Hi Marc,
On Tue, Apr 3, 2018 at 4:35 PM, Marc Hoemberger <hoemb...@brandeis.edu> wrote: > Hi Alex, > > I have had a similar issue on our cluster (different module files etc.) for > me it turned out that on the actual compute nodes this module was not > available. Thus if you run it from the command line on e.g. your login node > you might have access to this compiler / modulefile, but when moving to a > compute node it might not be there. > Yes, it think that is the reason. How did you solve it? > > Did you try running the command line invocation on the same node you are > submitting the script to? > Actually, I can not find the list of node, otherwise I could log in inside one of them (if I was allowed) to invoke gromacs there. The rest of my run script is juts gmx_mpi grompp and mpirun gmx_mpi mdrun . Best regards, Alex > > -Marc > > On Tue, Apr 3, 2018 at 4:13 PM, Alex <alexanderwie...@gmail.com> wrote: > > > On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > On Tue, Apr 3, 2018 at 8:56 PM Alex <alexanderwie...@gmail.com> wrote: > > > > > > > Thanks Marc. > > > > > > > > I removed the two EXPORT line in the script but still missing the > > library > > > > (removing only the second line also did not help): > > > > > > > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for > > > > 'intel/composerxe/2015.1.133' > > > > > > > > > > Why isn't this module being found? > > > > > I do not know. The funny point is that, the intel/composerxe/2015.1.133 > is > > needed when I invoke gmx_mpi in command line, and after loading it, the > > gmx_works fine. But I do not know why it can not be found inside script. > > > > > > > > > > > > ------------------------------------------------------------ > > > -------------- > > > > mpirun was unable to find the specified executable file, and > therefore > > > > did not launch the job. This error was first reported for process > > > > rank 0; it may have occurred for other processes as well. > > > > > > > > > > If this was the error message, then you won't get a log file from the > > > executable that wasn't found, so I presume that below you are looking > at > > an > > > old log file... > > > > > > No, it can generate .log file, I ran it again and a new log file was > > generated. > > > > > > > > > And .log file: > > > > > > > > gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: > > > cannot > > > > open shared object file: No such file or directory > > > > > > > > > > That's a library that has to come from the module that didn't load, so > > look > > > there. > > > > > > > > Best regards, > > Alex > > > > > > > Mark > > > > > > > > > > ------------------------------------------------------------ > > > -------------- > > > > mpirun was unable to find the specified executable file, and > therefore > > > > did not launch the job. This error was first reported for process > > > > rank 0; it may have occurred for other processes as well. > > > > > > > > Regards, > > > > Alex > > > > > > > > > > > > On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > > > > > wrote: > > > > > > > > > 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. > > > > > > > > > -- > > > > 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. > > > > > -- > > 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. > > > > > > -- > Marc Hoemberger > Ph.D. Candidate, Biochemistry and Biophysics, > Laboratory of Dorothee Kern > MS-009, 415 South St. > Brandeis University > Waltham, MA, 02453 > -- > 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? 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