> -------------- 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