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.moh...@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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