On Tue, Oct 8, 2019 at 11:38 AM Кирилл Максимович Шеповалов <[email protected]> wrote: > > Thank you, this error has disappeared. But now I have follow: > > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_thread_num' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_procs' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_start' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_max_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_end' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_set_num_threads' > collect2: error: ld returned 1 exit status This looks like -fopenmp is missing in compiler flags.
OpenMP is only used in ctp and xtp, so if you don't need these VOTCA modules, don't build them (-DBUILD_XTP=OFF -DBUILD_CTP=OFF). Christoph > make[2]: *** [csg/src/tools/csg_dump] Error 1 > make[1]: *** [csg/src/tools/CMakeFiles/csg_dump.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_thread_num' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_procs' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_start' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_max_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_end' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_set_num_threads' > collect2: error: ld returned 1 exit status > make[2]: *** [csg/src/tools/csg_resample] Error 1 > make[1]: *** [csg/src/tools/CMakeFiles/csg_resample.dir/all] Error 2 > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_thread_num' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_procs' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_start' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_max_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_end' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_set_num_threads' > collect2: error: ld returned 1 exit status > make[2]: *** [csg/src/tools/csg_gmxtopol] Error 1 > make[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2 > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_thread_num' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_num_procs' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_start' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_get_max_threads' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `GOMP_parallel_end' > /usr/lib64/gcc/x86_64-suse-linux/6/../../../../x86_64-suse-linux/bin/ld: > ../libcsg/libvotca_csg.so.6: undefined reference to `omp_set_num_threads' > collect2: error: ld returned 1 exit status > make[2]: *** [csg/src/tools/csg_stat] Error 1 > make[1]: *** [csg/src/tools/CMakeFiles/csg_stat.dir/all] Error 2 > =>> PBS: job killed: ncpus 2.84 exceeded limit 1 (sum) > -bash: line 1: 629 Terminated > /var/spool/PBS/mom_priv/jobs/1059153.vm-pbs.SC > make[2]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/calculatorfactory.cc.o] > Terminated > make[2]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/ewaldnd.cc.o] Terminated > make[2]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/extractorfactory.cc.o] > Terminated > make[2]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/fragment.cc.o] > Terminated > make[2]: *** wait: No child processes. Stop. > make[2]: *** Waiting for unfinished jobs.... > make[2]: *** wait: No child processes. Stop. > make[1]: *** [ctp/src/libctp/CMakeFiles/votca_ctp.dir/all] Error 2 > make: *** [all] Terminated > > > > вторник, 8 октября 2019 г., 21:09:32 UTC+7 пользователь Christoph Junghans > написал: >> >> On Tue, Oct 8, 2019 at 5:54 AM Кирилл Максимович Шеповалов >> <[email protected]> wrote: >> > >> > Greating all! >> > >> > Please, help me with VOTCA installation. >> > >> > I received the follow error massage, after entering "make": >> > >> > txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE >> This doesn't matter as txt2tags is just needed to build documentation. >> >> > CMake Warning: >> > Manually-specified variables were not used by the project: >> > >> > USE_CPU_MKL >> Yeah as CMake suggests USE_CPU_MKL is not used by VOTCA and hence >> changes nothing. >> >> MKL is really only needed for votca-xtp, you can compile without MKL, >> by setting CMAKE_DISABLE_FIND_PACKAGE_MKL=ON when you call CMake. >> >> Christoph >> > >> > >> > Current git revision is 1f6316d >> > make[2]: *** No rule to make target >> > 'MKL_ThreadLayer_LINK_LIBRARY-NOTFOUND', needed by >> > 'tools/src/libtools/libvotca_tools.so.6'. Stop. >> > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 >> > make: *** [all] Error 2 >> > make: *** No rule to make target 'check'. Stop. >> > Current git revision is 1f6316d >> > make[2]: *** No rule to make target >> > 'MKL_ThreadLayer_LINK_LIBRARY-NOTFOUND', needed by >> > 'tools/src/libtools/libvotca_tools.so.6'. Stop. >> > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 >> > make: *** [all] Error 2 >> > >> > If you have any ideas, answer me, please. >> > >> > Sinserely, >> > Kirill Shepovalov >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/ab2846c9-2ebb-4a71-8a14-a2a6eddada3d%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/2443d2f3-fe54-404d-93bc-5702af179832%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5jhyncvZQVcKJjfjA0B1US0CEwNbQr%3D_azJsHTy5RbNQ%40mail.gmail.com.
