I am running other softwares in parallel on glacier. GROMACS has shown such problem up to now!
On Thu, 2009-05-28 at 21:52 +0200, p.ya...@fz-juelich.de wrote: > It seems like your nodes cannot communicate. > you might want to check your job-submitting script: does it call mdrun > correctly? cpu/time allocation? try to see if mpi is installed correctly by > submitting any other mpi-enabled code. > > > Peyman Yamin > Institut fuer Strukturbiologie und Biophysik (ISB) > ISB-3: Strukturbiochemie > Forschungszentrum Juelich > D-52425 Juelich > Tel: (49)-2461-61-2875 > Fax: (49)-2461-61-2023 > mailto: p.yamin[at]fz-juelich.de > > ----- Original Message ----- > From: Paymon Pirzadeh <ppirz...@ucalgary.ca> > Date: Thursday, May 28, 2009 6:35 pm > Subject: [gmx-users] GROMACS on glacier.westgrid.ca > > > Hello all, > > A follow up from my previous problems on running the gromacs on > > glacierturned out that I had problems in installation. The guide in > > the manual > > was not clear enough. So, I installed the code fine this time, so, > > I get > > errors from 4.0.4 version. > > I ran the code interactively on the master node and everything went > > smooth and fine without any problems. But as soon as I started running > > it in parallel through que line, job gets killed. Following are the > > messages I received: > > > > PBS Job Id: 4686006.teva.westgrid.ubc > > > >> Job Name: sixsite-test > > > >> Exec host: ice1_2/1+ice1_2/0+ice1_1/1+ice1_1/0 > > > >> Aborted by PBS Server > > > >> Job cannot be executed > > > > The error messages I receive in error file: > > > >> Killed by signal 2.^M > > > >> Killed by signal 2.^M > > > >> Killed by signal 2.^M > > > > Running on 4 processors. > > > >> Starting run at: Mon May 25 20:29:34 PDT 2009 > > > >> p2_11876: p4_error: Timeout in establishing connection to remote > > > >> process: 0 > > > >> p0_4273: p4_error: net_recv read: probable EOF on socket: 1 > > > >> Job finished at: Mon May 25 20:34:40 PDT 2009 > > > > All the clues show that the program had started working, initial > > conditions were reviewed by the code, but suddenly everything > > crashed. I > > really do not know where the error originates from!!! This is while my > > friend has compiled the code in the same way as I did, and she is > > running fine on another cluster. > > Regards, > > > > Payman > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting!Please don't post (un)subscribe requests to the list. Use > > the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ------------------------------------------------------------------- > ------------------------------------------------------------------- > Forschungszentrum Juelich GmbH > 52425 Juelich > > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------- > ------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
