For an MPI enabled version you need to have the appropriate flags in your easyconfig: https://github.com/hpcugent/easybuild-easyblocks/blob/ master/easybuild/easyblocks/g/gromacs.py#L286
Here's an example: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb With the relevant part being https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb#L27 There's no explicit phi support in EasyBuild at the moment, you'd have to solve things on a case-by-case basis. On 31 May 2017 at 13:24, wahi <[email protected]> wrote: > One more question which version of Gromacs can I install with support of > Intel Phi processors, if there is such option ? > > On 05/31/2017 03:01 PM, wahi wrote: > > No we don't have such executable, only gmx > > On 05/31/2017 01:36 PM, Alan O'Cais wrote: > > Take a look in /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/ > there should be another executable there "gmx_mpi" which is the parallel > version. > > On 31 May 2017 at 11:30, wahi <[email protected]> wrote: > >> Just now I recognized that the installation of Gromacs is done without >> MPI or Openmpi support, do I need to enable something during eb install >> step, or I am missing something ? thank you once again for any suggestions. >> >> On 05/31/2017 01:03 PM, wahi wrote: >> >> Thank you very much indeed Alan, it solved the issue. >> >> On 05/31/2017 12:53 PM, Alan O'Cais wrote: >> >> You need to export the LD_LIBRARY_PATH envvar to your mpirun command (or >> build OpenMPI with support for your scheduler): >> https://stackoverflow.com/questions/11368215/loading-shared- >> library-in-open-mpi-mpi-run >> >> In other words: >> mpirun -x LD_LIBRARY_PATH -np 10 -machinefile machine gmx >> >> Alan >> >> On 31 May 2017 at 10:23, wahi <[email protected]> wrote: >> >>> Ok let put the Gromacs run away just now, what about this: >>> >>> mpirun -np 10 -machinefile machine gmx >>> ------------------------------------------------------- >>> Primary job terminated normally, but 1 process returned >>> a non-zero exit code.. Per user-direction, the job has been aborted. >>> ------------------------------------------------------- >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>> (required by gmx) >>> ------------------------------------------------------------ >>> -------------- >>> mpirun detected that one or more processes exited with non-zero status, >>> thus causing >>> the job to be terminated. The first process to do so was: >>> >>> Process name: [[6359,1],0] >>> Exit code: 1 >>> >>> On 05/31/2017 12:12 PM, Alan O'Cais wrote: >>> >>> Here''s the relevant comment: >>> https://github.com/hpcugent/easybuild-easyblocks/blob/master >>> /easybuild/easyblocks/g/gromacs.py#L351 >>> >>> You'll need t ocheck out the GROMACS website to see how to run it >>> properly. >>> >>> Alan >>> >>> On 31 May 2017 at 09:54, wahi <[email protected]> wrote: >>> >>>> Because I always compiled it by manually and mdrun is there by default. >>>> >>>> On 05/31/2017 11:52 AM, wahi wrote: >>>> >>>> Hi Alan, >>>> >>>> Thanks for your reply. >>>> >>>> ldd /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/gmx >>>> linux-vdso.so.1 => (0x00007ffcd13c6000) >>>> libgfortran.so.3 => >>>> /software/software/GCC/4.8.4/lib64/libgfortran.so.3 >>>> (0x00007fe08ee47000) >>>> libm.so.6 => /lib64/libm.so.6 (0x0000003e44000000) >>>> libz.so.1 => >>>> /software/software/zlib/1.2.8-goolf-1.7.20/lib/libz.so.1 >>>> (0x00007fe08ec27000) >>>> librt.so.1 => /lib64/librt.so.1 (0x0000003e44400000) >>>> libstdc++.so.6 => /software/software/GCC/4.8.4/lib64/libstdc++.so.6 >>>> (0x00007fe08e91d000) >>>> libgomp.so.1 => /software/software/GCC/4.8.4/lib64/libgomp.so.1 >>>> (0x00007fe08e70f000) >>>> libgcc_s.so.1 => /software/software/GCC/4.8.4/lib64/libgcc_s.so.1 >>>> (0x00007fe08e4f8000) >>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003e43800000) >>>> libc.so.6 => /lib64/libc.so.6 (0x0000003e43400000) >>>> libquadmath.so.0 => >>>> /software/software/GCC/4.8.4/lib/../lib64/libquadmath.so.0 >>>> (0x00007fe08e2bc000) >>>> /lib64/ld-linux-x86-64.so.2 (0x0000003e43000000) >>>> >>>> Sorry but I missed that mdrun is not installed with Gromacs, so maybe I >>>> miss how to run it ? >>>> >>>> On 05/31/2017 11:48 AM, Alan O'Cais wrote: >>>> >>>> When you have these modules loaded, what is the output of: >>>> ldd /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/gmx >>>> /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/mdrun >>>> >>>> On 31 May 2017 at 09:37, wahi <[email protected]> wrote: >>>> >>>>> Dear all, >>>>> >>>>> Here are the loaded modules: >>>>> >>>>> Currently Loaded Modules: >>>>> 1) GCC/4.8.4 >>>>> 2) numactl/2.0.10-GCC-4.8.4 >>>>> 3) hwloc/1.10.1-GCC-4.8.4 >>>>> 4) OpenMPI/1.8.4-GCC-4.8.4 >>>>> 5) OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0 >>>>> 6) gompi/1.7.20 >>>>> 7) FFTW/3.3.4-gompi-1.7.20 >>>>> 8) ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0 >>>>> 9) goolf/1.7.20 >>>>> 10) bzip2/1.0.6-goolf-1.7.20 >>>>> 11) zlib/1.2.8-goolf-1.7.20 >>>>> 12) Boost/1.53.0-goolf-1.7.20 >>>>> 13) GROMACS/5.1.2-goolf-1.7.20-mt >>>>> >>>>> As we see GCC is there. >>>>> >>>>> >>>>> >>>>> On 05/31/2017 11:27 AM, wahi wrote: >>>>> >>>>>> Dear Kenneth, >>>>>> >>>>>> Thanks for your reply. >>>>>> >>>>>> After loading GROMACS I am using this command: >>>>>> >>>>>> mpirun -np 10 -machinefile machine >>>>>> /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/gmx >>>>>> /software/software/GROMACS/5.1.2-goolf-1.7.20-mt/bin/mdrun -v >>>>>> >>>>>> As I said as a simple test >>>>>> >>>>>> >>>>>> Wahi >>>>>> >>>>>> >>>>>> On 05/31/2017 11:26 AM, Kenneth Hoste wrote: >>>>>> >>>>>>> Dear Wahi, >>>>>>> >>>>>>> On 31/05/2017 09:04, [email protected] wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> First of all thank you very much for this fantastic package. >>>>>>>> >>>>>>>> I installed Gromacs 5.1.2-goolf-1.7.20 on Linux cluster, the >>>>>>>> installation is >>>>>>>> done in NFS shared directory. >>>>>>>> >>>>>>>> When I am trying to run a test I am getting this: >>>>>>>> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >>>>>>>> >>>>>>> >>>>>>> How are you trying to use GROMACS exactly? Are you just calling the >>>>>>> binary directly, or are you loading the GROMACS module and then using >>>>>>> the >>>>>>> GROMACS main command (without specifying its full location)? >>>>>>> >>>>>>> You should do the latter, EasyBuild creates module files for you >>>>>>> that you should load in order to use the software (which takes cares of >>>>>>> setting $LD_LIBRARY_PATH, $PATH, etc.). >>>>>>> >>>>>>> >>>>>>> regards, >>>>>>> >>>>>>> Kenneth >>>>>>> >>>>>>> >>>>>>>> But this lib is in my shared directory, and I put LD_LIBRARY_PATH in >>>>>>>> my .bashrc >>>>>>>> >>>>>>>> Could you please help me to identify the problem. >>>>>>>> >>>>>>>> I used the same directory for other packages like WRF, Openmpi etc >>>>>>>> and it is >>>>>>>> working fine. >>>>>>>> >>>>>>>> Thank you very much in advance. >>>>>>>> >>>>>>>> >>>>>>>> Regards, >>>>>>>> Wahi >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> -- >>>>> Wahi Narsisian >>>>> Vice-Head of Center for Scientific Computing, >>>>> Institute for Informatics and Automation Problems, >>>>> National Academy of Sciences of the Republic of Armenia >>>>> 1, P. Sevak str., Yerevan 0014, Armenia >>>>> t: 374 91 557285 >>>>> e: [email protected] >>>>> >>>>> >>>> >>>> >>>> -- >>>> Dr. Alan O'Cais >>>> E-CAM Software Manager >>>> Juelich Supercomputing Centre >>>> Forschungszentrum Juelich GmbH >>>> 52425 Juelich, Germany >>>> >>>> Phone: +49 2461 61 5213 <02461%20615213> >>>> Fax: +49 2461 61 6656 <02461%20616656> >>>> E-mail: [email protected] >>>> WWW: