Hi Roland, The output of "mount" is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) 172.30.100.254:/home on /home type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254) 172.30.100.210:/opt on /opt type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) 172.30.100.210:/var/spool/torque/server_logs on /var/spool/pbs/server_logs type nfs (ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) none on /ipathfs type ipathfs (rw) 172.31.100....@o2ib,172.30.100....@tcp:172.31.100....@o2ib,172.30.100....@tcp:/lprod on /lustre/ws1 type lustre (rw,noatime,nodiratime) 172.31.100....@o2ib,172.30.100....@tcp:172.31.100....@o2ib,172.30.100....@tcp:/lbm on /lustre/lbm type lustre (rw,noatime,nodiratime) 172.30.100.219:/export/necbm on /nfs/nec type nfs (ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) 172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs (rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)
On 11/26/2010 05:41 PM, Roland Schulz wrote: > 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 >>>>>> >>>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >> -- >> 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