 >EDGE CHECK ************************************** > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graphalgorithm" end time: Jun 07 13:12 UTC >"unit_test_graphalgorithm" time elapsed: 00:00:00 >---------------------------------------------------------- > >14/157 Testing: unit_test_graph_base >14/157 Test: unit_test_graph_base >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_base" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graph_base" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 8 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graph_base" end time: Jun 07 13:12 UTC >"unit_test_graph_base" time elapsed: 00:00:00 >---------------------------------------------------------- > >15/157 Testing: unit_test_graph_bf_visitor >15/157 Test: unit_test_graph_bf_visitor >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_bf_visitor" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graph_bf_visitor" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graph_bf_visitor" end time: Jun 07 13:12 UTC >"unit_test_graph_bf_visitor" time elapsed: 00:00:00 >---------------------------------------------------------- > >16/157 Testing: unit_test_graph_df_visitor >16/157 Test: unit_test_graph_df_visitor >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graph_df_visitor" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graph_df_visitor" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graph_df_visitor" end time: Jun 07 13:12 UTC >"unit_test_graph_df_visitor" time elapsed: 00:00:00 >---------------------------------------------------------- > >17/157 Testing: unit_test_graphdistvisitor >17/157 Test: unit_test_graphdistvisitor >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphdistvisitor" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graphdistvisitor" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graphdistvisitor" end time: Jun 07 13:12 UTC >"unit_test_graphdistvisitor" time elapsed: 00:00:00 >---------------------------------------------------------- > >18/157 Testing: unit_test_graphnode >18/157 Test: unit_test_graphnode >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphnode" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graphnode" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 4 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graphnode" end time: Jun 07 13:12 UTC >"unit_test_graphnode" time elapsed: 00:00:00 >---------------------------------------------------------- > >19/157 Testing: unit_test_graphvisitor >19/157 Test: unit_test_graphvisitor >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_graphvisitor" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_graphvisitor" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_graphvisitor" end time: Jun 07 13:12 UTC >"unit_test_graphvisitor" time elapsed: 00:00:00 >---------------------------------------------------------- > >20/157 Testing: unit_test_histogramnew >20/157 Test: unit_test_histogramnew >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_histogramnew" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_histogramnew" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 6 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_histogramnew" end time: Jun 07 13:12 UTC >"unit_test_histogramnew" time elapsed: 00:00:00 >---------------------------------------------------------- > >21/157 Testing: unit_test_identity >21/157 Test: unit_test_identity >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_identity" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_identity" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_identity" end time: Jun 07 13:12 UTC >"unit_test_identity" time elapsed: 00:00:00 >---------------------------------------------------------- > >22/157 Testing: unit_test_linalg >22/157 Test: unit_test_linalg >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_linalg" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_linalg" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_linalg" end time: Jun 07 13:12 UTC >"unit_test_linalg" time elapsed: 00:00:00 >---------------------------------------------------------- > >23/157 Testing: unit_test_name >23/157 Test: unit_test_name >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_name" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_name" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_name" end time: Jun 07 13:12 UTC >"unit_test_name" time elapsed: 00:00:00 >---------------------------------------------------------- > >24/157 Testing: unit_test_objectfactory >24/157 Test: unit_test_objectfactory >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_objectfactory" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_objectfactory" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_objectfactory" end time: Jun 07 13:12 UTC >"unit_test_objectfactory" time elapsed: 00:00:00 >---------------------------------------------------------- > >25/157 Testing: unit_test_optionshandler >25/157 Test: unit_test_optionshandler >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_optionshandler" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_optionshandler" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 6 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_optionshandler" end time: Jun 07 13:12 UTC >"unit_test_optionshandler" time elapsed: 00:00:00 >---------------------------------------------------------- > >26/157 Testing: unit_test_property >26/157 Test: unit_test_property >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_property" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_property" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 8 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_property" end time: Jun 07 13:12 UTC >"unit_test_property" time elapsed: 00:00:00 >---------------------------------------------------------- > >27/157 Testing: unit_test_reducededge >27/157 Test: unit_test_reducededge >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_reducededge" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_reducededge" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 10 test cases... >Vertices >2 3 > > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_reducededge" end time: Jun 07 13:12 UTC >"unit_test_reducededge" time elapsed: 00:00:00 >---------------------------------------------------------- > >28/157 Testing: unit_test_reducedgraph >28/157 Test: unit_test_reducedgraph >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_reducedgraph" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_reducedgraph" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 9 test cases... >4 >3 >2 >0 > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_reducedgraph" end time: Jun 07 13:12 UTC >"unit_test_reducedgraph" time elapsed: 00:00:00 >---------------------------------------------------------- > >29/157 Testing: unit_test_structureparameters >29/157 Test: unit_test_structureparameters >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_structureparameters" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_structureparameters" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_structureparameters" end time: Jun 07 13:12 UTC >"unit_test_structureparameters" time elapsed: 00:00:00 >---------------------------------------------------------- > >30/157 Testing: unit_test_table >30/157 Test: unit_test_table >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_table" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_table" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 10 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_table" end time: Jun 07 13:12 UTC >"unit_test_table" time elapsed: 00:00:00 >---------------------------------------------------------- > >31/157 Testing: unit_test_thread >31/157 Test: unit_test_thread >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_thread" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_thread" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_thread" end time: Jun 07 13:12 UTC >"unit_test_thread" time elapsed: 00:00:00 >---------------------------------------------------------- > >32/157 Testing: unit_test_tokenizer >32/157 Test: unit_test_tokenizer >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_tokenizer" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_tokenizer" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 5 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_tokenizer" end time: Jun 07 13:12 UTC >"unit_test_tokenizer" time elapsed: 00:00:00 >---------------------------------------------------------- > >33/157 Testing: unit_test_random >33/157 Test: unit_test_random >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_random" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_random" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_random" end time: Jun 07 13:12 UTC >"unit_test_random" time elapsed: 00:00:00 >---------------------------------------------------------- > >34/157 Testing: unit_test_akimaspline >34/157 Test: unit_test_akimaspline >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_akimaspline" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_akimaspline" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_akimaspline" end time: Jun 07 13:12 UTC >"unit_test_akimaspline" time elapsed: 00:00:00 >---------------------------------------------------------- > >35/157 Testing: unit_test_linspline >35/157 Test: unit_test_linspline >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_linspline" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_linspline" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_linspline" end time: Jun 07 13:12 UTC >"unit_test_linspline" time elapsed: 00:00:00 >---------------------------------------------------------- > >36/157 Testing: unit_test_unitconverter >36/157 Test: unit_test_unitconverter >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_unitconverter" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_unitconverter" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 9 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_unitconverter" end time: Jun 07 13:12 UTC >"unit_test_unitconverter" time elapsed: 00:00:00 >---------------------------------------------------------- > >37/157 Testing: unit_test_NDimVector >37/157 Test: unit_test_NDimVector >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_NDimVector" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_NDimVector" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_NDimVector" end time: Jun 07 13:12 UTC >"unit_test_NDimVector" time elapsed: 00:00:00 >---------------------------------------------------------- > >38/157 Testing: unit_test_eigenio_matrixmarket >38/157 Test: unit_test_eigenio_matrixmarket >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests/unit_test_eigenio_matrixmarket" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/src/tests >"unit_test_eigenio_matrixmarket" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 4 test cases... >/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/tools/src/tests/DataFiles > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_eigenio_matrixmarket" end time: Jun 07 13:12 UTC >"unit_test_eigenio_matrixmarket" time elapsed: 00:00:00 >---------------------------------------------------------- > >39/157 Testing: integration_csg_reupdateHelp >39/157 Test: integration_csg_reupdateHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_reupdate" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_reupdateHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_reupdate, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >computes relative entropy update. > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file (only needed for > RE update) > >RE Specific options: > --options arg options file for coarse graining > --gentable arg (=0) only generate potential tables from given > parameters, NO RE update! > --interaction arg [OPTIONAL] generate potential tables only > for the specified interactions, > only valid when 'gentable' is true > --param-in-ext arg (=param.cur) Extension of the input parameter tables > --param-out-ext arg (=param.new) Extension of the output parameter tables > --pot-out-ext arg (=pot.new) Extension of the output potential tables > --hessian-check arg (=1) Disable the hessian check (mostly for > testing) > >Threading options: > --nt arg (=1) number of threads > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works > for Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_reupdateHelp" end time: Jun 07 13:12 UTC >"integration_csg_reupdateHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >40/157 Testing: integration_csg_mapHelp >40/157 Test: integration_csg_mapHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_mapHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_map, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Convert a reference atomistic trajectory or configuration into a coarse-grained one >based on a mapping xml-file. The mapping can be applied to either an entire trajectory >or a selected set of frames only (see options). >Examples: >* csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml >* csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg-map.xml >* csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map >* csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml >* csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV > > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --out arg output file for coarse-grained trajectory > --vel Write mapped velocities (if available) > --force Write mapped forces (if available) > --hybrid Create hybrid trajectory containing both atomistic > and coarse-grained > >Mapping options: > --cg arg coarse graining mapping and bond definitions > (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_mapHelp" end time: Jun 07 13:12 UTC >"integration_csg_mapHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >41/157 Testing: integration_csg_dumpHelp >41/157 Test: integration_csg_dumpHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_dumpHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_dump, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Print atoms that are read from topology file to help debugging atom naming. > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Mapping options: > --cg arg [OPTIONAL] coarse graining mapping and bond > definitions > (xml-file). If no file is given, program acts on > original trajectory > --map-ignore arg list of molecules to ignore if mapping is done > separated by ; > >Specific options: > --excl display exclusion list instead of molecule list > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_dumpHelp" end time: Jun 07 13:12 UTC >"integration_csg_dumpHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >42/157 Testing: integration_csg_propertyHelp >42/157 Test: integration_csg_propertyHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_property" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_propertyHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_property, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Helper program called by inverse scripts to parse xml file. > >Allowed options: > --help produce this help message > --path arg path to part of the xml file to print > --filter arg list option values that match