http://www.fz-juelich.de/ias/jsc/EN >>>> >>>> >>>> ------------------------------------------------------------ >>>> ------------------------------------ >>>> ------------------------------------------------------------ >>>> ------------------------------------ >>>> Forschungszentrum Juelich GmbH >>>> 52425 Juelich >>>> Sitz der Gesellschaft: Juelich >>>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >>>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >>>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >>>> Prof. Dr. Sebastian M. Schmidt >>>> ------------------------------------------------------------ >>>> ------------------------------------ >>>> ------------------------------------------------------------ >>>> ------------------------------------ >>>> >>>> >>>> -- >>>> Wahi Narsisian >>>> Vice-Head of Center for Scientific Computing, >>>> Institute for Informatics and Automation Problems, >>>> National Academy of Sciences of the Republic of Armenia >>>> 1, P. Sevak str., Yerevan 0014, Armenia >>>> t: 374 91 557285 >>>> e: [email protected] >>>> >>>> >>>> -- >>>> Wahi Narsisian >>>> Vice-Head of Center for Scientific Computing, >>>> Institute for Informatics and Automation Problems, >>>> National Academy of Sciences of the Republic of Armenia >>>> 1, P. Sevak str., Yerevan 0014, Armenia >>>> t: 374 91 557285 >>>> e: [email protected] >>>> >>>> >>> >>> >>> -- >>> Dr. Alan O'Cais >>> E-CAM Software Manager >>> Juelich Supercomputing Centre >>> Forschungszentrum Juelich GmbH >>> 52425 Juelich, Germany >>> >>> Phone: +49 2461 61 5213 <02461%20615213> >>> Fax: +49 2461 61 6656 <02461%20616656> >>> E-mail: [email protected] >>> WWW: http://www.fz-juelich.de/ias/jsc/EN >>> >>> >>> -- >>> Wahi Narsisian >>> Vice-Head of Center for Scientific Computing, >>> Institute for Informatics and Automation Problems, >>> National Academy of Sciences of the Republic of Armenia >>> 1, P. Sevak str., Yerevan 0014, Armenia >>> t: 374 91 557285 >>> e: [email protected] >>> >>> >> >> >> -- >> Dr. Alan O'Cais >> E-CAM Software Manager >> Juelich Supercomputing Centre >> Forschungszentrum Juelich GmbH >> 52425 Juelich, Germany >> >> Phone: +49 2461 61 5213 <02461%20615213> >> Fax: +49 2461 61 6656 <02461%20616656> >> E-mail: [email protected] >> WWW: http://www.fz-juelich.de/ias/jsc/EN >> >> >> -- >> Wahi Narsisian >> Vice-Head of Center for Scientific Computing, >> Institute for Informatics and Automation Problems, >> National Academy of Sciences of the Republic of Armenia >> 1, P. Sevak str., Yerevan 0014, Armenia >> t: 374 91 557285 >> e: [email protected] >> >> >> -- >> Wahi Narsisian >> Vice-Head of Center for Scientific Computing, >> Institute for Informatics and Automation Problems, >> National Academy of Sciences of the Republic of Armenia >> 1, P. Sevak str., Yerevan 0014, Armenia >> t: 374 91 557285 >> e: [email protected] >> >> > > > -- > Dr. Alan O'Cais > E-CAM Software Manager > Juelich Supercomputing Centre > Forschungszentrum Juelich GmbH > 52425 Juelich, Germany > > Phone: +49 2461 61 5213 <02461%20615213> > Fax: +49 2461 61 6656 <02461%20616656> > E-mail: [email protected] > WWW: http://www.fz-juelich.de/ias/jsc/EN > > > -- > Wahi Narsisian > Vice-Head of Center for Scientific Computing, > Institute for Informatics and Automation Problems, > National Academy of Sciences of the Republic of Armenia > 1, P. Sevak str., Yerevan 0014, Armenia > t: 374 91 557285 > e: [email protected] > > > -- > Wahi Narsisian > Vice-Head of Center for Scientific Computing, > Institute for Informatics and Automation Problems, > National Academy of Sciences of the Republic of Armenia > 1, P. Sevak str., Yerevan 0014, Armenia > t: 374 91 557285 > e: [email protected] > > -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected] WWW: http://www.fz-juelich.de/ias/jsc/EN
