Re: [gmx-users] Split Trajectory file into parts
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 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 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.
Re: [gmx-users] Split Trajectory file into parts
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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Split Trajectory file into parts
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. 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 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] Split Trajectory file into parts
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. Is it possible to ask gromacs to automatically split the trajectory files into parts? Or, I have to write a shell script to make gromacs restart the simulation every 15 minutes? Thank you. -- 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.
