No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4.
> Mark, > > The problem with one .tpr file set for 100ns is that when job number (say) > 4 hits the wall limit, it crashes and never gets a chance to submit the > next job. So it's not really automated. > > Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 > till job 4 ends. But the PBS queuing system is sometime weird and takes a > bit of time to recognize a job and give back its jobID. So I could submit > job 5 but be unable to change its status to /hold/ because PBS does not > return its ID. Another problem is that if resources are available, job 5 > could start before I ever get a chance to /hold/ it. > > > > > On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham > <mark.j.abra...@gmail.com>wrote: > >> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.grom...@gmail.com >> >wrote: >> >> > I have need to collect 100ns but I can collect only ~1ns (1000steps) >> per >> > run. Since I dont have .trr files, I rely on .cpt files for restarts. >> For >> > example, >> > >> > grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 >> > >> > This runs into a problem when the run gets killed due to walltime >> limits. I >> > now have a .xtc file which has run (say) 700 steps and a .cpt file >> which >> > was last written at 600th step. >> > >> >> You seem to have no need to use grompp, because you don't need to use a >> workflow that generates multiple .tpr files. Do the equivalent of what >> the >> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a >> .tpr >> for the whole 100ns run, and then keep doing >> >> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime >> >> with or without -append, perhaps with -maxh, keeping whatever manual >> backups you feel necessary. Then perhaps concatenate your final >> trajectory >> files, according to your earlier choices. >> >> - To set up the next run I use the .cpt file from 600th step. >> > - Now during analysis if I want to center the protein and such, >> /trjconv/ >> > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ >> know >> > to stop at 600th step? >> >> >> trjconv just operates on the contents of the trajectory file, as >> modified >> by things like -b -e and -dt. The .tpr just gives it context, such as >> atom >> names. You could give it a .tpr from any point during the run. >> >> Mark >> >> If this has to be put in manually, it becomes >> > cumbersome. >> > >> > Thoughts? >> > >> > >> > >> > >> > >> > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalem...@vt.edu> >> wrote: >> > >> > > >> > > >> > > On 10/27/13 9:37 AM, Pavan Ghatty wrote: >> > > >> > >> Hello All, >> > >> >> > >> Is there a way to make mdrun put out .cpt file with the same >> frequency >> > as >> > >> a >> > >> .xtc or .trr file. From here >> > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts< >> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that >> we >> > >> can choose how often (time in mins) the .cpt file is written. But >> > clearly >> > >> if the frequency of output of .cpt (frequency in mins) and .xtc >> > (frequency >> > >> in simulation steps) do not match, it can create problems during >> > analysis; >> > >> especially in the event of frequent crashes. Also, I am not storing >> .trr >> > >> file since I dont need that precision. >> > >> I am using Gromacs 4.6.1. >> > >> >> > >> >> > > What problems are you experiencing? There is no need for .cpt >> frequency >> > > to be the same as .xtc frequency, because any duplicate frames >> should >> be >> > > handled elegantly when appending. >> > > >> > > -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 >> > > >> > > jalemkul@outerbanks.umaryland.**edu >> <jalem...@outerbanks.umaryland.edu >> > >> > | (410) >> > > 706-7441 >> > > >> > > ==============================**==================== >> > > -- >> > > gmx-users mailing list gmx-users@gromacs.org >> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< >> > http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > > * Please search the archive at http://www.gromacs.org/** >> > > Support/Mailing_Lists/Search< >> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! >> > > * Please don't post (un)subscribe requests to the list. Use the www >> > > interface or send it to gmx-users-requ...@gromacs.org. >> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< >> > http://www.gromacs.org/Support/Mailing_Lists> >> > > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
