Hi Baofu, could you provide more information about the file system? The command "mount" provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest.
Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao <qia...@gmail.com> wrote: > Hi Roland, > > Thanks a lot! > > OS: Scientific Linux 5.5. But the system to store data is called as > WORKSPACE, different from the regular hardware system. Maybe this is the > reason. > > I'll try what you suggest! > > regards, > Baofu Qiao > > > On 11/26/2010 04:07 PM, Roland Schulz wrote: > > Baofu, > > > > what operating system are you using? On what file system do you try to > store > > the log file? The error (should) mean that the file system you use > doesn't > > support locking of files. > > Try to store the log file on some other file system. If you want you can > > still store the (large) trajectory files on the same file system. > > > > Roland > > > > On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao <qia...@gmail.com> wrote: > > > > > >> 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 > >>>> > >>>> > >>>> δΊ 2010-11-25 20:17, Baofu Qiao ει: > >>>> > >>>> > >>>>> 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 > >>>> > >>>> > >>> > >>> > >>> > >>> > >>> > > -- > 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 > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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