The file system seemed to have no quota, after checking with that command. The problem seems to be that the simulation I set up save too quickly for the file system. Splitting the trajectory into parts only alleviated but not solved the problem. in the end I ran the simulation at another place.
On Mon, Aug 31, 2015 at 3:50 AM, Peter Kroon <[email protected]> wrote: > > > On 29/08/15 16:22, Justin Lemkul wrote: > > > > > > On 8/29/15 9:10 AM, Johnny Lu wrote: > >> Dear Users, > >> > >> Simulation writes to a Lustre file system (a distributed file system > >> made > >> of many hard drives). > >> About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it > >> can't > >> write the trajectory file. > >> The file system still has lots of space. Not sure if that was because > >> one > >> of the many hard drives filled up. > Does your cluster implement filesystem quotas? Did you reach it? On our > cluster (which also uses Lustre) I use `lfs quota /home` to see my quota > and usage on the partition /home. > > Peter > >> > >> Is it possible to ask gromacs to automatically split the trajectory > >> files > >> into parts? > > > > No. > > > >> Or, I have to write a shell script to make gromacs restart the > >> simulation > >> every 15 minutes? > >> > > > > Yes. Or, heed what grompp tells you about how much data will be > > generated and simply construct a very trivial loop to execute mdrun > > for N steps, invoke convert-tpr, mdrun -cpi -noappend, etc. > > > > -Justin > > > > > > -- > 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 [email protected]. > -- 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 [email protected].
