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Gentoo's Bugzilla – Attachment 562866 Details for
Bug 359785
sci-chemistry/apbs fails tests
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build.log (1.4.1-r2, ppc)
apbs-1.4.1-r2:20190125-184202.log (text/plain), 99.42 KB, created by
ernsteiswuerfel
on 2019-01-26 13:39:44 UTC
(
hide
)
Description:
build.log (1.4.1-r2, ppc)
Filename:
MIME Type:
Creator:
ernsteiswuerfel
Created:
2019-01-26 13:39:44 UTC
Size:
99.42 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-chemistry/apbs-1.4.1-r2 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: sci-chemistry@gentoo.org >[32;01m * [39;49;00mUSE: abi_ppc_32 elibc_glibc kernel_linux openmp ppc python_targets_python2_7 userland_GNU >[32;01m * [39;49;00mFEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox >>>> Unpacking source... >>>> Unpacking apbs-1.4.1.zip to /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... > [32;01m*[0m Applying apbs-1.4.1-multilib.patch ... >[A[96C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying apbs-1.4.1-manip.patch ... >[A[96C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying apbs-1.4.1-python.patch ... >[A[96C [34;01m[ [32;01mok[34;01m ][0m >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build" >cmake -C /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_SKIP_RPATH=ON -DTOOLS_PATH=/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/image/usr -DSYS_LIBPATHS=/usr/lib -DLIBRARY_INSTALL_PATH=lib -DFETK_PATH=/usr/ -DBUILD_SHARED_LIBS=ON -DENABLE_QUIT=OFF -DBUILD_DOC=no -DBUILD_TOOLS=no -DENABLE_BEM=OFF -DENABLE_DEBUG=no -DENABLE_VERBOSE_DEBUG=no -DENABLE_FAST=no -DENABLE_FETK=no -DENABLE_MPI=no -DENABLE_PYTHON=no -DENABLE_iAPBS=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs >loading initial cache file /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/gentoo_common_config.cmake >-- The C compiler identification is GNU 7.4.0 >-- The CXX compiler identification is GNU 7.4.0 >-- Check for working C compiler: /usr/bin/powerpc-unknown-linux-gnu-gcc >-- Check for working C compiler: /usr/bin/powerpc-unknown-linux-gnu-gcc -- works >-- Detecting C compiler ABI info >-- Detecting C compiler ABI info - done >-- Detecting C compile features >-- Detecting C compile features - done >-- Check for working CXX compiler: /usr/bin/powerpc-unknown-linux-gnu-g++ >-- Check for working CXX compiler: /usr/bin/powerpc-unknown-linux-gnu-g++ -- works >-- Detecting CXX compiler ABI info >-- Detecting CXX compiler ABI info - done >-- Detecting CXX compile features >-- Detecting CXX compile features - done >-- Setting project paths >-- Setting lookup paths for headers and libraries >-- Computing machine epsilon values >-- Floating point epsilon is 2.220446e-16 >-- Double precision epsilon is 2.220446e-16 >-- Looking for time >-- Looking for time - found >-- Looking for rand >-- Looking for rand - found >-- Looking for srand >-- Looking for srand - found >-- Found fetk: /usr >-- External maloc library was found: /usr/lib/libmaloc.so >-- Looking for include file maloc/maloc.h >-- Looking for include file maloc/maloc.h - found >-- External maloc headers found >-- Inline functions enabled >-- Checking for OpenMP >CMake Warning (dev) at /usr/share/cmake/Modules/FindOpenMP.cmake:200 (if): > Policy CMP0054 is not set: Only interpret if() arguments as variables or > keywords when unquoted. Run "cmake --help-policy CMP0054" for policy > details. Use the cmake_policy command to set the policy and suppress this > warning. > > Quoted variables like "c" will no longer be dereferenced when the policy is > set to NEW. Since the policy is not set the OLD behavior will be used. >Call Stack (most recent call first): > /usr/share/cmake/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS) > CMakeLists.txt:473 (find_package) >This warning is for project developers. Use -Wno-dev to suppress it. > >-- Found OpenMP_C: -fopenmp (found version "4.5") >-- Found OpenMP_CXX: -fopenmp (found version "4.5") >-- OpenMP support enabled >libs: -lmaloc-lm-fopenmp >-- Adding apbs_generic >-- With source files nosh.c;mgparm.c;femparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c >-- With external header files nosh.h;mgparm.h;femparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h >-- With internal header files >-- With library dependencies -lmaloc;-lm;-fopenmp >-- Added apbs_generic >-- Adding apbs_pmgc >-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c >-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h >-- With internal header files >-- With library dependencies -lmaloc;-lm;-fopenmp;apbs_geoflow >-- Added apbs_pmgc >-- Adding apbs_mg >-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c >-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h >-- With internal header files >-- With library dependencies -lmaloc;-lm;-fopenmp;apbs_generic;apbs_pmgc >-- Added apbs_mg >-- Adding apbs_geoflow >-- With source files cpbconcz2.cpp;modules.cpp;pbsolvercz.cpp;solvationsub.cpp;subfunction.cpp;surfconcz.cpp >-- With external header files cpbconcz2.h >-- With internal header files >-- With library dependencies -lmaloc;-lm;-fopenmp >-- Added apbs_geoflow >-- >-- >-- -lmaloc;-lm;-fopenmp apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow >-- >-- -std=c99 >-- <<< Gentoo configuration >>> >Build type Gentoo >Install path /usr >Compiler flags: >C -std=c99 >C++ -O2 -mcpu=powerpc -pipe >Linker flags: >Executable -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu >Module -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu >Shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu > >-- Configuring done >-- Generating done >CMake Warning: > Manually-specified variables were not used by the project: > > ENABLE_QUIT > TOOLS_PATH > > >-- Build files have been written to: /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build" >make -j34 -l32 VERBOSE=1 >/usr/bin/cmake -H/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs -B/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build --check-build-system CMakeFiles/Makefile.cmake 0 >/usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles/progress.marks >make -f CMakeFiles/Makefile2 all >make[1]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >make -f src/geoflow/CMakeFiles/apbs_geoflow.dir/build.make src/geoflow/CMakeFiles/apbs_geoflow.dir/depend >make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/DependInfo.cmake --color= >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/generic /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= >Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/depend.internal". >Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow/CMakeFiles/apbs_geoflow.dir/depend.internal". >[35m[1mScanning dependencies of target apbs_geoflow[0m >Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/depend.internal". >Dependee "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic/CMakeFiles/apbs_generic.dir/depend.internal". >[35m[1mScanning dependencies of target apbs_generic[0m >make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >make -f src/geoflow/CMakeFiles/apbs_geoflow.dir/build.make src/geoflow/CMakeFiles/apbs_geoflow.dir/build >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >[ 1%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -pipe -fPIC -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/pbsolvercz.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/pbsolvercz.cpp >[ 3%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/solvationsub.cpp.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -pipe -fPIC -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/solvationsub.cpp.o -c 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-I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -pipe -fPIC -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/subfunction.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/subfunction.cpp >[ 9%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/modules.cpp.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -pipe -fPIC -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/modules.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/modules.cpp >[ 11%] [32mBuilding CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/geoflow && /usr/bin/powerpc-unknown-linux-gnu-g++ -Dapbs_geoflow_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -O2 -mcpu=powerpc -pipe -fPIC -fopenmp -std=c++0x -o CMakeFiles/apbs_geoflow.dir/surfconcz.cpp.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/geoflow/surfconcz.cpp >make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >[ 17%] [32mBuilding C object 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[[01;35m[K-Wimplicit-function-declaration[m[K] > [01;35m[KBEMparm_copy[m[K(thee->bemparm, source->bemparm); > [01;35m[K^~~~~~~~~~~~[m[K > [32m[KFEMparm_copy[m[K >[ 44%] [32m[1mLinking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 >/usr/bin/powerpc-unknown-linux-gnu-gcc -fPIC -std=c99 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -shared -Wl,-soname,libapbs_generic.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o 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>cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/pmgc/mgsubd.c >[ 73%] [32mBuilding C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o[0m >[ 75%] [32mBuilding C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/pmgc && /usr/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_pmgc_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c 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CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -lmaloc -lm -fopenmp /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp >make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >[ 82%] Built target apbs_pmgc >make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs 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'/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build >make[2]: Entering directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build' >[ 84%] [32mBuilding C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o[0m >[ 86%] [32mBuilding C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o[0m >cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src/mg && /usr/bin/powerpc-unknown-linux-gnu-gcc -Dapbs_mg_EXPORTS -I/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src -I/usr/include/eigen3 -DNDEBUG -std=c99 -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/src/mg/vgrid.c >[ 88%] [32mBuilding C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o[0m >cd 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>/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/environment: line 4277: python_export_best: command not found > > >---------------------------------------------------------------------- > APBS -- Adaptive Poisson-Boltzmann Solver > Version 1.4 > > Nathan A. Baker (nathan.baker@pnnl.gov) > Pacific Northwest National Laboratory > > Additional contributing authors listed in the code documentation. > > Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific > Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific > Northwest Division for the U.S. Department of Energy. > > Portions Copyright (c) 2002-2010, Washington University in St. Louis. > Portions Copyright (c) 2002-2010, Nathan A. Baker. > Portions Copyright (c) 1999-2002, The Regents of the University of California. > Portions Copyright (c) 1995, Michael Holst. > All rights reserved. > > Redistribution and use in source and binary forms, with or without > modification, are permitted provided that the following conditions are met: > > * Redistributions of source code must retain the above copyright