Strangely enough, I could install this time,and I do not know why. I followed exact same procedure except running make VERBOSE=1
Btw, here is the libgromacs_LIB_DEPENDS line in CMakeCache.txt if you want to know: libgromacs_LIB_DEPENDS:STATIC=general;/usr/lib64/libz.so;gen eral;dl;general;rt;general;m;general;gmxfftw;general;-lpthr ead;general;-fopenmp; S. Mostafa Razavi Graduate Research Assistant Molecular Simulation Lab Department of Chemical and Biomolecular Engineering The University of Akron, OH, USA On Fri, Jul 7, 2017 at 2:36 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > Strange. That means the GROAMCS build system somehow does not get the final > link command right. Without investigating deeper, I'm not sure what would > be the solution. > > I'd look a the actual link command that fails (make VERBOSE=1) and try to > see what and why is missing. > > BTW, cmake should know that libgromacs.so is linked against the OpenMP > library, can you check what's in the libgromacs_LIB_DEPENDS variable in > CMakeCache.txt? > > > -- > Szilárd > > On Fri, Jul 7, 2017 at 8:13 PM, Seyed Mostafa Razavi <s...@zips.uakron.edu > > > wrote: > > > 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.szil...@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 < > > > s...@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@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. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? 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