Dear All<br><br>I used again grompp and then mdrun with the same commands,<br>they run successfuluy!!<br>of course with the same error.<br>I copy and paste the command shell when these are completed:<br><br>Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty<br>
Source code file: /home/mohsen/src/gromacs/src/gromacs/gmxlib/checkpoint.c, line: 1287<br><br>File input/output error:<br>Cannot fsync 'nvt-4.log'; maybe you are out of disk space or quota?<br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br><br>"These are Ideas, They are Not Lies" (Magnapop)<br>
<br>step 4900, remaining runtime: 25 s vol 0.97 imb F 0% <br>Writing final coordinates.<br>step 5000, remaining runtime: 0 s <br> Average load imbalance: 10.9 %<br> Part of the total run time spent waiting due to load imbalance: 3.2 %<br>
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 %<br><br><br> Parallel run - timing based on wallclock.<br><br> NODE (s) Real (s) (%)<br> Time: 1252.469 1252.469 100.0<br>
20:52<br> (Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>Performance: 174.935 8.226 0.690 34.784<br><br>gcq#92: "Once Again Let Me Do This" (Urban Dance Squad)<br>
<br><br>what it means?<br>Why they worked if they were wrong??<br><br><br><div class="gmail_quote">On Wed, Apr 6, 2011 at 4:59 PM, mohsen ramezanpour <span dir="ltr"><<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear All<br>I used mdrun for generating NVT<br><br>It crashed and massage was:<br><br>Trying to get md5sum: nvt-1.trr: Stale NFS file handle<br>
<br>Trying to get md5sum: nvt-1.edr: Stale NFS file handle<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty<br>Source code file: /home/mohsen/src/gromacs/src/gromacs/gmxlib/checkpoint.c, line: 1287<br><br>File input/output error:<br>Cannot fsync 'nvt-1.trr'; maybe you are out of disk space or quota?<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br><br>But I have enough space on my cluster!<br>
it is excellent because I run 5 program with the same nvt.mdp file and all of them gave above error.<br>Of course 3 of them ended succesfully although they gave the same error too.<br>Is the problem from my mdp file?<br>
<br>
Thanks in advance<br>
</blockquote></div><br>