MKL_ThreadLayer_LINK_LIBRARY-NOTFOUND

25 views
Skip to first unread message

Кирилл Максимович Шеповалов

unread,
Oct 8, 2019, 7:54:45 AM10/8/19
to votca
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
CMake Warning:
  Manually-specified variables were not used by the project:

    USE_CPU_MKL


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

Christoph Junghans

unread,
Oct 8, 2019, 10:09:32 AM10/8/19
to vo...@googlegroups.com
On Tue, Oct 8, 2019 at 5:54 AM Кирилл Максимович Шеповалов
<k.shep...@g.nsu.ru> 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 votca+un...@googlegroups.com.
> 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

Кирилл Максимович Шеповалов

unread,
Oct 8, 2019, 1:38:00 PM10/8/19
to votca
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
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:
> To unsubscribe from this group and stop receiving emails from it, send an email to vo...@googlegroups.com.

Christoph Junghans

unread,
Oct 8, 2019, 3:15:37 PM10/8/19
to vo...@googlegroups.com
On Tue, Oct 8, 2019 at 11:38 AM Кирилл Максимович Шеповалов
<k.shep...@g.nsu.ru> 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
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/2443d2f3-fe54-404d-93bc-5702af179832%40googlegroups.com.

Кирилл Максимович Шеповалов

unread,
Oct 10, 2019, 10:14:17 AM10/10/19
to votca
Finally I have installed VOTCA. Thank you very much for help!


среда, 9 октября 2019 г., 2:15:37 UTC+7 пользователь Christoph Junghans написал:
Reply all
Reply to author
Forward
0 new messages