Thank you for your reply. When I try to run my job in a single processor through qsub command, (by feeding the gromacs mdrun command in script file), it says SEGMENTATION FAULT, CORE DUMPED...
But, when I run my job in login node (which we are not supposed to do), it works very well... Can you comment on this? Thanks, Vidya.R On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You're running a thread-MPI version of GROMACS, which is probably not what > you want to do if you're running mpirun. It should work even so, but > whatever quirks exist with SGE are unfortunately between you, its docs and > your cluster's docs and admins :-( > > Mark > > On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2...@gmail.com> wrote: > > > My log file is provided in the link below > > > > Can you please look into it and let me know why the error arises? > > > > I am feeding my commands in SGE cluster. When I run it in my login > node, > > gmx mdrun -v -deffnm eql runs well > > > > > > But, through qsub command, (with 8 processors) It says, > > > > mpirun noticed that process rank 7 with PID 19160 on node > > compute-0-28.local exited on signal 11 (Segmentation fault). > > > > Please help me. > > > > I am unable to figure out, as to whether the problem is with the version > of > > gromacs or the method of compiling. > > > > > > > > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/ > view?usp=sharing > > -- > > 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.