Hi, It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting the modules do it, since it is their job.
Mark On Tue, Apr 3, 2018, 20:29 Alex <alexanderwie...@gmail.com> wrote: > Dear all, > > I have installed the gromacs2018.1 parallel in a cluster, it works > perfectly in the command line, of course after loading some module. > But when I put the commands along with loading module commands in a bash > script to be submitted in the cluster, it crashes with the below massage: > > ++++++++++++++++++ > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for > 'intel/composerxe/2015.1.133' > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version > `GLIBCXX_3.4.20' not found (required by > /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3) > > And part of the log file: > > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version > `GLIBCXX_3.4.20' not found (required by > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3) > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version > `GLIBCXX_3.4.20' not found (required by > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3) > gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version > `GLIBCXX_3.4.20' not found (required by > /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3) > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot > open shared object file: No such file or directory > ++++++++++++++++++ > > Here is part of my script.sh file > ++++++++++++++++++ > . /etc/profile.d/modules.sh > module load intel/composerxe/2015.1.133 > module load shared > module load clusterA > module load gcc/4.8.1 > module load sge/univa > module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed > export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH > export > > LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH} > ++++++++++++++++ > > Do you know what I am missing? > Thanks > Alex > -- > 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? 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.