[gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

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.abraham at 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 <hus3nr at 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=hus3nr at 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 at head-node [CMAKE]
> >     checkpoint file: pro at 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
> > -------------------------------------------------------
> > ================================================================
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