Hi, Thank you for your reply !
md_test.xtc is exist and writable. I tried to restart from checkpoint file by excluding other node than compute-node and it works. only '--exclude=compute-node' that produces this error. is this has the same issue with this thread ? http://comments.gmane.org/gmane.science.biology.gromacs.user/40984 regards, Husen On Thu, Jun 16, 2016 at 2:20 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > The stuff about different nodes or numbers of nodes doesn't matter - it's > merely an advisory note from mdrun. mdrun failed when it tried to operate > upon md_test.xtc, so perhaps you need to consider whether the file exists, > is writable, etc. > > Mark > > On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote: > > > Hi all, > > > > I got the following error message when I tried to restart gromacs > > simulation from checkpoint file. > > I restart the simulation using fewer nodes and processes, and also I > > exclude one node using '--exclude=' option (in slurm) for experimental > > purpose. > > > > I'm sure fewer nodes and processes are not the cause of this error as I > > already test that. > > I have checked that the cause of this error is '--exclude=' usage. I > > excluded 1 node named 'compute-node' when restart from checkpoint (at > first > > run, I use all node including 'compute-node'). > > > > > > it seems that at first run, the submit job script was built at > > compute-node. So, at restart, build user mismatch appeared because > > compute-node was not found (excluded). > > > > Am I right ? is this behavior normal ? > > or is that a way to avoid this, so I can freely restart from checkpoint > > using any nodes without limitation. > > > > thank you in advance > > > > Regards, > > > > > > Husen > > > > ==========================restart script================= > > #!/bin/bash > > #SBATCH -J ayo > > #SBATCH -o md%j.out > > #SBATCH -A necis > > #SBATCH -N 2 > > #SBATCH -n 16 > > #SBATCH --exclude=compute-node > > #SBATCH --time=144:00:00 > > #SBATCH --mail-user=hus...@gmail.com > > #SBATCH --mail-type=begin > > #SBATCH --mail-type=end > > > > mpirun gmx_mpi mdrun -cpi md_test.cpt -deffnm md_test > > ===================================================== > > > > > > > > > > ==================================output error======================== > > Reading checkpoint file md_test.cpt generated: Wed Jun 15 16:30:44 2016 > > > > > > Build time mismatch, > > current program: Sel Apr 5 13:37:32 WIB 2016 > > checkpoint file: Rab Apr 6 09:44:51 WIB 2016 > > > > Build user mismatch, > > current program: pro@head-node [CMAKE] > > checkpoint file: pro@compute-node [CMAKE] > > > > #ranks mismatch, > > current program: 16 > > checkpoint file: 24 > > > > #PME-ranks mismatch, > > current program: -1 > > checkpoint file: 6 > > > > GROMACS patchlevel, binary or parallel settings differ from previous run. > > Continuation is exact, but not guaranteed to be binary identical. > > > > > > ------------------------------------------------------- > > Program gmx mdrun, VERSION 5.1.2 > > Source code file: > > /home/pro/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp, line: 2216 > > > > Fatal error: > > Truncation of file md_test.xtc failed. Cannot do appending because of > this > > failure. > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > ================================================================ > > -- > > 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.