Re: [gmx-users] restarting a simulation
Hi, Have you read and try what mdrun tells you, like -deffnm option? in recent version of gromacs, if you do not want to append the output to old output files, use option -noappend. On Mon, Apr 6, 2020 at 6:06 PM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > 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] restarting a simulation
You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > 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] restarting a simulation
On 4/7/20 11:47 AM, Daniel Burns wrote: You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". The issue is not with the naming of the checkpoint file but with the output files specified within the checkpoint. The simplest workaround here is simply to use -noappend and concatenate output later. If one moves files around, sometimes the appending mechanism can break for reasons that are still unclear to me. -Justin Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: Dear Gromacs users I am restarting a simulation with the following command:- mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append However, I am getting following error message. All the below-named files are there in my directory but it still complains the same. Inconsistency in user input: Some output files listed in the checkpoint file md10_prev.cpt are not present or not named as the output files by the current program:)Expected output files that are present: Expected output files that are not present or named differently: md10.log md10.xtc md10.trr md10.edr md10.xvg To keep your simulation files safe, this simulation will not restart. Either name your output files exactly the same as the previous simulation part (e.g. with -deffnm), or make sure all the output files are present (e.g. run from the same directory as the previous simulation part), or instruct mdrun to write new output files with mdrun -noappend. In the last case, you will not be able to use appending in future for this simulation. I also tried without -append option. Please correct me if I am wrong somewhere. Thanks. Sadaf -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] Restarting a simulation when checkpoint files are corrupted
Hi, On Fri, Mar 17, 2017 at 6:00 PM David Dotson wrote: > Greetings, > > I have a simulation that has been running for a long time, with many > trajectory segments (counting up to about 190). One of the segments ran on > a cluster that experienced a filesystem outage such that some of the files > for that run were corrupted, including its checkpoint files (both the *.cpt > and *_prev.cpt, somehow). Yeah, that's a recurring problem. mdrun tells the filesystem to flush to disk, but if it doesn't actually do that, then all we can suggest is that you request more conservative settings from your sysadmins. > Since I only have checkpoint files for the most recent run, I need to do > something like a manual restart. > > I'm aware I can do this with `gmx convert-tpr` using an existing TPR and > the most recent uncorrupted TRR and EDR file, but starting a run from this > restarts counting for the output files from `0001`. Is there some way to > make counting start from another value (like `0191`)? > Somehow it never got documented (I will fix that), but there is an .mdp field that lets you set "simulation-part = 191" that would let you take matters suitably into your own hands. Mark > If not, I can work around this I think by concatenating the existing parts > and moving forward with restarted counting, but being able to do this would > be the cleanest solution for me in this particular case to maintain some > consistency with other runs. > > Thanks! > > David > > -- > David L. Dotson * david.dot...@asu.edu > Beckstein Lab > Center for Biological Physics > Arizona State University > > becksteinlab.physics.asu.edu > > > -- > 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] Restarting a simulation when checkpoint files are corrupted
Excellent! Thanks Mark! Yeah, already had a discussion with the sysadmin of this particular system; it was definitely not something that should happen. Cheers! David On 03/17/2017 10:11 AM, Mark Abraham wrote: > Hi, > > > On Fri, Mar 17, 2017 at 6:00 PM David Dotson wrote: > >> Greetings, >> >> I have a simulation that has been running for a long time, with many >> trajectory segments (counting up to about 190). One of the segments ran on >> a cluster that experienced a filesystem outage such that some of the files >> for that run were corrupted, including its checkpoint files (both the *.cpt >> and *_prev.cpt, somehow). > > Yeah, that's a recurring problem. mdrun tells the filesystem to flush to > disk, but if it doesn't actually do that, then all we can suggest is that > you request more conservative settings from your sysadmins. > > >> Since I only have checkpoint files for the most recent run, I need to do >> something like a manual restart. >> >> I'm aware I can do this with `gmx convert-tpr` using an existing TPR and >> the most recent uncorrupted TRR and EDR file, but starting a run from this >> restarts counting for the output files from `0001`. Is there some way to >> make counting start from another value (like `0191`)? >> > Somehow it never got documented (I will fix that), but there is an .mdp > field that lets you set "simulation-part = 191" that would let you take > matters suitably into your own hands. > > Mark > > >> If not, I can work around this I think by concatenating the existing parts >> and moving forward with restarted counting, but being able to do this would >> be the cleanest solution for me in this particular case to maintain some >> consistency with other runs. >> >> Thanks! >> >> David >> >> -- >> David L. Dotson * david.dot...@asu.edu >> Beckstein Lab >> Center for Biological Physics >> Arizona State University >> >> becksteinlab.physics.asu.edu >> >> >> -- >> 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. >> -- David L. Dotson * david.dot...@asu.edu Beckstein Lab Center for Biological Physics Arizona State University becksteinlab.physics.asu.edu -- 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] Restarting a simulation: failed to lock the log file
> On 7. Jan 2019, at 11:55, morpheus wrote: > > Hi, > > I am running simulations on a cluster that terminates jobs after a hard > wall clock time limit. Normally this is not a problem as I just restart the > simulations using -cpi state.cpt but for the last batch of simulations I > got (for most but not all of them) the error: > > "Failed to lock: 1uao.md.log. Already running simulation?" > > There is definitely nothing running. I have tried to move the log file to > another directory and then moved it back (to get rid of any write locks) > but the error stays the same. If I delete the logfile it also crashes > because it cant find the file and if I replace the log file with an empty > new file then I get "Can't read 1048576 bytes of '1uao.md.log' to compute > checksum. The file has been replaced or its contents have been modified. > Cannot do appending because of this condition.". > Using "-noappend" and then concatenating is also not a great solution as > this becomes quite cumbersome with many simulations. > > Any ideas? You can move the simulation output files to some temporary location and then _copy_ them back into the original directory. Carsten > > Thanks! > -- > 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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.
