On Wed, Apr 29, 2015 at 1:20 PM Kutzner, Carsten <ckut...@gwdg.de> wrote:
> Hi JIom, > > > On 29 Apr 2015, at 11:50, gromacs query <gromacsqu...@gmail.com> wrote: > > > > Dear All, > > > > mdrun is not giving any error about missing cpt file. It runs using tpr > > from initial time zero. Sometimes my job get killed and I need to use cpt > > file in some script but if cpt is not found my job starts running from > zero > > time in tpr file which is harmful as it consumes my processors to run job > > again from time zero. I would expect it should get killed with error if > > some cpt file is not found. My command line in script goes like this: > This is not a bug but a feature :) > Debatable - if the other output files actually *are* present, then mdrun ignores it, which is not necessarily a good thing. https://gerrit.gromacs.org/#/c/4439/1 proposed to fix this and related issues (though as you point out, I'd need to change the doc string below, also). Mark > From mdrun -h: > "A simulation can be continued by > reading the full state from file with option -cpi. This option is > intelligent > in the way that if no checkpoint file is found, Gromacs just assumes a > normal > run and starts from the first step of the .tpr file.” > > > > > mdrun_mpi -s dyn.tpr -x dyn.xtc -e dyn.edr -c dyn.gro -g dyn.log -cpi > > previous.cpt -cpo dyn.cpt > > > > In this case if provious.cpt is not found mdrun still runs my job but > > starting from zero time. Why it should not get killed complaining about > > missing previous.cpt file? > > > > Do I need to force something? > If you specifically only want to run an MD if a .cpt file is found, > you could do that, e.g. in bash with: > > if [ -f previous.cpt ] ; then > mdrun … > else > printf “No checkpoint file found.” > fi > > Carsten > > > > > > > Thanks, > > JIom > > -- > > 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. -- 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.