given criteria > --print arg (=.) specifies which children or root to print > --file arg xml file to parse > --short short version of output > --with-path include path of node in output > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_propertyHelp" end time: Jun 07 13:12 UTC >"integration_csg_propertyHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >43/157 Testing: integration_csg_resampleHelp >43/157 Test: integration_csg_resampleHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_resample" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_resampleHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_resample, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Change grid and interval of any sort of table files. >Mainly called internally by inverse script, can also be >used to manually prepare input files for coarse-grained >simulations. > >Allowed options: > --help produce this help message > --in arg table to read > --out arg table to write > --derivative arg table to write > --grid arg new grid spacing (min:step:max). If 'grid' is specified > only, interpolation is performed. > --type arg (=akima) [cubic|akima|linear]. If option is not specified, the > default type 'akima' is assumed. > --fitgrid arg specify fit grid (min:step:max). If 'grid' and > 'fitgrid' are specified, a fit is performed. > --nocut Option for fitgrid: Normally, values out of fitgrid > boundaries are cut off. If they shouldn't, choose > --nocut. > --comment arg store a comment in the output table > --boundaries arg (natural|periodic|derivativezero) sets boundary > conditions > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_resampleHelp" end time: Jun 07 13:12 UTC >"integration_csg_resampleHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >44/157 Testing: integration_csg_statHelp >44/157 Test: integration_csg_statHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_stat" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_statHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_stat, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Calculate all distributions (bonded and non-bonded) specified in options file. >Optionally calculates update Eigen::Matrix3d for invere Monte Carlo. This program >is called inside the inverse scripts. Unlike csg_boltzmann, big systems >can be treated as well as non-bonded interactions can be evaluated. > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Mapping options: > --cg arg [OPTIONAL] coarse graining mapping and bond > definitions > (xml-file). If no file is given, program acts on > original trajectory > --map-ignore arg list of molecules to ignore if mapping is done > separated by ; > >Specific options: > --options arg options file for coarse graining > --do-imc write out additional Inverse Monte Carlo data > --include-intra do not exclude intramolecular neighbors > --block-length arg write blocks of this length, the averages are > cleared after every write > --ext arg (=dist.new) Extension of the output > >Threading options: > --nt arg (=1) number of threads > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_statHelp" end time: Jun 07 13:12 UTC >"integration_csg_statHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >45/157 Testing: integration_csg_fmatchHelp >45/157 Test: integration_csg_fmatchHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_fmatchHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_fmatch, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Perform force matching (also called multiscale coarse-graining) > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --options arg options file for coarse graining > --trj-force arg coarse-grained trajectory containing forces of > already known interactions > >Mapping options: > --cg arg coarse graining mapping and bond definitions > (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_fmatchHelp" end time: Jun 07 13:12 UTC >"integration_csg_fmatchHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >46/157 Testing: integration_csg_gmxtopolHelp >46/157 Test: integration_csg_gmxtopolHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_gmxtopol" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_gmxtopolHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_gmxtopol, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Create skeleton for gromacs topology based on atomistic topology >and a mapping file. File still needs to be modified by the user. > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --out arg output topology (will create .top and in future also > .itp) > >Mapping options: > --cg arg coarse graining mapping and bond definitions > (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_gmxtopolHelp" end time: Jun 07 13:12 UTC >"integration_csg_gmxtopolHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >47/157 Testing: integration_csg_dlptopolHelp >47/157 Test: integration_csg_dlptopolHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dlptopol" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_dlptopolHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_dlptopol, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Create a dlpoly topology template based on an existing (atomistic) topology and >a mapping xml-file. The created template file needs to be inspected and amended by the user! > >Examples: >* csg_dlptopol --top .dlpf --out .dlpf --cg cg-map.xml > convert FIELD to FIELD_CGV using cg-map.xml >* csg_dlptopol --top FA-dlpoly.dlpf --out CG-dlpoly.dlpf --cg cg-map.xml >* csg_dlptopol --top FA-gromacs.tpr --out FA-dlpoly.dlpf --no-map > > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --out arg output topology in dlpoly format > >Mapping options: > --cg arg coarse graining mapping and bond definitions > (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_dlptopolHelp" end time: Jun 07 13:12 UTC >"integration_csg_dlptopolHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >48/157 Testing: integration_csg_densityHelp >48/157 Test: integration_csg_densityHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_density" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_densityHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_density, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Calculates the mass density distribution along a box axis or radial density profile from reference point > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Mapping options: > --cg arg [OPTIONAL] coarse graining mapping and bond > definitions > (xml-file). If no file is given, program acts on > original trajectory > --map-ignore arg list of molecules to ignore if mapping is done > separated by ; > >Specific options:: > --type arg (=mass) density type: mass or number > --axis arg (=r) [x|y|z|r] density axis (r=spherical) > --step arg (=0.01) spacing of density > --block-length arg write blocks of this length, the averages are > cleared after every write > --out arg Output file > --rmax arg rmax (default for [r] =min of all box vectors/2, else > l ) > --scale arg (=1) scale factor for the density > --molname arg (=*) molname > --filter arg (=*) filter bead names > --ref arg reference zero point > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_densityHelp" end time: Jun 07 13:12 UTC >"integration_csg_densityHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >49/157 Testing: integration_csg_imc_solveHelp >49/157 Test: integration_csg_imc_solveHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_imc_solve" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools >"integration_csg_imc_solveHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_imc_solve, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Solves the linear system for IMCs > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > -r [ --regularization ] arg (=0) regularization factor > -i [ --imcfile ] arg imc statefile > -g [ --gmcfile ] arg gmc statefile > -n [ --idxfile ] arg idx statefile > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_csg_imc_solveHelp" end time: Jun 07 13:12 UTC >"integration_csg_imc_solveHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >103/157 Testing: integration_Run_gmx_grompp >103/157 Test: integration_Run_gmx_grompp >Command: "/usr/bin/gmx" "grompp" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_gmx_grompp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- > :-) GROMACS - gmx grompp, 2023.1 (-: > >Executable: /usr/bin/gmx >Data prefix: /usr >Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >Command line: > gmx grompp > >Ignoring obsolete mdp entry 'title' > >NOTE 1 [file grompp.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > >NOTE 2 [file grompp.mdp]: > You have set rlist larger than the interaction cut-off, but you also have > verlet-buffer-tolerance > 0. Will set rlist using > verlet-buffer-tolerance. > >Setting the LD random seed to -1126171682 >Generating 1-4 interactions: fudge = 0.5 >Number of degrees of freedom in T-Coupling group System is 15.00 > >There were 2 NOTEs > >GROMACS reminds you: "You're Insignificant" (Tricky) > > >Generated 330891 of the 330891 non-bonded parameter combinations > >Generated 330891 of the 330891 1-4 parameter combinations > >Excluding 2 bonded neighbours molecule type 'SOL' >Analysing residue names: >There are: 3 Water residues > >Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > >Calculated rlist for 1x1 atom pair-list as 0.900 nm, buffer size 0.000 nm > >Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm > >Note that mdrun will redetermine rlist based on the actual pair-list setup > >This run will generate roughly 0 Mb of data ><end of output> >Test time = 0.30 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_gmx_grompp" end time: Jun 07 13:12 UTC >"integration_Run_gmx_grompp" time elapsed: 00:00:00 >---------------------------------------------------------- > >51/157 Testing: integration_Compare_csg_reupdate_output >51/157 Test: integration_Compare_csg_reupdate_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.re" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate >"integration_Compare_csg_reupdate_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.re to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_reupdate_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_reupdate_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >53/157 Testing: integration_Compare_csg_reupdate_output2 >53/157 Test: integration_Compare_csg_reupdate_output2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 >"integration_Compare_csg_reupdate_output2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_reupdate_output2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_reupdate_output2" time elapsed: 00:00:00 >---------------------------------------------------------- > >54/157 Testing: integration_Compare_csg_reupdate_output3 >54/157 Test: integration_Compare_csg_reupdate_output3 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.param.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate2 >"integration_Compare_csg_reupdate_output3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.param.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_reupdate_output3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_reupdate_output3" time elapsed: 00:00:00 >---------------------------------------------------------- > >57/157 Testing: integration_Compare_csg_reupdate_gmx_output >57/157 Test: integration_Compare_csg_reupdate_gmx_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.pot.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re_gmx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx >"integration_Compare_csg_reupdate_gmx_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.pot.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pot.new.re_gmx to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_reupdate_gmx_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_reupdate_gmx_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >58/157 Testing: integration_Compare_csg_reupdate_gmx_output2 >58/157 Test: integration_Compare_csg_reupdate_gmx_output2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.param.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re_gmx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_reupdate_gmx >"integration_Compare_csg_reupdate_gmx_output2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.param.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.param.re_gmx to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_reupdate_gmx_output2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_reupdate_gmx_output2" time elapsed: 00:00:00 >---------------------------------------------------------- > >60/157 Testing: integration_Compare_csg_fmatch_output >60/157 Test: integration_Compare_csg_fmatch_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch >"integration_Compare_csg_fmatch_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.force and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_fmatch_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_fmatch_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >70/157 Testing: integration_Compare_csg_stat_output1 >70/157 Test: integration_Compare_csg_stat_output1 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.rdf" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat >"integration_Compare_csg_stat_output1" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.rdf to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat_output1" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat_output1" time elapsed: 00:00:00 >---------------------------------------------------------- > >78/157 Testing: integration_Compare_csg_stat-imc_output_4 >78/157 Test: integration_Compare_csg_stat-imc_output_4 >Command: "/usr/bin/cmake" "-E" "compare_files" "CG-CG.idx" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.idx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc >"integration_Compare_csg_stat-imc_output_4" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_output_4" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_output_4" time elapsed: 00:00:00 >---------------------------------------------------------- > >104/157 Testing: integration_Run_csg_dump_gmx_tpr >104/157 Test: integration_Run_csg_dump_gmx_tpr >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --top topol.tpr > csg_dump_tpr.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_csg_dump_gmx_tpr" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump_gmx_tpr" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump_gmx_tpr" time elapsed: 00:00:00 >---------------------------------------------------------- > >68/157 Testing: integration_Compare_csg_map_gro_output >68/157 Test: integration_Compare_csg_map_gro_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "conf_cg.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/conf_cg.gro" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map_gro >"integration_Compare_csg_map_gro_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing conf_cg.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/conf_cg.gro to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_map_gro_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_map_gro_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >71/157 Testing: integration_Compare_csg_stat_output2 >71/157 Test: integration_Compare_csg_stat_output2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pmf" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat >"integration_Compare_csg_stat_output2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.force.