Dear justin, The job was terminated as under:
vol 0.92 imb F 1% step 5860300, will finish Sun Nov 15 06:56:32 2009 =>> PBS: job killed: walltime 86438 exceeded limit 86400 mpiexec: killing job... i think due to queueing system and maximum time being 24hrs. i donot know how to know whether new cpt files are written all the files i have are the same 2 cpt files state.cpt and state_prev.cpt. when i did gmxcheck on both cpt files the output was Checking file state.cpt # Atoms 31609 Last frame -1 time 2928.000 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 for state_prev.cpt # Atoms 31609 Last frame -1 time 2896.000 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 when the run is extended for the second time do gromacs generate a new cpt file i mean with new name or same named files (state.cpt and state_prev.cpt) with new check points written.. Please help Thanks, Ram On Tue, Nov 10, 2009 at 7:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> As per the suggestions in the bug, i changed the line in >> src/gmxlib/checkpoint.c file on the cluster: >> >> from >> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) >> offset_low ); >> >> to >> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) >> offset_low & mask ); >> >> and was able to use the -append option, my command was >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state.cpt -append >> >> and this run generated another 3ns production data (from the step >> 2928600 - 5900000) and thus increasing the size of trr file to 4.8 GB >> from 2.1 GB, because my simulation is for 20ns, i submitted one more >> job with the same command after completing the 5.9 ns, >> > > So the job crashed again, then? > >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state.cpt -append >> >> now again the job is starting from same step 2928600, i also tried >> using the command >> >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state_prev.cpt >> >> -append >> >> here also the output is same that is starting from 2928600 step, >> >> i want to continue the run from 5900000 step, please let me know how >> to proceed, do i have to generate a new .tpr file (my mdp file is >> defined for 20 ns and the output is md20.tpr) or can i use the same >> tpr file (md20.tpr) or i require to change the command to continue.. >> > > Were new .cpt files actually written? What does gmxcheck tell you about > each of them? It would seem that the simulation did not run long enough for > new .cpt files to be generated, or there was otherwise some problem with > writing the new file. You should not need a new .tpr file if you have not > yet completed the required 20 ns. See here: > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > -Justin > >> Please help. >> >> Thanks, >> >> Ram >> >> >> >> >> On Fri, Nov 6, 2009 at 10:15 PM, ram bio <rmbio...@gmail.com> wrote: >>> >>> Dear Justin, >>> >>> Thanks for the information regarding the bug, will try the solutions >>> in the site. >>> >>> Ram >>> >>> On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>>> >>>> ram bio wrote: >>>>> >>>>> Dear Gromacs users, >>>>> >>>>> I am running a protein-lipid bilayer simulation for 20ns. I am using >>>>> Gromacs version 4.0.5 and when i want to continue the mdrun using >>>>> -append command , I am getting an error as follows: >>>>> >>>>> Getting Loaded... >>>>> Reading file md20.tpr, VERSION 4.0.5 (single precision) >>>>> >>>>> Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 >>>>> >>>>> >>>>> ------------------------------------------------------- >>>>> Program mdrun, VERSION 4.0.5 >>>>> Source code file: checkpoint.c, line: 1248 >>>>> >>>>> Fatal error: >>>>> Truncation of file traj.trr failed. >>>>> >>>>> Please suugest me how to overcome this error and continue the mdrun. >>>>> >>>> http://bugzilla.gromacs.org/show_bug.cgi?id=341 >>>> >>>> I believe this bug has been fixed in the development version (available >>>> through git). >>>> >>>> -Justin >>>> >>>>> Thanks, >>>>> >>>>> Ram >>>>> _______________________________________________ >>>>> 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/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/mailing_lists/users.php >>>>> >>>> -- >>>> ======================================== >>>> >>>> Justin A. Lemkul >>>> Ph.D. Candidate >>>> ICTAS Doctoral Scholar >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> _______________________________________________ >>>> 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/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/mailing_lists/users.php >>>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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/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/mailing_lists/users.php > -- 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/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/mailing_lists/users.php
