Re: [gmx-users] out of disk space error
On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] out of disk space error
If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the problem. On Thu, Dec 5, 2013 at 11:03 AM, vaani vsha...@imtech.res.in wrote: On 12/4/13 5:24 AM, amin@.res wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up someone's disk if it has several hundred GB available, but it can't hurt to reduce the output a bit. Frequent writing could be taxing the filesystem unnecessarily. It is also important to keep in mind that some desktop computers simply cannot handle a simulation that would be best run on a cluster with high-performance I/O. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 hi justin, i have already run simulations on this work station before also without any such disk space problem. i am facing this problem now only after installing ubuntu and gromacs freshly, best - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013086.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 and Regards,Bipin Singh* -- 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] out of disk space error
hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
Dear vaani, Please rerun the gmx executable. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote: hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
Dear vaani, Sorry for the unclear message. Try running the mdrun command once again and post the out put of the log file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote: i am sorry ..but i kind of dint get you .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013027.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
sure .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013029.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
vaani wrote nvt.log http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log find the attached nvt.log file .. i have been equilibrating for 200ps in this example..and getting this error , but when equilibrating for 100ps there is no such error ..in later case i am getting this error at the time of 10 ns dynamic run - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013032.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