notice, this > list of conditions and the following disclaimer. > > * Redistributions in binary form must reproduce the above copyright notice, > this list of conditions and the following disclaimer in the documentation > and/or other materials provided with the distribution. > > * Neither the name of the developer nor the names of its contributors may be > used to endorse or promote products derived from this software without > specific prior written permission. > > THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND > ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED > WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE > DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR > ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES > (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; > LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND > ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT > (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS > SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. >---------------------------------------------------------------------- > APBS uses FETK (the Finite Element ToolKit) to solve the > Poisson-Boltzmann equation numerically. FETK is a portable collection > of finite element modeling class libraries developed by the Michael Holst > research group and written in an object-oriented form of C. FEtk is > designed to solve general coupled systems of nonlinear partial differential > equations using adaptive finite element methods, inexact Newton methods, > and algebraic multilevel methods. More information about FEtk may be found > at <http://www.FEtk.ORG>. >---------------------------------------------------------------------- > APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. > Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG> > which has been modified by Patrice Koehl > <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and > memory usage when solving the Poisson-Boltzmann equation. >---------------------------------------------------------------------- > Please cite your use of APBS as: > > Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of > nanosystems: application to microtubules and the ribosome. Proc. > Natl. Acad. Sci. USA 98, 10037-10041 2001. > > >This executable compiled on Jan 25 2019 at 19:42:47 > >1.4 >Testing all sections >The following sections will be tested: born, actin-dimer, alkanes, FKBP, hca-bind, ionize, ion-pmf, ion-protein, pka-lig, point-pmf, solv, geoflow >================================================================================ >Running tests for born section >-------------------------------------------------------------------------------- >Testing forces from apbs-forces.in > >Checking forces for input file apbs-forces.in >Checking Polar Forces >Checking Apolar Forces >Elapsed time: 0.011241 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-mol-auto.in > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 >*** PASSED *** >Elapsed time: 13.007700 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-auto.in > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 >*** PASSED *** >Elapsed time: 21.280534 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-mol-parallel.in > >Splitting the input file into 4 separate files using the inputgen utility > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 0 results: > -5.761864094552E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 1 results: > -5.762728170718E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 2 results: > -5.761864257239E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 3 results: > -5.762728344954E+01 > >Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 >*** PASSED *** >Elapsed time: 45.825982 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-parallel.in > >Splitting the input file into 4 separate files using the inputgen utility > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 0 results: > -5.734895113069E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 1 results: > -5.734462051928E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 2 results: > -5.734895146550E+01 > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 3 results: > -5.734462084052E+01 > >Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 >*** PASSED *** >Elapsed time: 49.648748 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 129.774205 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for actin-dimer section >-------------------------------------------------------------------------------- >Testing input file apbs-mol-auto.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.048683058623E+02 against expected result 1.048683E+02 >*** PASSED *** >Elapsed time: 364.162788 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-auto.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.095841077687E+02 against expected result 1.095841E+02 >*** PASSED *** >Elapsed time: 253.498379 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-mol-parallel.in > >Splitting the input file into 8 separate files using the inputgen utility > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 0 results: > 8.344489735016E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 1 results: > -9.010749548092E-01 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 2 results: > 3.002011083291E+01 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 3 results: > 8.710240552182E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 4 results: > 2.108446480097E+01 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 5 results: > 2.371738924675E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 6 results: > -1.892943480838E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 7 results: > 3.043753521010E+01 > >Testing computed result 9.817456162021E+01 against expected result 