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.pmf to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat_output2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat_output2" time elapsed: 00:00:00 >---------------------------------------------------------- > >106/157 Testing: integration_Run_csg_dump_gmx_tpr_excl >106/157 Test: integration_Run_csg_dump_gmx_tpr_excl >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --excl --top topol.tpr > csg_dump_tpr_excl.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_csg_dump_gmx_tpr_excl" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump_gmx_tpr_excl" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump_gmx_tpr_excl" time elapsed: 00:00:00 >---------------------------------------------------------- > >76/157 Testing: integration_Compare_csg_stat-imc_output_2 >76/157 Test: integration_Compare_csg_stat-imc_output_2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.dist.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc >"integration_Compare_csg_stat-imc_output_2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.dist.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_output_2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_output_2" time elapsed: 00:00:00 >---------------------------------------------------------- > >108/157 Testing: integration_Run_csg_dump_gmx_tpr_cg >108/157 Test: integration_Run_csg_dump_gmx_tpr_cg >Command: "/bin/bash" "-c" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_dump --cg /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/../mapping.xml --top topol.tpr > csg_dump_tpr_cg.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_csg_dump_gmx_tpr_cg" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_dump_gmx_tpr_cg" end time: Jun 07 13:12 UTC >"integration_Run_csg_dump_gmx_tpr_cg" time elapsed: 00:00:00 >---------------------------------------------------------- > >66/157 Testing: integration_Compare_csg_map_output >66/157 Test: integration_Compare_csg_map_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "frame.dump" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_map >"integration_Compare_csg_map_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing frame.dump and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump to a tolerance of 5e-05 ><end of output> >Test time = 0.08 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_map_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_map_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >73/157 Testing: integration_Compare_csg_stat_angular_output >73/157 Test: integration_Compare_csg_stat_angular_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.dist.new" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.angular" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_angular >"integration_Compare_csg_stat_angular_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG-CG.dist.new and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.angular to a tolerance of 5e-05 ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat_angular_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat_angular_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >77/157 Testing: integration_Compare_csg_stat-imc_output_3 >77/157 Test: integration_Compare_csg_stat-imc_output_3 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.gmc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.gmc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc >"integration_Compare_csg_stat-imc_output_3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.gmc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.gmc to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_output_3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_output_3" time elapsed: 00:00:00 >---------------------------------------------------------- > >75/157 Testing: integration_Compare_csg_stat-imc_output >75/157 Test: integration_Compare_csg_stat-imc_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat-imc >"integration_Compare_csg_stat-imc_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.07 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >88/157 Testing: integration_Compare_csg_stat-imc_multi_output_3 >88/157 Test: integration_Compare_csg_stat-imc_multi_output_3 >Command: "/usr/bin/cmake" "-E" "compare_files" "all.idx" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.idx" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi >"integration_Compare_csg_stat-imc_multi_output_3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_multi_output_3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_multi_output_3" time elapsed: 00:00:00 >---------------------------------------------------------- > >98/157 Testing: integration_Compare_csg_dump_output >98/157 Test: integration_Compare_csg_dump_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/methanol-water//csg_dump.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump >"integration_Compare_csg_dump_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >100/157 Testing: integration_Compare_csg_dump_gro_output >100/157 Test: integration_Compare_csg_dump_gro_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_gro.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_gro.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_gro >"integration_Compare_csg_dump_gro_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_gro_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_gro_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >102/157 Testing: integration_Compare_csg_dump_data_output >102/157 Test: integration_Compare_csg_dump_data_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_data.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols_cg/csg_dump_data.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_dump_data >"integration_Compare_csg_dump_data_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_data_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_data_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >105/157 Testing: integration_Compare_csg_dump_gmx_tpr_output >105/157 Test: integration_Compare_csg_dump_gmx_tpr_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Compare_csg_dump_gmx_tpr_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_gmx_tpr_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_gmx_tpr_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >107/157 Testing: integration_Compare_csg_dump_gmx_tpr_excl_output >107/157 Test: integration_Compare_csg_dump_gmx_tpr_excl_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr_excl.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr_excl.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Compare_csg_dump_gmx_tpr_excl_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_gmx_tpr_excl_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_gmx_tpr_excl_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >80/157 Testing: integration_Compare_csg_imc_solve_output >80/157 Test: integration_Compare_csg_imc_solve_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.dpot.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve >"integration_Compare_csg_imc_solve_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing CG-CG.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/imc/CG-CG.dpot.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_imc_solve_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_imc_solve_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >109/157 Testing: integration_Compare_csg_dump_gmx_tpr_cg_output >109/157 Test: integration_Compare_csg_dump_gmx_tpr_cg_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_dump_tpr_cg.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/csg_dump_tpr_cg.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Compare_csg_dump_gmx_tpr_cg_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_dump_gmx_tpr_cg_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_dump_gmx_tpr_cg_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >83/157 Testing: integration_Compare_csg_imc_solve_reg_output_3 >83/157 Test: integration_Compare_csg_imc_solve_reg_output_3 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ1-LJ2.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ2.dpot.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg >"integration_Compare_csg_imc_solve_reg_output_3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing LJ1-LJ2.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ2.dpot.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_imc_solve_reg_output_3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_imc_solve_reg_output_3" time elapsed: 00:00:00 >---------------------------------------------------------- > >82/157 Testing: integration_Compare_csg_imc_solve_reg_output_2 >82/157 Test: integration_Compare_csg_imc_solve_reg_output_2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ1-LJ1.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ1.dpot.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg >"integration_Compare_csg_imc_solve_reg_output_2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing LJ1-LJ1.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ1-LJ1.dpot.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_imc_solve_reg_output_2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_imc_solve_reg_output_2" time elapsed: 00:00:00 >---------------------------------------------------------- > >116/157 Testing: integration_Compare_csg_property_output >116/157 Test: integration_Compare_csg_property_output >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Compare_csg_property_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_property_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_property_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >118/157 Testing: integration_Compare_csg_property_output2 >118/157 Test: integration_Compare_csg_property_output2 >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out2" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Compare_csg_property_output2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_property_output2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_property_output2" time elapsed: 00:00:00 >---------------------------------------------------------- > >84/157 Testing: integration_Compare_csg_imc_solve_reg_output_4 >84/157 Test: integration_Compare_csg_imc_solve_reg_output_4 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "LJ2-LJ2.dpot.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ2-LJ2.dpot.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_imc_solve_reg >"integration_Compare_csg_imc_solve_reg_output_4" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing LJ2-LJ2.dpot.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/LJ2-LJ2.dpot.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_imc_solve_reg_output_4" end time: Jun 07 13:12 UTC >"integration_Compare_csg_imc_solve_reg_output_4" time elapsed: 00:00:00 >---------------------------------------------------------- > >86/157 Testing: integration_Compare_csg_stat-imc_multi_output >86/157 Test: integration_Compare_csg_stat-imc_multi_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "all.imc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.imc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi >"integration_Compare_csg_stat-imc_multi_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing all.imc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.imc to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_multi_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_multi_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >120/157 Testing: integration_Compare_csg_property_output3 >120/157 Test: integration_Compare_csg_property_output3 >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out3" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out3" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Compare_csg_property_output3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_property_output3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_property_output3" time elapsed: 00:00:00 >---------------------------------------------------------- > >122/157 Testing: integration_Compare_csg_property_output4 >122/157 Test: integration_Compare_csg_property_output4 >Command: "/usr/bin/cmake" "-E" "compare_files" "csg_property.out4" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_property/csg_property.out4" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_property >"integration_Compare_csg_property_output4" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_property_output4" end time: Jun 07 13:12 UTC >"integration_Compare_csg_property_output4" time elapsed: 00:00:00 >---------------------------------------------------------- > >125/157 Testing: Compare_csg_boltzmann_output_ppy >125/157 Test: Compare_csg_boltzmann_output_ppy >Command: "/usr/bin/cmake" "-E" "compare_files" "excl.txt" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/ppy//excl.txt" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_ppy >"Compare_csg_boltzmann_output_ppy" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"Compare_csg_boltzmann_output_ppy" end time: Jun 07 13:12 UTC >"Compare_csg_boltzmann_output_ppy" time elapsed: 00:00:00 >---------------------------------------------------------- > >128/157 Testing: Compare_csg_boltzmann_output_mma >128/157 Test: Compare_csg_boltzmann_output_mma >Command: "/usr/bin/cmake" "-E" "compare_files" "excl.txt" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/mma//excl.txt" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_boltzmann_mma >"Compare_csg_boltzmann_output_mma" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"Compare_csg_boltzmann_output_mma" end time: Jun 07 13:12 UTC >"Compare_csg_boltzmann_output_mma" time elapsed: 00:00:00 >---------------------------------------------------------- > >90/157 Testing: integration_Compare_csg_resample_akima_output >90/157 Test: integration_Compare_csg_resample_akima_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_akima" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_akima" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Compare_csg_resample_akima_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing table_akima and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_akima to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_resample_akima_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_resample_akima_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >92/157 Testing: integration_Compare_csg_resample_cubic_output >92/157 Test: integration_Compare_csg_resample_cubic_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_cubic" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubic" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Compare_csg_resample_cubic_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing table_cubic and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubic to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_resample_cubic_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_resample_cubic_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >94/157 