[gmx-users] The mdrun can not continue to run from the last check point

Mark Abraham mark.j.abraham at gmail.com
Thu Nov 27 12:33:25 CET 2014


This means what it says. The crash means not all files got written to disk.
mdrun can only restart from the checkpoint, so it has to rewind the .log
file to that point. But something's wrong with the log file. You can
continue the simulation, but you cannot append to that output file, so
either fix the problem of missing files, or use mdrun -noappend.


On Thu, Nov 27, 2014 at 7:13 AM, liuyong_1007 at dicp.ac.cn <
liuyong_1007 at dicp.ac.cn> wrote:

> Dear gmx users.
> After been killed during the mdrun, the mdrun can not continue to run from
> the last check point.
> The gromacs shows error as :
> -------------------------------------------------------
> Program mdrun_mpi_d, VERSION 5.0
> Source code file:
> /lustre/home/liuyong/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line: 2218
> Fatal error:
> Can't read 404674 bytes of 'md.log' to compute checksum. The file has been
> replaced or its contents have been modified. Cannot do appending because of
> this condition.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>  The command line“mpirun.lsf mdrun_mpi_d -v -multidir sim* -s topol.tpr
> -cpi state.cpt -replex 500” are used.
> liuyong_1007 at dicp.ac.cn
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