Thanks Carsten and Mark
As of now I think Carsten's suggestion is good but this intelligent option seems harmful which I can see in the link provided by Mark is under consideration. Otherwise in code it will be good if somehow '-force' option is implemented which bounds to use file names as such without any compromise. regards, Jiom On Wed, Apr 29, 2015 at 12:36 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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. > -- 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.