[gmx-users] Gromacs installation fails in CentOS 6.5

[Seyed Mostafa Razavi]

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