[gmx-users] Re: not enough space

[mohsen ramezanpour]

Dear All

I used again grompp and then mdrun with the same commands,
they run successfuluy!!
of course with the same error.
I copy and paste the command shell when these are completed:

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-4.log'; maybe you are out of disk space or quota?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"These are Ideas, They are Not Lies" (Magnapop)

step 4900, remaining runtime:    25 s          vol 0.97  imb F  0%
Writing final coordinates.
step 5000, remaining runtime:     0 s
 Average load imbalance: 10.9 %
 Part of the total run time spent waiting due to load imbalance: 3.2 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
%


    Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:   1252.469   1252.469    100.0
                       20:52
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    174.935      8.226      0.690     34.784

gcq#92: "Once Again Let Me Do This" (Urban Dance Squad)


what it means?
Why they worked if they were wrong??


On Wed, Apr 6, 2011 at 4:59 PM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> 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
>
> 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 GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> But I have enough space on my cluster!
> 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?
>
> Thanks in advance
>
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