Testing: integration_Compare_csg_resample_linear_output >94/157 Test: integration_Compare_csg_resample_linear_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_linear" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_linear" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Compare_csg_resample_linear_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing table_linear and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_linear to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_resample_linear_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_resample_linear_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >96/157 Testing: integration_Compare_csg_resample_cubicfit_output >96/157 Test: integration_Compare_csg_resample_cubicfit_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "table_cubicfit" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubicfit" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_resample >"integration_Compare_csg_resample_cubicfit_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing table_cubicfit and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/csg_resample/table_cubicfit to a tolerance of 5e-05 ><end of output> >Test time = 0.06 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_resample_cubicfit_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_resample_cubicfit_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >129/157 Testing: fluctuationsHelp >129/157 Test: fluctuationsHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/fluctuations/csg_fluctuations" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"fluctuationsHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >fluctuations, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >calculate density fluctuations in subvolumes of the simulation box.Subolumes can be either cubic slabs in dimensions (x|y|z) or sphericalslabs with respect to either the center of box or a reference molecule > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Fluctuation options: > --filter arg (=*) filter molecule names > --rmax arg maximal distance to be considered > --rmin arg (=0) minimal distance to be considered > --refmol arg Reference molecule > --nbin arg (=100) Number of bins > --geometry arg (sphere|x|y|z) Take radial or x, y, z > slabs from rmin to rmax > --outfile arg (=fluctuations.dat) Output file > >Mapping options: > --cg arg coarse graining mapping and bond > definitions (xml-file) > --map-ignore arg list of molecules to ignore separated by > ; > --no-map disable mapping and act on original > trajectory > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works > for Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"fluctuationsHelp" end time: Jun 07 13:12 UTC >"fluctuationsHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >130/157 Testing: orientcorrHelp >130/157 Test: orientcorrHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/orientcorr/csg_orientcorr" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"orientcorrHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >orientcorr, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Calculates the orientational correlation function ><3/2*u(0)*u(r) - 1/2> >for a polymer melt, where u is the vector pointing along a bond and >r the distance between bond segments (centered on middle of bond). > >The output is correlation.dat (with intra-molecular contributions) and >correlation_excl.dat, where inter-molecular contributions are excluded. > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Neighbor search options: > -c [ --cutoff ] arg (=1) cutoff for the neighbor search > --nbins arg (=40) number of bins for the grid > --nbmethod arg (=grid) neighbor search algorithm (simple or grid) > >Threading options: > --nt arg (=1) number of threads > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"orientcorrHelp" end time: Jun 07 13:12 UTC >"orientcorrHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >131/157 Testing: part_distHelp >131/157 Test: part_distHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/part_dist/csg_part_dist" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"part_distHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_part_dist, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >This program reads a topology and (set of) trajectory(ies). For every >binned value of a chosen coordinate, it outputs the time-averaged number of >particles, listed by particle types. > >Allowed options: > --top arg topology file > --trj arg trajectory file > --grid arg output grid spacing (min:step:max) > --out arg output particle distribution table > --ptypes arg particle types to include in the analysis > arg: file - particle types separated by space > default: all particle types > --first_frame arg first frame considered for analysis > --last_frame arg last frame considered for analysis > --coord arg coordinate analyzed ('x', 'y', or 'z' (default)) > --shift_com shift center of mass to zero > --comment arg store a comment in the output table > --help produce this help message > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"part_distHelp" end time: Jun 07 13:12 UTC >"part_distHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >132/157 Testing: partial_rdfHelp >132/157 Test: partial_rdfHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/partial_rdf/csg_partial_rdf" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"partial_rdfHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >csg_partial_rdf, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Calculate spatially confined rdfs > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Mapping options: > --cg arg [OPTIONAL] coarse graining mapping and bond > definitions > (xml-file). If no file is given, program acts on > original trajectory > --map-ignore arg list of molecules to ignore if mapping is done > separated by ; > >Specific options: > --options arg options file defining the rdfs > --subvolume_radius arg Rdf calc. in spherical subvolume of this radius (from > center of box) > --do-vol-corr Correct for subvolume truncation in rdf > --write-every arg (UNIMPLEMENTED) write after every block of this > length, if --blocking is set, the averages are > cleared after every output > --do-blocks write output for blocking analysis > >Threading options: > --nt arg (=1) number of threads > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"partial_rdfHelp" end time: Jun 07 13:12 UTC >"partial_rdfHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >133/157 Testing: radiiHelp >133/157 Test: radiiHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/radii/csg_radii" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"radiiHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >radii, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >calculate gyration- and hydrodynamic radius for a specific molecule or molecule type > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >Molecule filter options: > --mol arg molecule number > --molname arg (=*) pattern for molecule name > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"radiiHelp" end time: Jun 07 13:12 UTC >"radiiHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >134/157 Testing: sphericalorderHelp >134/157 Test: sphericalorderHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/sphericalorder/csg_sphericalorder" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"sphericalorderHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >sphericalorder, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >!! EXPERIMENTAL !! Calculate spherical order parameter. > Needs non-spherical beads in mapping. > > > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --filter arg (=*) filter molecule names > --radialcut arg (=0) radial cutoff: distance from center where bead is > considered > --minrad arg (=0) minimal distance a parcle has to be apart from center > to be considerd > --refmol arg Reference molecule > --rbinw arg (=0) Do multiple r_bins multiple histograms > >Mapping options: > --cg arg coarse graining mapping and bond definitions > (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"sphericalorderHelp" end time: Jun 07 13:12 UTC >"sphericalorderHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >135/157 Testing: traj_forceHelp >135/157 Test: traj_forceHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps/traj_force/csg_traj_force" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/csgapps >"traj_forceHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >traj_force, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >Adds/subtracts forces from given atomistic trajectories > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > --scale arg (=-1) scaling factor for trajectory forces > --trj-force arg atomistic reference trajectory containing forces to > add/subtract > --out arg output trajectory file with resultant forces > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"traj_forceHelp" end time: Jun 07 13:12 UTC >"traj_forceHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >136/157 Testing: unit_test_bead >136/157 Test: unit_test_bead >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_bead" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_bead" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_bead" end time: Jun 07 13:12 UTC >"unit_test_bead" time elapsed: 00:00:00 >---------------------------------------------------------- > >137/157 Testing: unit_test_beadtriple >137/157 Test: unit_test_beadtriple >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadtriple" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadtriple" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadtriple" end time: Jun 07 13:12 UTC >"unit_test_beadtriple" time elapsed: 00:00:00 >---------------------------------------------------------- > >138/157 Testing: unit_test_basebead >138/157 Test: unit_test_basebead >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_basebead" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_basebead" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_basebead" end time: Jun 07 13:12 UTC >"unit_test_basebead" time elapsed: 00:00:00 >---------------------------------------------------------- > >61/157 Testing: integration_Run_csg_fmatch_3body >61/157 Test: integration_Run_csg_fmatch_3body >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_fmatch" "--top" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/topol.xml" "--trj" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/frame.dump" "--options" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/settings_fmatch_3body.xml" "--cg" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/mapping.xml" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body >"integration_Run_csg_fmatch_3body" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >I have 648 beads in 216 molecules >I have 216 beads in 216 molecules for the coarsegraining >Reading frame, timestep 0 >a: 0.37 ,sigma: 1 ,gamma: 0.12 >Number of spline functions for the interaction CG-CG:48 >a: 0.37 ,sigma: 1 ,gamma: 0.08 >Number of spline functions for the interaction CG-CG-CG:36 > >You are using VOTCA! > >hey, somebody wants to forcematch! > >Using constrained Least Squares! > ><end of output> >Test time = 0.43 sec >---------------------------------------------------------- >Test Failed. >"integration_Run_csg_fmatch_3body" end time: Jun 07 13:12 UTC >"integration_Run_csg_fmatch_3body" time elapsed: 00:00:00 >---------------------------------------------------------- > >139/157 Testing: unit_test_beadmotif_algorithms >139/157 Test: unit_test_beadmotif_algorithms >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_algorithms" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadmotif_algorithms" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 4 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadmotif_algorithms" end time: Jun 07 13:12 UTC >"unit_test_beadmotif_algorithms" time elapsed: 00:00:00 >---------------------------------------------------------- > >140/157 Testing: unit_test_beadmotif_base >140/157 Test: unit_test_beadmotif_base >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_base" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadmotif_base" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 4 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadmotif_base" end time: Jun 07 13:12 UTC >"unit_test_beadmotif_base" time elapsed: 00:00:00 >---------------------------------------------------------- > >141/157 Testing: unit_test_beadmotif_connector >141/157 Test: unit_test_beadmotif_connector >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadmotif_connector" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadmotif_connector" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadmotif_connector" end time: Jun 07 13:12 UTC >"unit_test_beadmotif_connector" time elapsed: 00:00:00 >---------------------------------------------------------- > >143/157 Testing: unit_test_beadstructure_algorithms >143/157 Test: unit_test_beadstructure_algorithms >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadstructure_algorithms" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadstructure_algorithms" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... >Calling break into structures >Bead Count 1 3 >Bead Count 2 5 > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadstructure_algorithms" end time: Jun 07 13:12 UTC >"unit_test_beadstructure_algorithms" time elapsed: 00:00:00 >---------------------------------------------------------- > >144/157 Testing: unit_test_bondedstatistics >144/157 Test: unit_test_bondedstatistics >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_bondedstatistics" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_bondedstatistics" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_bondedstatistics" end time: Jun 07 13:12 UTC >"unit_test_bondedstatistics" time elapsed: 00:00:00 >---------------------------------------------------------- > >142/157 Testing: unit_test_beadstructure_base >142/157 Test: unit_test_beadstructure_base >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_beadstructure_base" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_beadstructure_base" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 10 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_beadstructure_base" end time: Jun 07 13:12 UTC >"unit_test_beadstructure_base" time elapsed: 00:00:00 >---------------------------------------------------------- > >145/157 Testing: unit_test_csg_topology >145/157 Test: unit_test_csg_topology >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_csg_topology" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_csg_topology" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 6 test cases... >interaction name :bond >interaction name :bond > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_csg_topology" end time: Jun 07 13:12 UTC >"unit_test_csg_topology" time elapsed: 00:00:00 >---------------------------------------------------------- > >146/157 Testing: unit_test_interaction >146/157 Test: unit_test_interaction >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_interaction" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_interaction" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 