Hi Servaas, I often had similar problems when running on mpich-1.2.x. In my case they all vanished when I was using any other MPI implementation, like LAM, OpenMPI, or mpich-2.x.
Carsten servaas michielssens wrote: >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.gromacs.org/pipermail/gmx-users/attachments/20071128/e80a1638/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 28 Nov 2007 14:39:29 +0100 >> From: David van der Spoel <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] parallel simulation crash on 6 processors >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <[EMAIL PROTECTED]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> servaas michielssens wrote: >>> I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on >>> 2 systems: >>> >>> Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network >>> and >>> AMD Opteron(tm) Processor 250 with 1Gbit network >>> On both systems I had a crash when I tried to run with more then 5 >>> processors. From 1-5 there was no problem. >>> >> more details please. >>> > > I ran same the simulation on 1,2,3,4 and 5 processors without any > problem, so I there is no problem with the system that I'm using. But > from to moment I tried to use 6 processors of the same cluster the > simulation crashes, this is the error: > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun on CPU 0 out of 6 > > > On AMD: > [0] MPI Abort by user Aborting program ! > [0] Aborting program! > p4_error: latest msg from perror: No such file or directory > p0_3303: p4_error: : -1 > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > p0_3303: (1.088153) net_send: could not write to fd=4, errno = 32 > error while executing run nb 1 > > > On intel: > p4_1781: p4_error: Timeout in establishing connection to remote > process: 0 > rm_l_4_1786: (318.577125) net_send: could not write to fd=5, errno = 32 > p4_1781: (318.580132) net_send: could not write to fd=5, errno = 32 > p0_26458: (319.239545) net_recv failed for fd = 8 > p0_26458: p4_error: net_recv read, errno = : 104 > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > Killed by signal 2.^M > p0_26458: (325.249810) net_send: could not write to fd=4, errno = 32 > error while executing run nb 1 > > > > hope this is the information you need, > > greets, > > servaas > >>> kind regards, >>> >>> servaas michielssens >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> -- >> David. >> ________________________________________________________________________ >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: 46 18 471 4205 fax: 46 18 511 755 >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> > > > _______________________________________________ > 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 [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php