[gmx-users] question about mdrun -append

[Berk Hess]

My guess would be that for some reason (which I don't know),
your xtc file has not been written to disk completely.
You can check this by using gmxdump -cp on your checkpoint file
and looking at the size of the xtc file.

Berk

> Date: Fri, 7 Aug 2009 10:19:35 +0200
> From: qiaobf at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] question about mdrun -append
> 
> Hi all,
> 
> I meet one problem when I am using mdrun -append. In some cases, the
> following error information happens, and mdrun is halted
> *************************************************
> Program mdrun, VERSION 4.0.5
> Source code file: checkpoint.c, line: 1248
> Fatal error:
> Truncation of file T298.xtc failed.
> *************************************************
> Line 1248 in checkpoint.c is the inner loop as follows
> *********************************************************************************
>         if(bAppendOutputFiles) {
>                 for(i=0;i<nfiles;i++)  {
>                         if(0 !=
> truncate(outputfiles[i].filename,outputfiles[i].offset) )  {
>                                gmx_fatal(FARGS,"Truncation of file %s
> failed.",outputfiles[i].filename);
>                         }
>                 }
>         }
> *********************************************************************************
> 
> But I don't know how to solve it. Please give some suggestions! Thanks a
> lot!
> 
> The following script is used
> grompp -f T298.mdp -c pre2.gro -p system.top -o T298
> mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5
> mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 -cpi T298.cpt -append
> 
> regards,
> Baofu Qiao
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