9.817463E+01 >*** PASSED *** >Elapsed time: 1288.451413 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-parallel.in > >Splitting the input file into 8 separate files using the inputgen utility > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 0 results: > 8.732209150876E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 1 results: > -1.155195837104E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 2 results: > 3.228473728525E+01 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 3 results: > 9.405155087970E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 4 results: > 3.637600005479E+01 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 5 results: > 1.004590063265E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 6 results: > -1.699465221507E+00 > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Processor 7 results: > 3.059403714563E+01 > >Testing computed result 1.155420677292E+02 against expected result 1.155422E+02 >*** PASSED *** >Elapsed time: 1096.482537 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 3002.595117 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for alkanes section >-------------------------------------------------------------------------------- >Testing input file alkanes.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 >*** PASSED *** >Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 >*** PASSED *** >Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 >*** PASSED *** >Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 >*** PASSED *** >Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 >*** PASSED *** >Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 >*** PASSED *** >Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 >*** PASSED *** >Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 >*** PASSED *** >Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 >*** PASSED *** >Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 >*** PASSED *** >Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 >*** PASSED *** >Elapsed time: 71.358532 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 71.358532 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for FKBP section >-------------------------------------------------------------------------------- >Testing input file 1d7h-dmso-mol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.500810086371E+01 against expected result 1.500769E+01 >*** FAILED *** > APBS returned 1.500810000000e+01 > Expected result is 1.500770000000e+01 (0.0026653% error) >Elapsed time: 51.063102 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file 1d7h-dmso-smol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.624454192072E+01 against expected result 1.624455E+01 >*** FAILED *** > APBS returned 1.624450000000e+01 > Expected result is 1.624460000000e+01 (0.000615589% error) >Elapsed time: 46.249726 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file 1d7i-dss-mol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.442499933668E+01 against expected result 1.442501E+01 >*** PASSED *** >Elapsed time: 50.890618 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file 1d7i-dss-smol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.545150742844E+01 against expected result 1.545150E+01 >*** PASSED *** >Elapsed time: 46.844032 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 195.047478 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for hca-bind section >-------------------------------------------------------------------------------- >Testing input file apbs-mol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -5.246475812665E+01 against expected result -5.246468E+01 >*** FAILED *** > APBS returned -5.246480000000e+01 > Expected result is -5.246470000000e+01 (0.000190604% error) >Elapsed time: 48.678982 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -5.405979017066E+01 against expected result -5.405978E+01 >*** PASSED *** >Elapsed time: 42.935228 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 91.614210 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for ionize section >-------------------------------------------------------------------------------- >Testing input file apbs-mol.in > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 >*** PASSED *** >Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 >*** PASSED *** >Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 >*** PASSED *** >Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 >*** PASSED *** >Elapsed time: 16.868836 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol.in > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 >*** PASSED *** >Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 >*** PASSED *** >Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 >*** PASSED *** >Testing computed result -4.721246714829E+02 against expected result -4.721247E+02 >*** PASSED *** >Elapsed time: 17.345739 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 34.214575 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for ion-pmf section >-------------------------------------------------------------------------------- >Testing input file ion-pmf.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Vpmg_ibForce: No force for zero ionic strength! >Vpmg_ibForce: No force for zero ionic strength! >Vpmg_ibForce: No force for zero ionic strength! >Vpmg_ibForce: No force for zero ionic strength! >Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 >*** PASSED *** >Elapsed time: 45.586889 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 45.586889 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for ion-protein section >-------------------------------------------------------------------------------- >Testing input file apbs-mol-pdiel2.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.559159533658E+01 against expected result 1.559160E+01 >*** PASSED *** >Elapsed time: 45.794249 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-pdiel2.