MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1? On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li <lida...@gmail.com> wrote:
> Yes it is. Now everything is fine with openmpi instead of mvapich2. > > dawei > > On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham <mark.abra...@anu.edu.au> > wrote: > > > > > > ----- Original Message ----- > > From: Da-Wei Li <lida...@gmail.com> > > Date: Wednesday, August 11, 2010 6:23 > > Subject: Re: [gmx-users] New beta release: 4.5-beta3 > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > >> Hi,all > >> > >> Unfortunately, it still crash. Here it is the output of mdrun. Both > >> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use > >> mvapich2 and intel compiler. > > > > MPICH variants are known to cause problems. Try OpenMPI. > > > > Mark > > > >> *************************** > >> Getting Loaded... > >> Reading file em.tpr, VERSION 4.5-beta3 (single precision) > >> Loaded with Money > >> > >> > >> Will use 9 particle-particle and 7 PME only nodes > >> This is a guess, check the performance at the end of the log file > >> Making 1D domain decomposition 9 x 1 x 1 > >> > >> Back Off! I just backed up em.trr to ./#em.trr.4# > >> > >> Back Off! I just backed up em.edr to ./#em.edr.4# > >> > >> Steepest Descents: > >> Tolerance (Fmax) = 1.00000e+03 > >> Number of steps > >> = 50000 > >> rank 9 in job 1 hpc-8-6.local_58777 caused > >> collective abort of all ranks > >> exit status of rank 9: killed by signal 9 > >> > >> ******************************* > >> > >> dawei > >> > >> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov > >> <rossen.aposto...@cbr.su.se> wrote: > >> > > >> > New beta release of gromacs is available for testing: > >> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz. > >> > > >> > Many bugs have been fixed in this release, mainly double > >> precision support > >> > with icc compilers, SSE2. Have a look at the release note on > >> the website for > >> > more details. There are still some issues on Windows platofrms > >> that will be > >> > resolved before the final release. > >> > > >> > Please try it out and see if it works as expected! Hopefully > >> there won't be > >> > many more betas :)) > >> > > >> > Rossen > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.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://lists.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://lists.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://lists.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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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