5 test cases... >molecule 1:large 1:index 1 >molecule 1:medium 1:index 1 >molecule 1:small 1:index 1 > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_interaction" end time: Jun 07 13:12 UTC >"unit_test_interaction" time elapsed: 00:00:00 >---------------------------------------------------------- > >148/157 Testing: unit_test_lammpsdumpreaderwriter >148/157 Test: unit_test_lammpsdumpreaderwriter >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_lammpsdumpreaderwriter" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_lammpsdumpreaderwriter" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... >Reading frame, timestep 1 >Reading frame, timestep 1 > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_lammpsdumpreaderwriter" end time: Jun 07 13:12 UTC >"unit_test_lammpsdumpreaderwriter" time elapsed: 00:00:00 >---------------------------------------------------------- > >149/157 Testing: unit_test_nblist_3body >149/157 Test: unit_test_nblist_3body >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_nblist_3body" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_nblist_3body" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_nblist_3body" end time: Jun 07 13:12 UTC >"unit_test_nblist_3body" time elapsed: 00:00:00 >---------------------------------------------------------- > >150/157 Testing: unit_test_nblistgrid_3body >150/157 Test: unit_test_nblistgrid_3body >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_nblistgrid_3body" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_nblistgrid_3body" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_nblistgrid_3body" end time: Jun 07 13:12 UTC >"unit_test_nblistgrid_3body" time elapsed: 00:00:00 >---------------------------------------------------------- > >147/157 Testing: unit_test_lammpsdatareader >147/157 Test: unit_test_lammpsdatareader >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_lammpsdatareader" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_lammpsdatareader" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: >angle >atom >bond >full >molecule > >These styles use the following formats in the atom block: >atom-ID molecule-ID atom-type charge x y z >atom-ID molecule-ID atom-type charge x y z nx ny nz >atom-ID molecule-ID atom-type x y z >atom-ID molecule-ID atom-type x y z nx ny nz >atom-ID atom-type x y z >atom-ID atom-type x y z nx ny nz > > >WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: >angle >atom >bond >full >molecule > >These styles use the following formats in the atom block: >atom-ID molecule-ID atom-type charge x y z >atom-ID molecule-ID atom-type charge x y z nx ny nz >atom-ID molecule-ID atom-type x y z >atom-ID molecule-ID atom-type x y z nx ny nz >atom-ID atom-type x y z >atom-ID atom-type x y z nx ny nz > >6.57991 >5.10424 >5.84802 >6.57991 >5.10424 >5.84802 >10.8431 > 8.3947 >6.85254 >10.8431 > 8.3947 >6.85254 > >WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: >angle >atom >bond >full >molecule > >These styles use the following formats in the atom block: >atom-ID molecule-ID atom-type charge x y z >atom-ID molecule-ID atom-type charge x y z nx ny nz >atom-ID molecule-ID atom-type x y z >atom-ID molecule-ID atom-type x y z nx ny nz >atom-ID atom-type x y z >atom-ID atom-type x y z nx ny nz > >WARNING: Lammps Atoms 1 and 6 belong to different molecules (1:2) >WARNING: Lammps Atoms 0 and 5 belong to different molecules (1:2) >WARNING: Lammps Atoms -1 and 4 belong to different molecules (1:2) > >WARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles: >angle >atom >bond >full >molecule > >These styles use the following formats in the atom block: >atom-ID molecule-ID atom-type charge x y z >atom-ID molecule-ID atom-type charge x y z nx ny nz >atom-ID molecule-ID atom-type x y z >atom-ID molecule-ID atom-type x y z nx ny nz >atom-ID atom-type x y z >atom-ID atom-type x y z nx ny nz > > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.04 sec >---------------------------------------------------------- >Test Passed. >"unit_test_lammpsdatareader" end time: Jun 07 13:12 UTC >"unit_test_lammpsdatareader" time elapsed: 00:00:00 >---------------------------------------------------------- > >151/157 Testing: unit_test_boundarycondition >151/157 Test: unit_test_boundarycondition >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_boundarycondition" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_boundarycondition" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.03 sec >---------------------------------------------------------- >Test Passed. >"unit_test_boundarycondition" end time: Jun 07 13:12 UTC >"unit_test_boundarycondition" time elapsed: 00:00:00 >---------------------------------------------------------- > >152/157 Testing: unit_test_pdbreader >152/157 Test: unit_test_pdbreader >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_pdbreader" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_pdbreader" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 1 test case... >The VOTCA pdb reader attempts to follow the official format: >http://www.wwpdb.org/documentation/file-format > >NOTE the element symbol is important for associating a mass with >each atom, if no element symbol is specified the atom name will be >used and assumed to be an element symbol. >The pdb file format does not support pseudo atoms such as a CH3 >and thus VOTCA cannot read such atoms in when using a .pdb file. >If you need to use pseudo atoms consider using a different file >format such as the lammps data format. >WARNING no charge was specified for >HETATM 1 C UNL 1 -5.249 1.055 -0.000 1.00 0.00 C >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 2 H UNL 1 -6.202 1.521 -0.141 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 3 H UNL 1 -5.390 0.026 0.255 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 4 H UNL 1 -4.682 1.124 -0.904 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 5 H UNL 1 -4.724 1.550 0.790 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 6 C UNL 2 -2.248 1.671 -0.000 1.00 0.00 C >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 7 H UNL 2 -1.518 2.451 0.051 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 8 H UNL 2 -3.153 1.999 0.467 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 9 H UNL 2 -2.442 1.430 -1.024 1.00 0.00 H >Assuming a charge of 0 >WARNING no charge was specified for >HETATM 10 H UNL 2 -1.880 0.804 0.507 1.00 0.00 H >Assuming a charge of 0 >Consistency check for pdbreader >Molecule 0 >Atoms: 6 7 8 9 10 >Molecule 1 >Atoms: 1 2 3 4 5 > > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"unit_test_pdbreader" end time: Jun 07 13:12 UTC >"unit_test_pdbreader" time elapsed: 00:00:00 >---------------------------------------------------------- > >155/157 Testing: template_serialHelp >155/157 Test: template_serialHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template/template_serial" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template >"template_serialHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >template_nblist, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >rough template for rdf calculations > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >RDF options: > --c arg (=1) the cutoff > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"template_serialHelp" end time: Jun 07 13:12 UTC >"template_serialHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >157/157 Testing: regression_UninstallExists >157/157 Test: regression_UninstallExists >Command: "/usr/bin/cmake" "-DFileToCheck=/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials/cmake_uninstall.cmake" "-P" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg-tutorials/CMakeModules/FileExists.cmake" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials >"regression_UninstallExists" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg-tutorials/cmake_uninstall.cmake exists. ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"regression_UninstallExists" end time: Jun 07 13:12 UTC >"regression_UninstallExists" time elapsed: 00:00:00 >---------------------------------------------------------- > >156/157 Testing: template_threadedHelp >156/157 Test: template_threadedHelp >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template/template_threaded" "--help" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/share/template >"template_threadedHelp" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >please submit bugs to https://github.com/votca/csg/issues > >template_threaded_rdf, version 2022.1 (compiled Jun 7 2023, 13:11:39) >votca_tools, version 2022.1 (compiled Jun 7 2023, 13:11:02) >gromacs, 2023.1 (single precision) > >template for threaded rdf calculations > > >Allowed options: > -h [ --help ] display this help and exit > --verbose be loud and noisy > --verbose1 be very loud and noisy > -v [ --verbose2 ] be extremly loud and noisy > --top arg atomistic topology file > >RDF options: > --c arg (=1) the cutoff > >Threading options: > --nt arg (=1) number of threads > >Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time (only works for > Gromacs files) > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > ><end of output> >Test time = 0.01 sec >---------------------------------------------------------- >Test Passed. >"template_threadedHelp" end time: Jun 07 13:12 UTC >"template_threadedHelp" time elapsed: 00:00:00 >---------------------------------------------------------- > >154/157 Testing: unit_test_triplelist >154/157 Test: unit_test_triplelist >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_triplelist" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_triplelist" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 2 test cases... > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"unit_test_triplelist" end time: Jun 07 13:12 UTC >"unit_test_triplelist" time elapsed: 00:00:00 >---------------------------------------------------------- > >87/157 Testing: integration_Compare_csg_stat-imc_multi_output_2 >87/157 Test: integration_Compare_csg_stat-imc_multi_output_2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "all.gmc" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.gmc" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_stat_imc_multi >"integration_Compare_csg_stat-imc_multi_output_2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing all.gmc and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/LJ1-LJ2/smaller_system/all.gmc to a tolerance of 5e-05 ><end of output> >Test time = 0.14 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_stat-imc_multi_output_2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_stat-imc_multi_output_2" time elapsed: 00:00:00 >---------------------------------------------------------- > >62/157 Testing: integration_Compare_csg_fmatch_3body_output1 >62/157 Test: integration_Compare_csg_fmatch_3body_output1 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG.force.fmatch_3body" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body >"integration_Compare_csg_fmatch_3body_output1" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >THE VOTCA::TOOLS FILE COMPARISON > >please submit bugs to bugs@votca.org >votca_compare, version 2022.1 >votca_compare: error: argument -f1/--file1: can't open 'CG-CG.force': [Errno 2] No such file or directory: 'CG-CG.force' ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Failed. >"integration_Compare_csg_fmatch_3body_output1" end time: Jun 07 13:12 UTC >"integration_Compare_csg_fmatch_3body_output1" time elapsed: 00:00:00 >---------------------------------------------------------- > >63/157 Testing: integration_Compare_csg_fmatch_3body_output2 >63/157 Test: integration_Compare_csg_fmatch_3body_output2 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.force" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.force.fmatch_3body" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body >"integration_Compare_csg_fmatch_3body_output2" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >THE VOTCA::TOOLS FILE COMPARISON > >please submit bugs to bugs@votca.org >votca_compare, version 2022.1 >votca_compare: error: argument -f1/--file1: can't open 'CG-CG-CG.force': [Errno 2] No such file or directory: 'CG-CG-CG.force' ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Failed. >"integration_Compare_csg_fmatch_3body_output2" end time: Jun 07 13:12 UTC >"integration_Compare_csg_fmatch_3body_output2" time elapsed: 00:00:00 >---------------------------------------------------------- > >64/157 Testing: integration_Compare_csg_fmatch_3body_output3 >64/157 Test: integration_Compare_csg_fmatch_3body_output3 >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "CG-CG-CG.pot" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/CG-CG-CG.pot.fmatch_3body" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_csg_fmatch_3body >"integration_Compare_csg_fmatch_3body_output3" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >================================================== >======== VOTCA (http://www.votca.org) ======== >================================================== > >THE VOTCA::TOOLS FILE COMPARISON > >please submit bugs to bugs@votca.org >votca_compare, version 2022.1 >votca_compare: error: argument -f1/--file1: can't open 'CG-CG-CG.pot': [Errno 2] No such file or directory: 'CG-CG-CG.pot' ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Failed. >"integration_Compare_csg_fmatch_3body_output3" end time: Jun 07 13:12 UTC >"integration_Compare_csg_fmatch_3body_output3" time elapsed: 00:00:00 >---------------------------------------------------------- > >110/157 Testing: integration_Run_gmx_mdrun >110/157 Test: integration_Run_gmx_mdrun >Command: "/usr/bin/gmx" "mdrun" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_gmx_mdrun" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- > :-) GROMACS - gmx mdrun, 2023.1 (-: > >Executable: /usr/bin/gmx >Data prefix: /usr >Working dir: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >Command line: > gmx mdrun > >hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. >CPU phase discovery... >CPU phase discovery in component linux... >hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. >Found sysfs cpu files under /sys/devices/system/cpu with new topology filenames > > > * Topology extraction from /proc/cpuinfo * > >processor 0 >processor 1 >processor 2 >processor 3 >processor 4 >processor 5 >processor 6 >processor 7 >processor 8 >processor 9 >processor 10 >processor 11 >processor 12 >processor 13 >processor 14 >processor 15 >processor 16 >processor 17 >processor 18 >processor 19 >processor 20 >processor 21 >processor 22 >processor 23 >processor 24 >processor 25 >processor 26 >processor 27 >processor 28 >processor 29 >processor 30 >processor 31 >processor 32 >processor 33 >processor 34 >processor 35 >processor 36 >processor 37 >processor 38 >processor 39 >processor 40 >processor 41 >processor 42 >processor 43 >processor 44 >processor 45 >processor 46 >processor 47 >processor 48 >processor 49 >processor 50 >processor 51 >processor 52 >processor 53 >processor 54 >processor 55 >processor 56 >processor 57 >processor 58 >processor 59 >processor 60 >processor 61 >processor 62 >processor 63 >Found cgroup2 mount point on /sys/fs/cgroup/unified >Failed to read cgroup2 controllers from `/sys/fs/cgroup/unified/cgroup.controllers' >Found cgroup1/cpuset