It could be a quota issue (there is free space, but your group has used its entire allocation). Also, file systems often have limits not only on the total amount of space, but also on the total number of files that a group is allowed to create. Talk to your system administrator. There is likely a special command that you can run to find the relevant information (e.g., quota, diskUsage, prquota, etc... these are usually scripts written by your administrators so the name could in theory be anything).
Chris. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Pavan Kumar <kumar.pavan...@gmail.com> Sent: 04 March 2014 09:38 To: gmx-users Subject: Re: [gmx-users] Out of Disk Space Hello THOMMAS, Exactly, it showed 2.2GB of trajectory is going to be created. But i have 17GB of free space on my cluster on which i am running. So any other reasons for the error. Thanks in advance. On Tue, Mar 4, 2014 at 8:00 PM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Hi Pavan, > When you use the grompp command to prepare the md.tpr file for the final > mdrun, do you notice such a statement "This run will generate roughly XXXXX > Mb of data". I suspect the resultant trajectory could be exceeding the > available space. > > > On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar <kumar.pavan...@gmail.com > >wrote: > > > Hi everybody, > > I am running mdrun_mpi V 4.6.5 for nsteps=10000000; 20 ns > > My simulation is getting stopped at 500ps and I am getting following > error > > even though i have enough space on my cluster around 17 GB. > > > > *Cannot fsync 'md1.trr'; maybe you are out of disk space?* > > *Cannot fsync 'md1.log'; maybe you are out of disk space?* > > > > > > I have executed for two times, each time i get different error. > > > > What is the reason for the above error. I am sharing my mdp file. > > Any help is appreciated. > > -- > > Thanks & Regards, > > Pavan Kumar > > Project Engineer > > CDAC -KP > > Ph +91-7676367646 > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Thanks & Regards, Pavan Kumar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
