Yes this is to continue a crashed run, but I dont know why my runs crash at the very beginnig of the simulation. I am using 4.5.4 so -append should work by default. I tried a simulation from time zero and it works as before ( mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x ) but as soon as I include the -cpi flag the it doesn work and I get:
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. While as I said if I try to start from the very beginning it doesnt crash... Any ideas.. Thanks On 13 August 2012 15:51, Matthias Ernst <matthias.ern...@student.kit.edu> wrote: > > > Am 13.08.2012 21:42, schrieb Juliette N.: > >> Thank you. I am using >> >> mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt > > I see a "md_prev.cpt". If I presume correctly that this is for the > continuation of the crashed run: Why and did you read what I wrote? > > >> >> but I dont get any output and the issued command terminates in the >> terminal. >> >> Do I have to remove the -o -c -g -e -x flags from the command line? >> >> Appreciate your help, >> >> >> On 13 August 2012 15:28, Matthias Ernst <matthias.ern...@student.kit.edu> >> wrote: >>> >>> Long story short: backup everything (since it's a backup, and hopefully >>> you >>> won't need it), then use the [whatever].cpt file. You don't want to do >>> work >>> twice, do you? If you use the [whatever]_prev.cpi file, you will >>> calculate >>> some frames *again* that are already there. >>> If you use an up-to-date version of Gromacs (4.5.5 is the most recent >>> one), >>> then the files will be continued and not overwritten. This is stated on >>> the >>> page you already found (hint: "remaining output will be appended to the >>> existing files (energy, trajectory, log, etc).") >>> >>> Good luck, >>> Matthias >>> >>> Am 13.08.2012 21:07, schrieb Juliette N.: >>> >>>> Hello all, >>>> >>>> I am going to restart my crashed simulations, but I am not sure which >>>> of *_prev.cpt or *.cpt to use as they contain different written >>>> frames. >>>> >>>> *_prev.cpt >>>> Last frame -1 time 7462.900 >>>> >>>> *.cpt >>>> Last frame -1 time 7468.965 >>>> >>>> Also on the gmx site it is stated that : >>>> >>>> Before doing anything, back up your files! Then use >>>> >>>> mdrun -s topol.tpr -cpi state.cpt >>>> >>>> >>>> What files do I need to back up? the edr. trr .. files that were >>>> written before crash? Is the new run going to overwrite the old files? >>>> >>>> >>>> Thanks, >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * 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 > * Only plain text messages are allowed! > * 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 -- Thanks, J. N. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