mount point on /sys/fs/cgroup/cpuset >Found cgroup name `/' >Trying to read cgroup1 file </sys/fs/cgroup/cpuset//cpuset.cpus> >cpuset includes 0xffffffff,0xffffffff >Trying to read cgroup1 file </sys/fs/cgroup/cpuset//cpuset.mems> >cpuset includes 0x00000001 > > > * Topology extraction from /sys/devices/system/cpu/ * > >online CPUs 0xffffffff,0xffffffff >found 64 cpu topologies, cpuset 0xffffffff,0xffffffff >os core 0 has cpuset 0x00000001,0x00000001 >os package 0 has cpuset 0xffffffff,0xffffffff >os cluster 65535 has cpuset 0x00000001,0x00000001 >thread 0 has cpuset 0x00000001 >cache depth 1 has cpuset 0x00000001,0x00000001 >cache depth 2 has cpuset 0x00000001,0x00000001 >cache depth 3 has cpuset 0x000000ff,0x000000ff >os core 1 has cpuset 0x00000002,0x00000002 >os cluster 65535 has cpuset 0x00000002,0x00000002 >thread 1 has cpuset 0x00000002 >cache depth 1 has cpuset 0x00000002,0x00000002 >cache depth 2 has cpuset 0x00000002,0x00000002 >os core 2 has cpuset 0x00000004,0x00000004 >os cluster 65535 has cpuset 0x00000004,0x00000004 >thread 2 has cpuset 0x00000004 >cache depth 1 has cpuset 0x00000004,0x00000004 >cache depth 2 has cpuset 0x00000004,0x00000004 >os core 3 has cpuset 0x00000008,0x00000008 >os cluster 65535 has cpuset 0x00000008,0x00000008 >thread 3 has cpuset 0x00000008 >cache depth 1 has cpuset 0x00000008,0x00000008 >cache depth 2 has cpuset 0x00000008,0x00000008 >os core 4 has cpuset 0x00000010,0x00000010 >os cluster 65535 has cpuset 0x00000010,0x00000010 >thread 4 has cpuset 0x00000010 >cache depth 1 has cpuset 0x00000010,0x00000010 >cache depth 2 has cpuset 0x00000010,0x00000010 >os core 5 has cpuset 0x00000020,0x00000020 >os cluster 65535 has cpuset 0x00000020,0x00000020 >thread 5 has cpuset 0x00000020 >cache depth 1 has cpuset 0x00000020,0x00000020 >cache depth 2 has cpuset 0x00000020,0x00000020 >os core 6 has cpuset 0x00000040,0x00000040 >os cluster 65535 has cpuset 0x00000040,0x00000040 >thread 6 has cpuset 0x00000040 >cache depth 1 has cpuset 0x00000040,0x00000040 >cache depth 2 has cpuset 0x00000040,0x00000040 >os core 7 has cpuset 0x00000080,0x00000080 >os cluster 65535 has cpuset 0x00000080,0x00000080 >thread 7 has cpuset 0x00000080 >cache depth 1 has cpuset 0x00000080,0x00000080 >cache depth 2 has cpuset 0x00000080,0x00000080 >os core 8 has cpuset 0x00000100,0x00000100 >os cluster 65535 has cpuset 0x00000100,0x00000100 >thread 8 has cpuset 0x00000100 >cache depth 1 has cpuset 0x00000100,0x00000100 >cache depth 2 has cpuset 0x00000100,0x00000100 >cache depth 3 has cpuset 0x0000ff00,0x0000ff00 >os core 9 has cpuset 0x00000200,0x00000200 >os cluster 65535 has cpuset 0x00000200,0x00000200 >thread 9 has cpuset 0x00000200 >cache depth 1 has cpuset 0x00000200,0x00000200 >cache depth 2 has cpuset 0x00000200,0x00000200 >os core 10 has cpuset 0x00000400,0x00000400 >os cluster 65535 has cpuset 0x00000400,0x00000400 >thread 10 has cpuset 0x00000400 >cache depth 1 has cpuset 0x00000400,0x00000400 >cache depth 2 has cpuset 0x00000400,0x00000400 >os core 11 has cpuset 0x00000800,0x00000800 >os cluster 65535 has cpuset 0x00000800,0x00000800 >thread 11 has cpuset 0x00000800 >cache depth 1 has cpuset 0x00000800,0x00000800 >cache depth 2 has cpuset 0x00000800,0x00000800 >os core 12 has cpuset 0x00001000,0x00001000 >os cluster 65535 has cpuset 0x00001000,0x00001000 >thread 12 has cpuset 0x00001000 >cache depth 1 has cpuset 0x00001000,0x00001000 >cache depth 2 has cpuset 0x00001000,0x00001000 >os core 13 has cpuset 0x00002000,0x00002000 >os cluster 65535 has cpuset 0x00002000,0x00002000 >thread 13 has cpuset 0x00002000 >cache depth 1 has cpuset 0x00002000,0x00002000 >cache depth 2 has cpuset 0x00002000,0x00002000 >os core 14 has cpuset 0x00004000,0x00004000 >os cluster 65535 has cpuset 0x00004000,0x00004000 >thread 14 has cpuset 0x00004000 >cache depth 1 has cpuset 0x00004000,0x00004000 >cache depth 2 has cpuset 0x00004000,0x00004000 >os core 15 has cpuset 0x00008000,0x00008000 >os cluster 65535 has cpuset 0x00008000,0x00008000 >thread 15 has cpuset 0x00008000 >cache depth 1 has cpuset 0x00008000,0x00008000 >cache depth 2 has cpuset 0x00008000,0x00008000 >os core 16 has cpuset 0x00010000,0x00010000 >os cluster 65535 has cpuset 0x00010000,0x00010000 >thread 16 has cpuset 0x00010000 >cache depth 1 has cpuset 0x00010000,0x00010000 >cache depth 2 has cpuset 0x00010000,0x00010000 >cache depth 3 has cpuset 0x00ff0000,0x00ff0000 >os core 17 has cpuset 0x00020000,0x00020000 >os cluster 65535 has cpuset 0x00020000,0x00020000 >thread 17 has cpuset 0x00020000 >cache depth 1 has cpuset 0x00020000,0x00020000 >cache depth 2 has cpuset 0x00020000,0x00020000 >os core 18 has cpuset 0x00040000,0x00040000 >os cluster 65535 has cpuset 0x00040000,0x00040000 >thread 18 has cpuset 0x00040000 >cache depth 1 has cpuset 0x00040000,0x00040000 >cache depth 2 has cpuset 0x00040000,0x00040000 >os core 19 has cpuset 0x00080000,0x00080000 >os cluster 65535 has cpuset 0x00080000,0x00080000 >thread 19 has cpuset 0x00080000 >cache depth 1 has cpuset 0x00080000,0x00080000 >cache depth 2 has cpuset 0x00080000,0x00080000 >os core 20 has cpuset 0x00100000,0x00100000 >os cluster 65535 has cpuset 0x00100000,0x00100000 >thread 20 has cpuset 0x00100000 >cache depth 1 has cpuset 0x00100000,0x00100000 >cache depth 2 has cpuset 0x00100000,0x00100000 >os core 21 has cpuset 0x00200000,0x00200000 >os cluster 65535 has cpuset 0x00200000,0x00200000 >thread 21 has cpuset 0x00200000 >cache depth 1 has cpuset 0x00200000,0x00200000 >cache depth 2 has cpuset 0x00200000,0x00200000 >os core 22 has cpuset 0x00400000,0x00400000 >os cluster 65535 has cpuset 0x00400000,0x00400000 >thread 22 has cpuset 0x00400000 >cache depth 1 has cpuset 0x00400000,0x00400000 >cache depth 2 has cpuset 0x00400000,0x00400000 >os core 23 has cpuset 0x00800000,0x00800000 >os cluster 65535 has cpuset 0x00800000,0x00800000 >thread 23 has cpuset 0x00800000 >cache depth 1 has cpuset 0x00800000,0x00800000 >cache depth 2 has cpuset 0x00800000,0x00800000 >os core 24 has cpuset 0x01000000,0x01000000 >os cluster 65535 has cpuset 0x01000000,0x01000000 >thread 24 has cpuset 0x01000000 >cache depth 1 has cpuset 0x01000000,0x01000000 >cache depth 2 has cpuset 0x01000000,0x01000000 >cache depth 3 has cpuset 0xff000000,0xff000000 >os core 25 has cpuset 0x02000000,0x02000000 >os cluster 65535 has cpuset 0x02000000,0x02000000 >thread 25 has cpuset 0x02000000 >cache depth 1 has cpuset 0x02000000,0x02000000 >cache depth 2 has cpuset 0x02000000,0x02000000 >os core 26 has cpuset 0x04000000,0x04000000 >os cluster 65535 has cpuset 0x04000000,0x04000000 >thread 26 has cpuset 0x04000000 >cache depth 1 has cpuset 0x04000000,0x04000000 >cache depth 2 has cpuset 0x04000000,0x04000000 >os core 27 has cpuset 0x08000000,0x08000000 >os cluster 65535 has cpuset 0x08000000,0x08000000 >thread 27 has cpuset 0x08000000 >cache depth 1 has cpuset 0x08000000,0x08000000 >cache depth 2 has cpuset 0x08000000,0x08000000 >os core 28 has cpuset 0x10000000,0x10000000 >os cluster 65535 has cpuset 0x10000000,0x10000000 >thread 28 has cpuset 0x10000000 >cache depth 1 has cpuset 0x10000000,0x10000000 >cache depth 2 has cpuset 0x10000000,0x10000000 >os core 29 has cpuset 0x20000000,0x20000000 >os cluster 65535 has cpuset 0x20000000,0x20000000 >thread 29 has cpuset 0x20000000 >cache depth 1 has cpuset 0x20000000,0x20000000 >cache depth 2 has cpuset 0x20000000,0x20000000 >os core 30 has cpuset 0x40000000,0x40000000 >os cluster 65535 has cpuset 0x40000000,0x40000000 >thread 30 has cpuset 0x40000000 >cache depth 1 has cpuset 0x40000000,0x40000000 >cache depth 2 has cpuset 0x40000000,0x40000000 >os core 31 has cpuset 0x80000000,0x80000000 >os cluster 65535 has cpuset 0x80000000,0x80000000 >thread 31 has cpuset 0x80000000 >cache depth 1 has cpuset 0x80000000,0x80000000 >cache depth 2 has cpuset 0x80000000,0x80000000 >thread 32 has cpuset 0x00000001,0x0 >thread 33 has cpuset 0x00000002,0x0 >thread 34 has cpuset 0x00000004,0x0 >thread 35 has cpuset 0x00000008,0x0 >thread 36 has cpuset 0x00000010,0x0 >thread 37 has cpuset 0x00000020,0x0 >thread 38 has cpuset 0x00000040,0x0 >thread 39 has cpuset 0x00000080,0x0 >thread 40 has cpuset 0x00000100,0x0 >thread 41 has cpuset 0x00000200,0x0 >thread 42 has cpuset 0x00000400,0x0 >thread 43 has cpuset 0x00000800,0x0 >thread 44 has cpuset 0x00001000,0x0 >thread 45 has cpuset 0x00002000,0x0 >thread 46 has cpuset 0x00004000,0x0 >thread 47 has cpuset 0x00008000,0x0 >thread 48 has cpuset 0x00010000,0x0 >thread 49 has cpuset 0x00020000,0x0 >thread 50 has cpuset 0x00040000,0x0 >thread 51 has cpuset 0x00080000,0x0 >thread 52 has cpuset 0x00100000,0x0 >thread 53 has cpuset 0x00200000,0x0 >thread 54 has cpuset 0x00400000,0x0 >thread 55 has cpuset 0x00800000,0x0 >thread 56 has cpuset 0x01000000,0x0 >thread 57 has cpuset 0x02000000,0x0 >thread 58 has cpuset 0x04000000,0x0 >thread 59 has cpuset 0x08000000,0x0 >thread 60 has cpuset 0x10000000,0x0 >thread 61 has cpuset 0x20000000,0x0 >thread 62 has cpuset 0x40000000,0x0 >thread 63 has cpuset 0x80000000,0x0 >linux/cpufreq: max frequency values will be adjusted by up to 10% > > > * Topology extraction from /sys/devices/system/node * > >possible NUMA nodes 0x00000001 >NUMA indexes: 0 >os node 0 has cpuset 0xffffffff,0xffffffff >found DMIProductName 'PowerEdge R6515' >found DMIProductVersion '' >found DMIBoardVendor 'Dell Inc.' >found DMIBoardName '035YY8' >found DMIBoardVersion 'A03' >found DMIChassisVendor 'Dell Inc.' >found DMIChassisType '23' >found DMIChassisVersion '' >found DMIChassisAssetTag '' >found DMIBIOSVendor 'Dell Inc.' >found DMIBIOSVersion '2.6.6' >found DMIBIOSDate '01/13/2022' >found DMISysVendor 'Dell Inc.' >CPU phase discovery in component x86... >--- Package level has number 1 > >--- L3Cache level has number 2 > >--- L2Cache level has number 3 > >--- L1Cache level has number 4 > >--- Core level has number 5 > >--- PU level has number 6 > >hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. >highest cpuid 10, cpuid type 1 >highest extended cpuid 80000023 >possible CPUs are 0xffffffff,0xffffffff >binding to CPU0 >APIC ID 0x00 legacy_max_log_proc 64 >phys 0 legacy thread 0 >topoext 00000000, 0 nodes, node 4294967295, 2 threads in core 0 >x2APIC 00000000 0: nextshift 1 num 2 type 1 id 0 >x2APIC 00000000 1: nextshift 6 num 64 type 2 id 0 >x2APIC remainder: 0 >this is thread 0 of core 0 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU1 >APIC ID 0x02 legacy_max_log_proc 64 >phys 0 legacy thread 2 >topoext 00000002, 0 nodes, node 4294967295, 2 threads in core 1 >x2APIC 00000002 0: nextshift 1 num 2 type 1 id 2 >x2APIC 00000002 1: nextshift 6 num 64 type 2 id 1 >x2APIC remainder: 0 >this is thread 2 of core 1 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU2 >APIC ID 0x04 legacy_max_log_proc 64 >phys 0 legacy thread 4 >topoext 00000004, 0 nodes, node 4294967295, 2 threads in core 2 >x2APIC 00000004 0: nextshift 1 num 2 type 1 id 4 >x2APIC 00000004 1: nextshift 6 num 64 type 2 id 2 >x2APIC remainder: 0 >this is thread 4 of core 2 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU3 >APIC ID 0x06 legacy_max_log_proc 64 >phys 0 legacy thread 6 >topoext 00000006, 0 nodes, node 4294967295, 2 threads in core 3 >x2APIC 00000006 0: nextshift 1 num 2 type 1 id 6 >x2APIC 00000006 1: nextshift 6 num 64 type 2 id 3 >x2APIC remainder: 0 >this is thread 6 of core 3 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU4 >APIC ID 0x08 legacy_max_log_proc 64 >phys 0 legacy thread 8 >topoext 00000008, 0 nodes, node 4294967295, 2 threads in core 4 >x2APIC 00000008 0: nextshift 1 num 2 type 1 id 8 >x2APIC 00000008 1: nextshift 6 num 64 type 2 id 4 >x2APIC remainder: 0 >this is thread 8 of core 4 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU5 >APIC ID 0x0a legacy_max_log_proc 64 >phys 0 legacy thread 10 >topoext 0000000a, 0 nodes, node 4294967295, 2 threads in core 5 >x2APIC 0000000a 0: nextshift 1 num 2 type 1 id 10 >x2APIC 0000000a 1: nextshift 6 num 64 type 2 id 5 >x2APIC remainder: 0 >this is thread 10 of core 5 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU6 >APIC ID 0x0c legacy_max_log_proc 64 >phys 0 legacy thread 12 >topoext 0000000c, 0 nodes, node 4294967295, 2 threads in core 6 >x2APIC 0000000c 0: nextshift 1 num 2 type 1 id 12 >x2APIC 0000000c 1: nextshift 6 num 64 type 2 id 6 >x2APIC remainder: 0 >this is thread 12 of core 6 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU7 >APIC ID 0x0e legacy_max_log_proc 64 >phys 0 legacy thread 14 >topoext 0000000e, 0 nodes, node 4294967295, 2 threads in core 7 >x2APIC 0000000e 0: nextshift 1 num 2 type 1 id 14 >x2APIC 0000000e 1: nextshift 6 num 64 type 2 id 7 >x2APIC remainder: 0 >this is thread 14 of core 7 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU8 >APIC ID 0x10 legacy_max_log_proc 64 >phys 0 legacy thread 16 >topoext 00000010, 0 nodes, node 4294967295, 2 threads in core 8 >x2APIC 00000010 0: nextshift 1 num 2 type 1 id 16 >x2APIC 00000010 1: nextshift 6 num 64 type 2 id 8 >x2APIC remainder: 0 >this is thread 16 of core 8 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU9 >APIC ID 0x12 legacy_max_log_proc 64 >phys 0 legacy thread 18 >topoext 00000012, 0 nodes, node 4294967295, 2 threads in core 9 >x2APIC 00000012 0: nextshift 1 num 2 type 1 id 18 >x2APIC 00000012 1: nextshift 6 num 64 type 2 id 9 >x2APIC remainder: 0 >this is thread 18 of core 9 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU10 >APIC ID 0x14 legacy_max_log_proc 64 >phys 0 legacy thread 20 >topoext 00000014, 0 nodes, node 4294967295, 2 threads in core 10 >x2APIC 00000014 0: nextshift 1 num 2 type 1 id 20 >x2APIC 00000014 1: nextshift 6 num 64 type 2 id 10 >x2APIC remainder: 0 >this is thread 20 of core 10 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU11 >APIC ID 0x16 legacy_max_log_proc 64 >phys 0 legacy thread 22 >topoext 00000016, 0 nodes, node 4294967295, 2 threads in core 11 >x2APIC 00000016 0: nextshift 1 num 2 type 1 id 22 >x2APIC 00000016 1: nextshift 6 num 64 type 2 id 11 >x2APIC remainder: 0 >this is thread 22 of core 11 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU12 >APIC ID 0x18 legacy_max_log_proc 64 >phys 0 legacy thread 24 >topoext 00000018, 0 nodes, node 4294967295, 2 threads in core 12 >x2APIC 00000018 0: nextshift 1 num 2 type 1 id 24 >x2APIC 00000018 1: nextshift 6 num 64 type 2 id 12 >x2APIC remainder: 0 >this is thread 24 of core 12 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU13 >APIC ID 0x1a legacy_max_log_proc 64 >phys 0 legacy thread 26 >topoext 0000001a, 0 nodes, node 4294967295, 2 threads in core 13 >x2APIC 0000001a 0: nextshift 1 num 2 type 1 id 26 >x2APIC 0000001a 1: nextshift 6 num 64 type 2 id 13 >x2APIC remainder: 0 >this is thread 26 of core 13 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU14 >APIC ID 0x1c legacy_max_log_proc 64 >phys 0 legacy thread 28 >topoext 0000001c, 0 nodes, node 4294967295, 2 threads in core 14 >x2APIC 0000001c 0: nextshift 1 num 2 type 1 id 28 >x2APIC 0000001c 1: nextshift 6 num 64 type 2 id 14 >x2APIC remainder: 0 >this is thread 28 of core 14 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU15 >APIC ID 0x1e legacy_max_log_proc 64 >phys 0 legacy thread 30 >topoext 0000001e, 0 nodes, node 4294967295, 2 threads in core 15 >x2APIC 0000001e 0: nextshift 1 num 2 type 1 id 30 >x2APIC 0000001e 1: nextshift 6 num 64 type 2 id 15 >x2APIC remainder: 0 >this is thread 30 of core 15 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU16 >APIC ID 0x20 legacy_max_log_proc 64 >phys 0 legacy thread 32 >topoext 00000020, 0 nodes, node 4294967295, 2 threads in core 16 >x2APIC 00000020 0: nextshift 1 num 2 type 1 id 32 >x2APIC 00000020 1: nextshift 6 num 64 type 2 id 16 >x2APIC remainder: 0 >this is thread 32 of core 16 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU17 >APIC ID 0x22 legacy_max_log_proc 64 >phys 0 legacy thread 34 >topoext 00000022, 0 nodes, node 4294967295, 2 threads in core 17 >x2APIC 00000022 0: nextshift 1 num 2 type 1 id 34 >x2APIC 00000022 1: nextshift 6 num 64 type 2 id 17 >x2APIC remainder: 0 >this is thread 34 of core 17 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU18 >APIC ID 0x24 legacy_max_log_proc 64 >phys 0 legacy thread 36 >topoext 00000024, 0 nodes, node 4294967295, 2 threads in core 18 >x2APIC 00000024 0: nextshift 1 num 2 type 1 id 36 >x2APIC 00000024 1: nextshift 6 num 64 type 2 id 18 >x2APIC remainder: 0 >this is thread 36 of core 18 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU19 >APIC ID 0x26 legacy_max_log_proc 64 >phys 0 legacy thread 38 >topoext 00000026, 0 nodes, node 4294967295, 2 threads in core 19 >x2APIC 00000026 0: nextshift 1 num 2 type 1 id 38 >x2APIC 00000026 1: nextshift 6 num 64 type 2 id 19 >x2APIC remainder: 0 >this is thread 38 of core 19 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU20 >APIC ID 0x28 legacy_max_log_proc 64 >phys 0 legacy thread 40 >topoext 00000028, 0 nodes, node 4294967295, 2 threads in core 20 >x2APIC 00000028 0: nextshift 1 num 2 type 1 id 40 >x2APIC 00000028 1: nextshift 6 num 64 type 2 id 20 >x2APIC remainder: 0 >this is thread 40 of core 20 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU21 >APIC ID 0x2a legacy_max_log_proc 64 >phys 0 legacy thread 42 >topoext 0000002a, 0 nodes, node 4294967295, 2 threads in core 21 >x2APIC 0000002a 0: nextshift 1 num 2 type 1 id 42 >x2APIC 0000002a 1: nextshift 6 num 64 type 2 id 21 >x2APIC remainder: 0 >this is thread 42 of core 21 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU22 >APIC ID 0x2c legacy_max_log_proc 64 >phys 0 legacy thread 44 >topoext 0000002c, 0 nodes, node 4294967295, 2 threads in core 22 >x2APIC 0000002c 0: nextshift 1 num 2 type 1 id 44 >x2APIC 0000002c 1: nextshift 6 num 64 type 2 id 22 >x2APIC remainder: 0 >this is thread 44 of core 22 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU23 >APIC ID 0x2e legacy_max_log_proc 64 >phys 0 legacy thread 46 >topoext 0000002e, 0 nodes, node 4294967295, 2 threads in core 23 >x2APIC 0000002e 0: nextshift 1 num 2 type 1 id 46 >x2APIC 0000002e 1: nextshift 6 num 64 type 2 id 23 >x2APIC remainder: 0 >this is thread 46 of core 23 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU24 >APIC ID 0x30 legacy_max_log_proc 64 >phys 0 legacy thread 48 >topoext 00000030, 0 nodes, node 4294967295, 2 threads in core 24 >x2APIC 00000030 0: nextshift 1 num 2 type 1 id 48 >x2APIC 00000030 1: nextshift 6 num 64 type 2 id 24 >x2APIC remainder: 0 >this is thread 48 of core 24 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU25 >APIC ID 0x32 legacy_max_log_proc 64 >phys 0 legacy thread 50 >topoext 00000032, 0 nodes, node 4294967295, 2 threads in core 25 >x2APIC 00000032 0: nextshift 1 num 2 type 1 id 50 >x2APIC 00000032 1: nextshift 6 num 64 type 2 id 25 >x2APIC remainder: 0 >this is thread 50 of core 25 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU26 >APIC ID 0x34 legacy_max_log_proc 64 >phys 0 legacy thread 52 >topoext 00000034, 0 nodes, node 4294967295, 2 threads in core 26 >x2APIC 00000034 0: nextshift 1 num 2 type 1 id 52 >x2APIC 00000034 1: nextshift 6 num 64 type 2 id 26 >x2APIC remainder: 0 >this is thread 52 of core 26 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU27 >APIC ID 0x36 legacy_max_log_proc 64 >phys 0 legacy thread 54 >topoext 00000036, 0 nodes, node 4294967295, 2 threads in core 27 >x2APIC 00000036 0: nextshift 1 num 2 type 1 id 54 >x2APIC 00000036 1: nextshift 6 num 64 type 2 id 27 >x2APIC remainder: 0 >this is thread 54 of core 27 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU28 >APIC ID 0x38 legacy_max_log_proc 64 >phys 0 legacy thread 56 >topoext 00000038, 0 nodes, node 4294967295, 2 threads in core 28 >x2APIC 00000038 0: nextshift 1 num 2 type 1 id 56 >x2APIC 00000038 1: nextshift 6 num 64 type 2 id 28 >x2APIC remainder: 0 >this is thread 56 of core 28 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU29 >APIC ID 0x3a legacy_max_log_proc 64 >phys 0 legacy thread 58 >topoext 0000003a, 0 nodes, node 4294967295, 2 threads in core 29 >x2APIC 0000003a 0: nextshift 1 num 2 type 1 id 58 >x2APIC 0000003a 1: nextshift 6 num 64 type 2 id 29 >x2APIC remainder: 0 >this is thread 58 of core 29 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU30 >APIC ID 0x3c legacy_max_log_proc 64 >phys 0 legacy thread 60 >topoext 0000003c, 0 nodes, node 4294967295, 2 threads in core 30 >x2APIC 0000003c 0: nextshift 1 num 2 type 1 id 60 >x2APIC 0000003c 1: nextshift 6 num 64 type 2 id 30 >x2APIC remainder: 0 >this is thread 60 of core 30 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU31 >APIC ID 0x3e legacy_max_log_proc 64 >phys 0 legacy thread 62 >topoext 0000003e, 0 nodes, node 4294967295, 2 threads in core 31 >x2APIC 0000003e 0: nextshift 1 num 2 type 1 id 62 >x2APIC 0000003e 1: nextshift 6 num 64 type 2 id 31 >x2APIC remainder: 0 >this is thread 62 of core 31 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU32 >APIC ID 0x01 legacy_max_log_proc 64 >phys 0 legacy thread 1 >topoext 00000001, 0 nodes, node 4294967295, 2 threads in core 0 >x2APIC 00000001 0: nextshift 1 num 2 type 1 id 1 >x2APIC 00000001 1: nextshift 6 num 64 type 2 id 0 >x2APIC remainder: 0 >this is thread 1 of core 0 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU33 >APIC ID 0x03 legacy_max_log_proc 64 >phys 0 legacy thread 3 >topoext 00000003, 0 nodes, node 4294967295, 2 threads in core 1 >x2APIC 00000003 0: nextshift 1 num 2 type 1 id 3 >x2APIC 00000003 1: nextshift 6 num 64 type 2 id 1 >x2APIC remainder: 0 >this is thread 3 of core 1 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU34 >APIC ID 0x05 legacy_max_log_proc 64 >phys 0 legacy thread 5 >topoext 00000005, 0 nodes, node 4294967295, 2 threads in core 2 >x2APIC 00000005 0: nextshift 1 num 2 type 1 id 5 >x2APIC 00000005 1: nextshift 6 num 64 type 2 id 2 >x2APIC remainder: 0 >this is thread 5 of core 2 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU35 >APIC ID 0x07 legacy_max_log_proc 64 >phys 0 legacy thread 7 >topoext 00000007, 0 nodes, node 4294967295, 2 threads in core 3 >x2APIC 00000007 0: nextshift 1 num 2 type 1 id 7 >x2APIC 00000007 1: nextshift 6 num 64 type 2 id 3 >x2APIC remainder: 0 >this is thread 7 of core 3 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU36 >APIC ID 0x09 legacy_max_log_proc 64 >phys 0 legacy thread 9 >topoext 00000009, 0 nodes, node 4294967295, 2 threads in core 4 >x2APIC 00000009 0: nextshift 1 num 2 type 1 id 9 >x2APIC 00000009 1: nextshift 6 num 64 type 2 id 4 >x2APIC remainder: 0 >this is thread 9 of core 4 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU37 >APIC ID 0x0b legacy_max_log_proc 64 >phys 0 legacy thread 11 >topoext 0000000b, 0 nodes, node 4294967295, 2 threads in core 5 >x2APIC 0000000b 0: nextshift 1 num 2 type 1 id 11 >x2APIC 0000000b 1: nextshift 6 num 64 type 2 id 5 >x2APIC remainder: 0 >this is thread 11 of core 5 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU38 >APIC ID 0x0d legacy_max_log_proc 64 >phys 0 legacy thread 13 >topoext 0000000d, 0 nodes, node 4294967295, 2 threads in core 6 >x2APIC 0000000d 0: nextshift 1 num 2 type 1 id 13 >x2APIC 0000000d 1: nextshift 6 num 64 type 2 id 6 >x2APIC remainder: 0 >this is thread 13 of core 6 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU39 >APIC ID 0x0f legacy_max_log_proc 64 >phys 0 legacy thread 15 >topoext 0000000f, 0 nodes, node 4294967295, 2 threads in core 7 >x2APIC 0000000f 0: nextshift 1 num 2 type 1 id 15 >x2APIC 0000000f 1: nextshift 6 num 64 type 2 id 7 >x2APIC remainder: 0 >this is thread 15 of core 7 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU40 >APIC ID 0x11 legacy_max_log_proc 64 >phys 0 legacy thread 17 >topoext 00000011, 0 nodes, node 4294967295, 2 threads in core 8 >x2APIC 00000011 0: nextshift 1 num 2 type 1 id 17 >x2APIC 00000011 1: nextshift 6 num 64 type 2 id 8 >x2APIC remainder: 0 >this is thread 17 of core 8 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU41 >APIC ID 0x13 legacy_max_log_proc 64 >phys 0 legacy thread 19 >topoext 00000013, 0 nodes, node 4294967295, 2 threads in core 9 >x2APIC 00000013 0: nextshift 1 num 2 type 1 id 19 >x2APIC 00000013 1: nextshift 6 num 64 type 2 id 9 >x2APIC remainder: 0 >this is thread 19 of core 9 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU42 >APIC ID 0x15 legacy_max_log_proc 64 >phys 0 legacy thread 21 >topoext 00000015, 0 nodes, node 4294967295, 2 threads in core 10 >x2APIC 00000015 0: nextshift 1 num 2 type 1 id 21 >x2APIC 00000015 1: nextshift 6 num 64 type 2 id 10 >x2APIC remainder: 0 >this is thread 21 of core 10 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU43 >APIC ID 0x17 legacy_max_log_proc 64 >phys 0 legacy thread 23 >topoext 00000017, 0 nodes, node 4294967295, 2 threads in core 11 >x2APIC 00000017 0: nextshift 1 num 2 type 1 id 23 >x2APIC 00000017 1: nextshift 6 num 64 type 2 id 11 >x2APIC remainder: 0 >this is thread 23 of core 11 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU44 >APIC ID 0x19 legacy_max_log_proc 64 >phys 0 legacy thread 25 >topoext 00000019, 0 nodes, node 4294967295, 2 threads in core 12 >x2APIC 00000019 0: nextshift 1 num 2 type 1 id 25 >x2APIC 00000019 1: nextshift 6 num 64 type 2 id 12 >x2APIC remainder: 0 >this is thread 25 of core 12 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU45 >APIC ID 0x1b legacy_max_log_proc 64 >phys 0 legacy thread 27 >topoext 0000001b, 0 nodes, node 4294967295, 2 threads in core 13 >x2APIC 0000001b 0: nextshift 1 num 2 type 1 id 27 >x2APIC 0000001b 1: nextshift 6 num 64 type 2 id 13 >x2APIC remainder: 0 >this is thread 27 of core 13 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU46 >APIC ID 0x1d legacy_max_log_proc 64 >phys 0 legacy thread 29 >topoext 0000001d, 0 nodes, node 4294967295, 2 threads in core 14 >x2APIC 0000001d 0: nextshift 1 num 2 type 1 id 29 >x2APIC 0000001d 1: nextshift 6 num 64 type 2 id 14 >x2APIC remainder: 0 >this is thread 29 of core 14 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU47 >APIC ID 0x1f legacy_max_log_proc 64 >phys 0 legacy thread 31 >topoext 0000001f, 0 nodes, node 4294967295, 2 threads in core 15 >x2APIC 0000001f 0: nextshift 1 num 2 type 1 id 31 >x2APIC 0000001f 1: nextshift 6 num 64 type 2 id 15 >x2APIC remainder: 0 >this is thread 31 of core 15 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU48 >APIC ID 0x21 legacy_max_log_proc 64 >phys 0 legacy thread 33 >topoext 00000021, 0 nodes, node 4294967295, 2 threads in core 16 >x2APIC 00000021 0: nextshift 1 num 2 type 1 id 33 >x2APIC 00000021 1: nextshift 6 num 64 type 2 id 16 >x2APIC remainder: 0 >this is thread 33 of core 16 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU49 >APIC ID 0x23 legacy_max_log_proc 64 >phys 0 legacy thread 35 >topoext 00000023, 0 nodes, node 4294967295, 2 threads in core 17 >x2APIC 00000023 0: nextshift 1 num 2 type 1 id 35 >x2APIC 00000023 1: nextshift 6 num 64 type 2 id 17 >x2APIC remainder: 0 >this is thread 35 of core 17 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU50 >APIC ID 0x25 legacy_max_log_proc 64 >phys 0 legacy thread 37 >topoext 00000025, 0 nodes, node 4294967295, 2 threads in core 18 >x2APIC 00000025 0: nextshift 1 num 2 type 1 id 37 >x2APIC 00000025 1: nextshift 6 num 64 type 2 id 18 >x2APIC remainder: 0 >this is thread 37 of core 18 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU51 >APIC ID 0x27 legacy_max_log_proc 64 >phys 0 legacy thread 39 >topoext 00000027, 0 nodes, node 4294967295, 2 threads in core 19 >x2APIC 00000027 0: nextshift 1 num 2 type 1 id 39 >x2APIC 00000027 1: nextshift 6 num 64 type 2 id 19 >x2APIC remainder: 0 >this is thread 39 of core 19 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU52 >APIC ID 0x29 legacy_max_log_proc 64 >phys 0 legacy thread 41 >topoext 00000029, 0 nodes, node 4294967295, 2 threads in core 20 >x2APIC 00000029 0: nextshift 1 num 2 type 1 id 41 >x2APIC 00000029 1: nextshift 6 num 64 type 2 id 20 >x2APIC remainder: 0 >this is thread 41 of core 20 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU53 >APIC ID 0x2b legacy_max_log_proc 64 >phys 0 legacy thread 43 >topoext 0000002b, 0 nodes, node 4294967295, 2 threads in core 21 >x2APIC 0000002b 0: nextshift 1 num 2 type 1 id 43 >x2APIC 0000002b 1: nextshift 6 num 64 type 2 id 21 >x2APIC remainder: 0 >this is thread 43 of core 21 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU54 >APIC ID 0x2d legacy_max_log_proc 64 >phys 0 legacy thread 45 >topoext 0000002d, 0 nodes, node 4294967295, 2 threads in core 22 >x2APIC 0000002d 0: nextshift 1 num 2 type 1 id 45 >x2APIC 0000002d 1: nextshift 6 num 64 type 2 id 22 >x2APIC remainder: 0 >this is thread 45 of core 22 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU55 >APIC ID 0x2f legacy_max_log_proc 64 >phys 0 legacy thread 47 >topoext 0000002f, 0 nodes, node 4294967295, 2 threads in core 23 >x2APIC 0000002f 0: nextshift 1 num 2 type 1 id 47 >x2APIC 0000002f 1: nextshift 6 num 64 type 2 id 23 >x2APIC remainder: 0 >this is thread 47 of core 23 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU56 >APIC ID 0x31 legacy_max_log_proc 64 >phys 0 legacy thread 49 >topoext 00000031, 0 nodes, node 4294967295, 2 threads in core 24 >x2APIC 00000031 0: nextshift 1 num 2 type 1 id 49 >x2APIC 00000031 1: nextshift 6 num 64 type 2 id 24 >x2APIC remainder: 0 >this is thread 49 of core 24 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU57 >APIC ID 0x33 legacy_max_log_proc 64 >phys 0 legacy thread 51 >topoext 00000033, 0 nodes, node 4294967295, 2 threads in core 25 >x2APIC 00000033 0: nextshift 1 num 2 type 1 id 51 >x2APIC 00000033 1: nextshift 6 num 64 type 2 id 25 >x2APIC remainder: 0 >this is thread 51 of core 25 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU58 >APIC ID 0x35 legacy_max_log_proc 64 >phys 0 legacy thread 53 >topoext 00000035, 0 nodes, node 4294967295, 2 threads in core 26 >x2APIC 00000035 0: nextshift 1 num 2 type 1 id 53 >x2APIC 00000035 1: nextshift 6 num 64 type 2 id 26 >x2APIC remainder: 0 >this is thread 53 of core 26 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU59 >APIC ID 0x37 legacy_max_log_proc 64 >phys 0 legacy thread 55 >topoext 00000037, 0 nodes, node 4294967295, 2 threads in core 27 >x2APIC 00000037 0: nextshift 1 num 2 type 1 id 55 >x2APIC 00000037 1: nextshift 6 num 64 type 2 id 27 >x2APIC remainder: 0 >this is thread 55 of core 27 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU60 >APIC ID 0x39 legacy_max_log_proc 64 >phys 0 legacy thread 57 >topoext 00000039, 0 nodes, node 4294967295, 2 threads in core 28 >x2APIC 00000039 0: nextshift 1 num 2 type 1 id 57 >x2APIC 00000039 1: nextshift 6 num 64 type 2 id 28 >x2APIC remainder: 0 >this is thread 57 of core 28 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU61 >APIC ID 0x3b legacy_max_log_proc 64 >phys 0 legacy thread 59 >topoext 0000003b, 0 nodes, node 4294967295, 2 threads in core 29 >x2APIC 0000003b 0: nextshift 1 num 