[gmx-users] not enough space

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 6 14:45:30 CEST 2011

On 6/04/2011 10:29 PM, mohsen ramezanpour wrote:
> Dear All
> I used mdrun for generating NVT
> It crashed and massage was:
> Trying to get md5sum: nvt-1.trr: Stale NFS file handle

You have an intermittent problem with your Network File System. For some 
reason GROMACS can't keep writing to the same file, because it can't see 
it any more. The problem is not anything to do with GROMACS. Consult 
your system admins.

> Trying to get md5sum: nvt-1.edr: Stale NFS file handle
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty
> Source code file: 
> /home/mohsen/src/gromacs/src/gromacs/gmxlib/checkpoint.c, line: 1287
> File input/output error:
> Cannot fsync 'nvt-1.trr'; maybe you are out of disk space or quota?
> For more information and tips for troubleshooting, please check the 
> website at http://www.gromacs.org/Documentation/Errors
> But I have enough space on my cluster!

Sure... The above is only a guess, but it is often a good one.

> it is excellent because I run 5 program with the same nvt.mdp file and 
> all of them gave above error.
> Of course 3 of them ended succesfully although they gave the same 
> error too.
> Is the problem from my mdp file?



More information about the gromacs.org_gmx-users mailing list