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 2.355542126539E+01 against expected result 2.355542E+01 >*** PASSED *** >Elapsed time: 36.784904 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-mol-pdiel12.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.802722643145E+01 against expected result 1.802723E+01 >*** PASSED *** >Elapsed time: 34.036622 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-pdiel12.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.928245019843E+01 against expected result 1.928245E+01 >*** PASSED *** >Elapsed time: 52.172931 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 168.788706 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for pka-lig section >-------------------------------------------------------------------------------- >Testing input file apbs-mol-vdw.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 8.083515648730E+00 against expected result 8.083540E+00 >*** FAILED *** > APBS returned 8.083520000000e+00 > Expected result is 8.083540000000e+00 (0.000247416% error) >Elapsed time: 58.118194 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-vdw.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 2.096300255723E+01 against expected result 2.096296E+01 >*** PASSED *** >Elapsed time: 47.286675 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-mol-surf.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.192607686581E+02 against expected result 1.192608E+02 >*** PASSED *** >Elapsed time: 38.805691 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol-surf.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >[focusFillBound()]: WARNING: > Unusually large potential values > detected on the focusing boundary! > Convergence not guaranteed for NPBE/NRPBE calculations! > >Testing computed result 1.088773280806E+02 against expected result 1.088748E+02 >*** FAILED *** > APBS returned 1.088770000000e+02 > Expected result is 1.088750000000e+02 (0.00183697% error) >Elapsed time: 37.337951 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 181.548511 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for point-pmf section >-------------------------------------------------------------------------------- >Testing input file complex-0_1.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 >*** PASSED *** >Elapsed time: 3.520228 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file complex-0_2.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 8.906694086750E+00 against expected result 8.906694E+00 >*** PASSED *** >Elapsed time: 3.501550 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file complex-0_3.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 >*** PASSED *** >Elapsed time: 3.563157 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file complex-0_4.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 >*** PASSED *** >Elapsed time: 3.628952 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 14.213887 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for solv section >-------------------------------------------------------------------------------- >Testing input file apbs-mol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result -3.624863488074E+01 against expected result -3.624863E+01 >*** PASSED *** >Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 >*** PASSED *** >Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 >*** FAILED *** > APBS returned -3.541640000000e+02 > Expected result is -3.541630000000e+02 (0.000282356% error) >Elapsed time: 5.563866 seconds >-------------------------------------------------------------------------------- >-------------------------------------------------------------------------------- >Testing input file apbs-smol.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result -3.757593772493E+01 against expected result -3.757594E+01 >*** PASSED *** >Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 >*** PASSED *** >Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 >*** PASSED *** >Elapsed time: 5.051407 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 10.615273 seconds >Test results have been logged >-------------------------------------------------------------------------------- >Running tests for geoflow section >-------------------------------------------------------------------------------- >Testing input file geoflow.in > >asc_getToken: Error occurred (bailing out). >Vio_scanf: Format problem with input. >Testing computed result -1.030356323723E+01 against expected result -1.048931E+01 >*** FAILED *** > APBS returned -1.030360000000e+01 > Expected result is -1.048930000000e+01 (1.77038% error) >Testing computed result 5.417419024399E-01 against expected result 5.417419E-01 >*** PASSED *** >Elapsed time: 7.796164 seconds >-------------------------------------------------------------------------------- >Total elapsed time: 7.796164 seconds >Test results have been logged >-------------------------------------------------------------------------------- > [31;01m*[0m ERROR: sci-chemistry/apbs-1.4.1-r2::gentoo failed (test phase): > [31;01m*[0m Tests failed > [31;01m*[0m > [31;01m*[0m Call stack: > [31;01m*[0m ebuild.sh, line 124: Called src_test > [31;01m*[0m environment, line 4280: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m grep -q 'FAILED' log && die "Tests failed" > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-chemistry/apbs-1.4.1-r2::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/apbs-1.4.1-r2::gentoo'`. > [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-chemistry/apbs-1.4.1-r2:20190125-184202.log'. > [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/tests' > [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs'
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