[gmx-users] Gromacs installation fails in CentOS 6.5

[Szilárd Páll]

Hi,

That looks weird. Can you compile a sample OpenMP code, e.g. this
https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c

--
Szilárd

On Fri, Jul 7, 2017 at 11:59 AM, Seyed Mostafa Razavi <sr87 at zips.uakron.edu>
wrote:

> Hello,
>
> I'm trying to install Gromacs (gromacs-2016.3) on my CentOS 6.5 system. I
> exactly follow the installation instruction in http://manual.gromacs.org/
> documentation/2016.3/install-guide/index.html. After I run "make", the
> installation process starts and proceeds to %97, then it gives me an error.
>
> [Ahmad at chem30 build]$ make
>
> .
> .(lots of output)
> .
>
> [ 97%] Building C object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/
> tng_io/src/lib/tng_io.c.o
> [ 97%] Building C object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/
> tng_io/src/lib/md5.c.o
> [ 97%] Building CXX object src/gromacs/CMakeFiles/
> libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> [ 97%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/
> baseversion-gen.c.o
> [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> [ 97%] Built target libgromacs
> Scanning dependencies of target template
> [ 97%] Building CXX object share/template/CMakeFiles/
> template.dir/template.cpp.o
> [ 97%] Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> "make check" command gives me the following output:
>
> [Ahmad at chem30 build]$ make check
> Scanning dependencies of target mdrun_objlib
> [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/md.cpp.o
> [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/resource-division.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/runner.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/repl_ex.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/mdrun.cpp.o
> [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> objlib.dir/mdrun/membed.cpp.o
> [  1%] Built target mdrun_objlib
> [  2%] Built target fftwBuild
> [ 87%] Built target libgromacs
> Scanning dependencies of target view_objlib
> [ 87%] Building CXX object src/programs/CMakeFiles/view_
> objlib.dir/view/view.cpp.o
> [ 87%] Built target view_objlib
> Scanning dependencies of target gmx
> [ 88%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o
> [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> dir/legacymodules.cpp.o
> [ 88%] Linking CXX executable ../../bin/gmx
> ../../lib/libgromacs.so.2.3.0: undefined reference to `GOMP_parallel'
> collect2: error: ld returned 1 exit status
> make[3]: *** [bin/gmx] Error 1
> make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> make: *** [check] Error 2
>
>
> Here are some other information about my system:
>
> [Ahmad at chem30 Downloads]$ cat /etc/centos-release
> CentOS release 6.5 (Final)
>
> [Ahmad at chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
> #define _OPENMP 200805
>
>
> [Ahmad at chem30 Downloads]$ cmake --version
> cmake version 3.5.0
>
> [Ahmad at chem30 Downloads]$ gcc --version
> gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
> Copyright (C) 2010 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> ------------------------------------------------------------
> ------------------------
> Thank you,
> S. Mostafa Razavi
> --
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