[gmx-users] Re: not enough space
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Wed Apr 6 14:36:48 CEST 2011
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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