Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories!
Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: > Hi, > > as a workaround you could run with -noappend and later > concatenate the output files. Then you should have no > problems with locking. > > Carsten > > > On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: > > >> Hi all, >> >> I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% >> slower than 4.5.3. So I really appreciate if anyone can help me with it! >> >> best regards, >> Baofu Qiao >> >> >> 于 2010-11-25 20:17, Baofu Qiao 写道: >> >>> Hi all, >>> >>> I got the error message when I am extending the simulation using the >>> following command: >>> mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt >>> -append >>> >>> The previous simuluation is succeeded. I wonder why pre.log is locked, and >>> the strange warning of "Function not implemented"? >>> >>> Any suggestion is appreciated! >>> >>> ********************************************************************* >>> Getting Loaded... >>> Reading file pre.tpr, VERSION 4.5.3 (single precision) >>> >>> Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 >>> >>> ------------------------------------------------------- >>> Program mdrun, VERSION 4.5.3 >>> Source code file: checkpoint.c, line: 1750 >>> >>> Fatal error: >>> Failed to lock: pre.log. Function not implemented. >>> For more information and tips for troubleshooting, please check the GROMACS >>> website at http://www.gromacs.org/Documentation/Errors >>> ------------------------------------------------------- >>> >>> "It Doesn't Have to Be Tip Top" (Pulp Fiction) >>> >>> Error on node 0, will try to stop all the nodes >>> Halting parallel program mdrun on CPU 0 out of 64 >>> >>> gcq#147: "It Doesn't Have to Be Tip Top" (Pulp Fiction) >>> >>> -------------------------------------------------------------------------- >>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> with errorcode -1. >>> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> You may or may not see output from other processes, depending on >>> exactly when Open MPI kills them. >>> -------------------------------------------------------------------------- >>> -------------------------------------------------------------------------- >>> mpiexec has exited due to process rank 0 with PID 32758 on >>> >>> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > -- ************************************ Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
