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@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@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@chem30 Downloads]$ cat /etc/centos-release CentOS release 6.5 (Final) [Ahmad@chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open #define _OPENMP 200805 [Ahmad@chem30 Downloads]$ cmake --version cmake version 3.5.0 [Ahmad@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 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.