According to our HPC manage, our MVAPICH2's version is 1.0.3. thanks for the information.
dawei On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz <rol...@utk.edu> wrote: > 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-us...@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-us...@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-us...@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 > > -- > gmx-users mailing list gmx-us...@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
