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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
