This works well until you use a system that permits job suspension. Then -maxh gets double-crossed... :-)
Mark On Apr 25, 2013 3:41 PM, "Richard Broadbent" < richard.broadben...@imperial.ac.uk> wrote: > I generally build a tpr for the whole simulation then submit one job using > a command such as: > > mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh > ${WALL_TIME_IN_HOURS} > > copy all the files back at the end of the script if necessary then: > > then resubmit it (sending out all the files again if necessary) this time > using the command > > mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh > ${WALL_TIME_IN_HOURS} -cpi > > you can then keep resubmitting with that line till the job is finished. > > In my case I have a maximum wall clock of 24hrs on some machines so this > gets used a lot > > I also think that 1.6ns/day which is what you seem to be getting is very > low performance and you might want to consider using more processors. Check > the log file as the profiling information at the end will indicate whether > this might be beneficial. > > Richard > > > On 25/04/13 13:58, Francesco wrote: > >> You can split the simulation in different part (for example 5 ns each), >> every time you'll finish one you will extend it adding more time. >> http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulations?** >> highlight=extend<http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend> >> >> My cluster uses a different "script system" than yours so I can't help >> with it, but basically you have to submit more than 1 job with different >> command to execute: >> >> 1) first production >> mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 >> 2) modify the tpr file >> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr >> 3) next X ns >> mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt >> 4) modify the tpr file >> 5) production md >> and so on >> >> with qsub you can submit a depending job (-hold_jid) that will run only >> when the previous step will finish, in your case there should be a >> similar way to do it. >> >> cheers >> >> Fra >> >> On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote: >> >>> Hey all, >>> >>> I recently ran 20ns simulation of protein ligand complex on cluster i >>> used >>> following script to run simulation >>> >>> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o >>> md_test.tpr >>> >>> mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 >>> >>> *I saved this as MD.sh And then submited to cluster using following >>> script* >>> >>> #!/bin/bash >>> #BSUB -J testgromacs # the job's name/array job >>> #BSUB -W 120:00 # max. wall clock time in hh:mm >>> #BSUB -n 8,8 # number of processors Min,Max >>> #BSUB -o test/output_%J.log # output file >>> #BSUB -e test/errors_%J.log # error file >>> #BSUB -M 8192 #Memory limit in MB >>> >>> echo "Started at `date`" >>> echo >>> >>> cd test >>> >>> echo "Running gromacs test in `pwd`" >>> >>> ./MD.sh >>> >>> echo "Finished at `date`" >>> >>> >>> It gave result but when checked files .xtc and created RMSD plots in that >>> x-axis of this plot i see only 8ns ...but in MD.MDP file i specified >>> 20ns.. >>> >>> Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF >>> run >>> time limit. >>> Exited with exit code 140". i gave maximum cluster time 120 hours..still >>> it >>> is not sufficient .. >>> >>> Can any body tell me how do it split script i such that i will get all >>> 20ns simulation >>> >>> >>> Thanks in advance , >>> >>> Sainitin >>> -- >>> 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<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