I wish the error would come from the quota. But the disk quota is fine, we still have 2.0TB on the scratch space which is shared by everyone. And I have other jobs running and no problem with writing outputs. I've tried smaller REMD jobs on the cluster using only 1 node (8 cpus) and seems to be no problem. But using 7 nodes and one (or two) node complains about that. And several weird files are generated: mdrun_mpi.80s-12939,v002.local.btr, mdrun_mpi.80s-12940,v002.local.btr, .... v002 is the name of the node.
Chuanyin Shi Department of Chemistry & Biochemistry University of Oklahoma Email: c...@ou.edu ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of David van der Spoel [sp...@xray.bmc.uu.se] Sent: Monday, October 25, 2010 11:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Job crash: checkpoint file On 2010-10-25 17.58, Shi, Chuanyin wrote: > I am having exactly the same problem recently. > The replica exchange job stops around 11000 steps. > Switch to another cluster and the job is running fine. > I wonder how often you've seen this type of crashing and any solutions for > this? > Thanks. Have you checked your quota? I had the same problem recently, and I was indeed out of quota. > > > > Chuanyin Shi > Department of Chemistry& Biochemistry > University of Oklahoma > Email: c...@ou.edu > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: Friday, October 08, 2010 1:19 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Job crash: checkpoint file > > Jianhui Tian wrote: >> Dear GMX users, >> >> I am running a replica simulation and the job crashed with the following >> message: >> >> File input/output error: >> Cannot rename checkpoint file; maybe you are out of quota? >> >> From the mailling list, I see this might be a permission problem. >> However, I checked the file permission and nothing wrong was noticed. >> If I rerun the crashed simulation, it goes through the second time. This >> seems strong. Any suggestion is welcomed. >> > > I've seen this happen when our filesystem blips. It seems like you're able to > run your job, so I don't think there's anything to do about it, except perhaps > inquire with your sysadmins about the stability of the filesystem, and whether > or not you can expect to have this happen frequently. > > -Justin > >> JH >> > > -- > ======================================== > > 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 list gmx-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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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/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 mailing list gmx-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
