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

[Husen R]

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
-------------------------------------------------------
================================================================