2 type 1 id 59 >x2APIC 0000003b 1: nextshift 6 num 64 type 2 id 29 >x2APIC remainder: 0 >this is thread 59 of core 29 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU62 >APIC ID 0x3d legacy_max_log_proc 64 >phys 0 legacy thread 61 >topoext 0000003d, 0 nodes, node 4294967295, 2 threads in core 30 >x2APIC 0000003d 0: nextshift 1 num 2 type 1 id 61 >x2APIC 0000003d 1: nextshift 6 num 64 type 2 id 30 >x2APIC remainder: 0 >this is thread 61 of core 30 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB >binding to CPU63 >APIC ID 0x3f legacy_max_log_proc 64 >phys 0 legacy thread 63 >topoext 0000003f, 0 nodes, node 4294967295, 2 threads in core 31 >x2APIC 0000003f 0: nextshift 1 num 2 type 1 id 63 >x2APIC 0000003f 1: nextshift 6 num 64 type 2 id 31 >x2APIC remainder: 0 >this is thread 63 of core 31 >cache 0 L1d t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 1 L1i t2 linesize 64 linepart 1 ways 8 sets 64, size 32KB >cache 2 L2u t2 linesize 64 linepart 1 ways 8 sets 1024, size 512KB >cache 3 L3u t16 linesize 64 linepart 1 ways 16 sets 32768, size 32768KB > >Summary of x86 CPUID topology: >PU 0 present=1 apicid=0 on PKG 0 CORE 0 DIE -1 NODE -1 >PU 1 present=1 apicid=2 on PKG 0 CORE 1 DIE -1 NODE -1 >PU 2 present=1 apicid=4 on PKG 0 CORE 2 DIE -1 NODE -1 >PU 3 present=1 apicid=6 on PKG 0 CORE 3 DIE -1 NODE -1 >PU 4 present=1 apicid=8 on PKG 0 CORE 4 DIE -1 NODE -1 >PU 5 present=1 apicid=10 on PKG 0 CORE 5 DIE -1 NODE -1 >PU 6 present=1 apicid=12 on PKG 0 CORE 6 DIE -1 NODE -1 >PU 7 present=1 apicid=14 on PKG 0 CORE 7 DIE -1 NODE -1 >PU 8 present=1 apicid=16 on PKG 0 CORE 8 DIE -1 NODE -1 >PU 9 present=1 apicid=18 on PKG 0 CORE 9 DIE -1 NODE -1 >PU 10 present=1 apicid=20 on PKG 0 CORE 10 DIE -1 NODE -1 >PU 11 present=1 apicid=22 on PKG 0 CORE 11 DIE -1 NODE -1 >PU 12 present=1 apicid=24 on PKG 0 CORE 12 DIE -1 NODE -1 >PU 13 present=1 apicid=26 on PKG 0 CORE 13 DIE -1 NODE -1 >PU 14 present=1 apicid=28 on PKG 0 CORE 14 DIE -1 NODE -1 >PU 15 present=1 apicid=30 on PKG 0 CORE 15 DIE -1 NODE -1 >PU 16 present=1 apicid=32 on PKG 0 CORE 16 DIE -1 NODE -1 >PU 17 present=1 apicid=34 on PKG 0 CORE 17 DIE -1 NODE -1 >PU 18 present=1 apicid=36 on PKG 0 CORE 18 DIE -1 NODE -1 >PU 19 present=1 apicid=38 on PKG 0 CORE 19 DIE -1 NODE -1 >PU 20 present=1 apicid=40 on PKG 0 CORE 20 DIE -1 NODE -1 >PU 21 present=1 apicid=42 on PKG 0 CORE 21 DIE -1 NODE -1 >PU 22 present=1 apicid=44 on PKG 0 CORE 22 DIE -1 NODE -1 >PU 23 present=1 apicid=46 on PKG 0 CORE 23 DIE -1 NODE -1 >PU 24 present=1 apicid=48 on PKG 0 CORE 24 DIE -1 NODE -1 >PU 25 present=1 apicid=50 on PKG 0 CORE 25 DIE -1 NODE -1 >PU 26 present=1 apicid=52 on PKG 0 CORE 26 DIE -1 NODE -1 >PU 27 present=1 apicid=54 on PKG 0 CORE 27 DIE -1 NODE -1 >PU 28 present=1 apicid=56 on PKG 0 CORE 28 DIE -1 NODE -1 >PU 29 present=1 apicid=58 on PKG 0 CORE 29 DIE -1 NODE -1 >PU 30 present=1 apicid=60 on PKG 0 CORE 30 DIE -1 NODE -1 >PU 31 present=1 apicid=62 on PKG 0 CORE 31 DIE -1 NODE -1 >PU 32 present=1 apicid=1 on PKG 0 CORE 0 DIE -1 NODE -1 >PU 33 present=1 apicid=3 on PKG 0 CORE 1 DIE -1 NODE -1 >PU 34 present=1 apicid=5 on PKG 0 CORE 2 DIE -1 NODE -1 >PU 35 present=1 apicid=7 on PKG 0 CORE 3 DIE -1 NODE -1 >PU 36 present=1 apicid=9 on PKG 0 CORE 4 DIE -1 NODE -1 >PU 37 present=1 apicid=11 on PKG 0 CORE 5 DIE -1 NODE -1 >PU 38 present=1 apicid=13 on PKG 0 CORE 6 DIE -1 NODE -1 >PU 39 present=1 apicid=15 on PKG 0 CORE 7 DIE -1 NODE -1 >PU 40 present=1 apicid=17 on PKG 0 CORE 8 DIE -1 NODE -1 >PU 41 present=1 apicid=19 on PKG 0 CORE 9 DIE -1 NODE -1 >PU 42 present=1 apicid=21 on PKG 0 CORE 10 DIE -1 NODE -1 >PU 43 present=1 apicid=23 on PKG 0 CORE 11 DIE -1 NODE -1 >PU 44 present=1 apicid=25 on PKG 0 CORE 12 DIE -1 NODE -1 >PU 45 present=1 apicid=27 on PKG 0 CORE 13 DIE -1 NODE -1 >PU 46 present=1 apicid=29 on PKG 0 CORE 14 DIE -1 NODE -1 >PU 47 present=1 apicid=31 on PKG 0 CORE 15 DIE -1 NODE -1 >PU 48 present=1 apicid=33 on PKG 0 CORE 16 DIE -1 NODE -1 >PU 49 present=1 apicid=35 on PKG 0 CORE 17 DIE -1 NODE -1 >PU 50 present=1 apicid=37 on PKG 0 CORE 18 DIE -1 NODE -1 >PU 51 present=1 apicid=39 on PKG 0 CORE 19 DIE -1 NODE -1 >PU 52 present=1 apicid=41 on PKG 0 CORE 20 DIE -1 NODE -1 >PU 53 present=1 apicid=43 on PKG 0 CORE 21 DIE -1 NODE -1 >PU 54 present=1 apicid=45 on PKG 0 CORE 22 DIE -1 NODE -1 >PU 55 present=1 apicid=47 on PKG 0 CORE 23 DIE -1 NODE -1 >PU 56 present=1 apicid=49 on PKG 0 CORE 24 DIE -1 NODE -1 >PU 57 present=1 apicid=51 on PKG 0 CORE 25 DIE -1 NODE -1 >PU 58 present=1 apicid=53 on PKG 0 CORE 26 DIE -1 NODE -1 >PU 59 present=1 apicid=55 on PKG 0 CORE 27 DIE -1 NODE -1 >PU 60 present=1 apicid=57 on PKG 0 CORE 28 DIE -1 NODE -1 >PU 61 present=1 apicid=59 on PKG 0 CORE 29 DIE -1 NODE -1 >PU 62 present=1 apicid=61 on PKG 0 CORE 30 DIE -1 NODE -1 >PU 63 present=1 apicid=63 on PKG 0 CORE 31 DIE -1 NODE -1 > >CPU phase discovery in component no_os... > >Fixup root sets > >Propagate sets > >Removing unauthorized sets from all sets > >Ok, finished tweaking, now connect >PCI phase discovery... >PCI phase discovery in component linux... >hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. > >PCI hierarchy: >0000:00:00.0 Device [1022:1480 (1028:08fc) rev=00 class=0600] > >Adding new PCI hostbridge 0000:00 > new PCI hostbridge covers 0000:[00-02] >Adding new PCI hostbridge 0000:40 > new PCI hostbridge covers 0000:[40-47] >Adding new PCI hostbridge 0000:80 > new PCI hostbridge covers 0000:[80-84] >Adding new PCI hostbridge 0000:c0 > new PCI hostbridge covers 0000:[c0-c9] >Looking for parent of PCI busid 0000:00:00.0 > will attach PCI bus to cpuset 0xffffffff,0xffffffff >Adding PCI locality Machine P#0 for bus 0000:[00:02] >Looking for parent of PCI busid 0000:40:00.0 > will attach PCI bus to cpuset 0xffffffff,0xffffffff >Adding PCI locality Machine P#0 for bus 0000:[40:47] >Looking for parent of PCI busid 0000:80:00.0 > will attach PCI bus to cpuset 0xffffffff,0xffffffff >Adding PCI locality Machine P#0 for bus 0000:[80:84] >Looking for parent of PCI busid 0000:c0:00.0 > will attach PCI bus to cpuset 0xffffffff,0xffffffff >Adding PCI locality Machine P#0 for bus 0000:[c0:c9] >IO phase discovery... >IO phase discovery in component linux... >pcidisc looking for bus id 0000:81:00.0 > found pci locality for 0000:[80:84] > looking for bus 0000:81:00.0 below Machine P#0 > found busid 0000:81:00.0 >pcidisc looking for bus id 0000:c3:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c3:00.0 below Machine P#0 > found busid 0000:c3:00.0 >pcidisc looking for bus id 0000:82:00.0 > found pci locality for 0000:[80:84] > looking for bus 0000:82:00.0 below Machine P#0 > found busid 0000:82:00.0 >pcidisc looking for bus id 0000:c3:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c3:00.0 below Machine P#0 > found busid 0000:c3:00.0 >pcidisc looking for bus id 0000:41:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:41:00.0 below Machine P#0 > found busid 0000:41:00.0 >pcidisc looking for bus id 0000:41:00.1 > found pci locality for 0000:[40:47] > looking for bus 0000:41:00.1 below Machine P#0 > found busid 0000:41:00.1 >pcidisc looking for bus id 0000:41:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:41:00.0 below Machine P#0 > found busid 0000:41:00.0 >pcidisc looking for bus id 0000:41:00.1 > found pci locality for 0000:[40:47] > looking for bus 0000:41:00.1 below Machine P#0 > found busid 0000:41:00.1 >MISC phase discovery... >MISC phase discovery in component linux... >ANNOTATE phase discovery... >ANNOTATE phase discovery in component linux... >pcidisc looking for bus id 0000:c7:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c7:00.0 below Machine P#0 > found busid 0000:c0:03.4 >pcidisc looking for bus id 0000:c5:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c5:00.0 below Machine P#0 > found busid 0000:c0:03.2 >pcidisc looking for bus id 0000:81:00.0 > found pci locality for 0000:[80:84] > looking for bus 0000:81:00.0 below Machine P#0 > found busid 0000:81:00.0 >pcidisc looking for bus id 0000:40:01.0 > found pci locality for 0000:[40:47] > looking for bus 0000:40:01.0 below Machine P#0 > found busid 0000:40:01.0 >pcidisc looking for bus id 0000:44:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:44:00.0 below Machine P#0 > found busid 0000:40:03.3 >pcidisc looking for bus id 0000:00:03.0 > found pci locality for 0000:[00:02] > looking for bus 0000:00:03.0 below Machine P#0 > found busid 0000:00:03.0 >pcidisc looking for bus id 0000:42:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:42:00.0 below Machine P#0 > found busid 0000:40:03.1 >pcidisc looking for bus id 0000:c6:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c6:00.0 below Machine P#0 > found busid 0000:c0:03.3 >pcidisc looking for bus id 0000:c4:00.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c4:00.0 below Machine P#0 > found busid 0000:c0:03.1 >pcidisc looking for bus id 0000:82:00.0 > found pci locality for 0000:[80:84] > looking for bus 0000:82:00.0 below Machine P#0 > found busid 0000:82:00.0 >pcidisc looking for bus id 0000:c0:01.0 > found pci locality for 0000:[c0:c9] > looking for bus 0000:c0:01.0 below Machine P#0 > found busid 0000:c0:01.0 >pcidisc looking for bus id 0000:45:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:45:00.0 below Machine P#0 > found busid 0000:40:03.4 >pcidisc looking for bus id 0000:43:00.0 > found pci locality for 0000:[40:47] > looking for bus 0000:43:00.0 below Machine P#0 > found busid 0000:40:03.2 >ANNOTATE phase discovery in component pci... >--- Package level has number 1 > >--- L3Cache level has number 2 > >--- L2Cache level has number 3 > >--- L1Cache level has number 4 > >--- Core level has number 5 > >--- PU level has number 6 > > >Removing bridge objects if needed > >Removing empty objects > >Removing levels with HWLOC_TYPE_FILTER_KEEP_STRUCTURE >--- Package level has number 1 > >--- L3Cache level has number 2 > >--- L2Cache level has number 3 > >--- L1Cache level has number 4 > >--- Core level has number 5 > >--- PU level has number 6 > > >Propagate total memory up >hwloc verbose debug enabled, may be disabled with HWLOC_DEBUG_VERBOSE=0 in the environment. >Sorting memory tiers... > tier 0 = node L#0 P#0 with tier type 0 and local BW #0 >UNKNOWN-memory-tier max bandwidth 0 >SPM-memory-tier min bandwidth 0 >cannot assume SPM means HBM >Reading file topol.tpr, VERSION 2023.1 (single precision) > >NOTE: Parallelization is limited by the small number of atoms, > only starting 1 thread-MPI ranks. > You can use the -nt and/or -ntmpi option to optimize the number of threads. > >Using 1 MPI thread >Using 16 OpenMP threads > >starting mdrun 'Flex water' >1 steps, 0.0 ps. > >Writing final coordinates. > >NOTE: 27 % of the run time was spent in pair search, > you might want to increase nstlist (this has no effect on accuracy) > > Core t (s) Wall t (s) (%) > Time: 3.202 3.543 90.4 > (ns/day) (hour/ns) >Performance: 0.098 246.073 > >GROMACS reminds you: "I Used To Care, But Things Have Changed" (Bob Dylan) > ><end of output> >Test time = 4.97 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_gmx_mdrun" end time: Jun 07 13:12 UTC >"integration_Run_gmx_mdrun" time elapsed: 00:00:04 >---------------------------------------------------------- > >111/157 Testing: integration_Run_csg_map_gmx >111/157 Test: integration_Run_csg_map_gmx >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "topol.tpr" "--trj" "traj.trr" "--out" "traj.gro" "--no-map" "--nframes" "1" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_csg_map_gmx" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) >I have 9 beads in 3 molecules >trr version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 >writing coarse-grained trajectory to traj.gro ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_map_gmx" end time: Jun 07 13:12 UTC >"integration_Run_csg_map_gmx" time elapsed: 00:00:00 >---------------------------------------------------------- > >113/157 Testing: integration_Run_csg_map_gmx_xtc >113/157 Test: integration_Run_csg_map_gmx_xtc >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/csg_map" "--top" "topol.tpr" "--trj" "traj_comp.xtc" "--out" "traj_comp.gro" "--no-map" "--nframes" "1" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Run_csg_map_gmx_xtc" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Reading file topol.tpr, VERSION 2023.1 (single precision) >I have 9 beads in 3 molecules > Reading frame 0 time 0.000 >writing coarse-grained trajectory to traj_comp.gro ><end of output> >Test time = 0.02 sec >---------------------------------------------------------- >Test Passed. >"integration_Run_csg_map_gmx_xtc" end time: Jun 07 13:12 UTC >"integration_Run_csg_map_gmx_xtc" time elapsed: 00:00:00 >---------------------------------------------------------- > >112/157 Testing: integration_Compare_csg_map_gmx_output >112/157 Test: integration_Compare_csg_map_gmx_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "traj.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Compare_csg_map_gmx_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing traj.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_map_gmx_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_map_gmx_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >114/157 Testing: integration_Compare_csg_map_gmx_xtc_output >114/157 Test: integration_Compare_csg_map_gmx_xtc_output >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/tools/scripts/votca_compare" "--etol" "5e-5" "-f1" "traj_comp.gro" "-f2" "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tools/Run_gmx_3mols >"integration_Compare_csg_map_gmx_xtc_output" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Comparing traj_comp.gro and /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1/csg/src/tools/references/spce/3mols/conf.gro to a tolerance of 5e-05 ><end of output> >Test time = 0.05 sec >---------------------------------------------------------- >Test Passed. >"integration_Compare_csg_map_gmx_xtc_output" end time: Jun 07 13:12 UTC >"integration_Compare_csg_map_gmx_xtc_output" time elapsed: 00:00:00 >---------------------------------------------------------- > >153/157 Testing: unit_test_tabulatedpotential >153/157 Test: unit_test_tabulatedpotential >Command: "/var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests/unit_test_tabulatedpotential" >Directory: /var/tmp/portage/sci-chemistry/votca-2022.1/work/votca-2022.1_build/csg/src/tests >"unit_test_tabulatedpotential" start time: Jun 07 13:12 UTC >Output: >---------------------------------------------------------- >Running 3 test cases... >Number of H2 96 >bonded_values after pulling out of statistics 4560 >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt >histogram created using 4560 data-rows, written to file_interactions.txt > >[1;32;49m*** No errors detected >[0;39;49m ><end of output> >Test time = 5.86 sec >---------------------------------------------------------- >Test Passed. >"unit_test_tabulatedpotential" end time: Jun 07 13:12 UTC >"unit_test_tabulatedpotential" time elapsed: 00:00:05 >---------------------------------------------------------- > >End testing: Jun 07 13:12 UTC > >csg = 16.39 sec*proc > >csg-tutorials = 0.01 sec*proc > >csgapps = 0.22 sec*proc > >integration = 9.19 sec*proc > >tools = 11.71 sec*proc > >unit = 8.15 sec*proc > >votca = 18.16 sec*proc >
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