Re: [gmx-users] problem of paralleled running
fancy2012 wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! To get a faster resolution, you should provide substantially more detail, including: 1. Commands given to install Gromacs 2. Description of hardware, compilers, etc. 3. Command issued that causes the problem 4. The actual error message (from Gromacs, OS, MPI, etc.), if any -Justin All the best, fancy -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] problem of paralleled running
Can't help you directly, other than suggestion you provide a lot more information than you have. Direct copy/paste of the command lines used, error messages and log files generated, how GROMACS was installed etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of fancy2012 Sent: Thursday, 28 October 2010 1:05 PM To: gmx-users Subject: [gmx-users] problem of paralleled running Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! All the best, fancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem of paralleled running
On October 28, 2010 at 4:11 AM TJ Mustard wrote: On October 28, 2010 at 4:05 AM fancy2012 wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! Gromacs 4.5.1 is somewhat viral on cpu (takes all of them if not told otherwise). I you submit multiple jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure. If you use SGE, you may want to use SMP or MPI. All the best, fancy TJ Mustard Email: musta...@onid.orst.edu TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem of paralleled running
On October 28, 2010 at 4:05 AM fancy2012 wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! Gromacs 4.5.1 is somewhat viral on cpu (takes all of them if not told otherwise). I you submit multiple jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure. All the best, fancy TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] problem of paralleled running
Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! All the best, fancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
