[gmx-users] Gromacs installation fails in CentOS 6.5

[Seyed Mostafa Razavi]

Here is what I did:

$ gcc -o omp_helloc -fopenmp omp_hello.c
$ ./omp_helloc
Hello World from thread = 0
Number of threads = 4
Hello World from thread = 3
Hello World from thread = 1
Hello World from thread = 2




Thank you,

S. Mostafa Razavi


On Fri, Jul 7, 2017 at 9:12 AM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
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