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Gentoo's Bugzilla – Attachment 736600 Details for
Bug 810892
sci-chemistry/gromacs-2021.2 - -- Could NOT find MPI_C (missing: MPI_C_WORKS)
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CMakeError.log
CMakeError.log (text/plain), 6.36 KB, created by
Toralf Förster
on 2021-08-29 09:22:11 UTC
(
hide
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Description:
CMakeError.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2021-08-29 09:22:11 UTC
Size:
6.36 KB
patch
obsolete
>Compiling the C compiler identification source file "CMakeCCompilerId.c" failed. >Compiler: /usr/bin/mpicc >Build flags: -pipe;-march=native;-fno-diagnostics-color;-O2 >Id flags: > >The output was: >1 >/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `MPIR_being_debugged' >/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `orte_data_server_uri' >collect2: error: ld returned 1 exit status > > >Determining if files io.h exist failed with the following output: >Change Dir: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp > >Run Build Command(s):/usr/bin/ninja cmTC_2821e && [1/2] Building C object CMakeFiles/cmTC_2821e.dir/HAVE_IO_H.c.o >FAILED: CMakeFiles/cmTC_2821e.dir/HAVE_IO_H.c.o >/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -o CMakeFiles/cmTC_2821e.dir/HAVE_IO_H.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c:2:10: fatal error: io.h: No such file or directory > 2 | #include <io.h> > | ^~~~~~ >compilation terminated. >ninja: build stopped: subcommand failed. > > >Source: >/* */ >#include <io.h> > > >int main(void){return 0;} > >Determining if the _fileno exist failed with the following output: >Change Dir: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp > >Run Build Command(s):/usr/bin/ninja cmTC_095dd && [1/2] Building CXX object CMakeFiles/cmTC_095dd.dir/CheckSymbolExists.cxx.o >FAILED: CMakeFiles/cmTC_095dd.dir/CheckSymbolExists.cxx.o >/usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -std=c++17 -o CMakeFiles/cmTC_095dd.dir/CheckSymbolExists.cxx.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function âint main(int, char**)â: >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: â_filenoâ was not declared in this scope; did you mean âfilenoâ? > 8 | return ((int*)(&_fileno))[argc]; > | ^~~~~~~ > | fileno >ninja: build stopped: subcommand failed. > > >File /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: >/* */ >#include <stdio.h> > >int main(int argc, char** argv) >{ > (void)argv; >#ifndef _fileno > return ((int*)(&_fileno))[argc]; >#else > (void)argc; > return 0; >#endif >} >Determining if the _commit exist failed with the following output: >Change Dir: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp > >Run Build Command(s):/usr/bin/ninja cmTC_536f0 && [1/2] Building CXX object CMakeFiles/cmTC_536f0.dir/CheckSymbolExists.cxx.o >FAILED: CMakeFiles/cmTC_536f0.dir/CheckSymbolExists.cxx.o >/usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -std=c++17 -o CMakeFiles/cmTC_536f0.dir/CheckSymbolExists.cxx.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:2:10: fatal error: io.h: No such file or directory > 2 | #include <io.h> > | ^~~~~~ >compilation terminated. >ninja: build stopped: subcommand failed. > > >File /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: >/* */ >#include <io.h> > >int main(int argc, char** argv) >{ > (void)argv; >#ifndef _commit > return ((int*)(&_commit))[argc]; >#else > (void)argc; > return 0; >#endif >} >Determining if the memalign exist failed with the following output: >Change Dir: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp > >Run Build Command(s):/usr/bin/ninja cmTC_f252e && [1/2] Building CXX object CMakeFiles/cmTC_f252e.dir/CheckSymbolExists.cxx.o >FAILED: CMakeFiles/cmTC_f252e.dir/CheckSymbolExists.cxx.o >/usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -std=c++17 -o CMakeFiles/cmTC_f252e.dir/CheckSymbolExists.cxx.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function âint main(int, char**)â: >/var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: âmemalignâ was not declared in this scope > 8 | return ((int*)(&memalign))[argc]; > | ^~~~~~~~ >ninja: build stopped: subcommand failed. > > >File /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: >/* */ >#include <stdlib.h> > >int main(int argc, char** argv) >{ > (void)argv; >#ifndef memalign > return ((int*)(&memalign))[argc]; >#else > (void)argc; > return 0; >#endif >} >The MPI test test_mpi for C in mode normal failed to compile with the following output: >Change Dir: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float_mpi/CMakeFiles/CMakeTmp > >Run Build Command(s):/usr/bin/ninja cmTC_92f4d && [1/2] Building C object CMakeFiles/cmTC_92f4d.dir/test_mpi.c.o >[2/2] Linking C executable cmTC_92f4d >FAILED: cmTC_92f4d >: && /usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/usr/lib64 -Wl,--enable-new-dtags -pthread CMakeFiles/cmTC_92f4d.dir/test_mpi.c.o -o cmTC_92f4d /usr/lib64/libmpi.so && : >/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `MPIR_being_debugged' >/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `orte_data_server_uri' >collect2: error: ld returned 1 exit status >ninja: build stopped: subcommand failed. > > >
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bug 810892
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736597
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736603
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736606
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736609
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736612
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736615
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736618
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736621