-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 To make things short. The used file system is lustre.
/Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: > 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 <[email protected]> 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 <[email protected]> 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 [email protected] >>>>>>> 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 [email protected]. >>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >> >> > > - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzwHkkACgkQLpNNBb9GiPkTDACfYqLGXTdRuyg5cZB82pEdF1L4 LGAAoObjD2XR1T2Ypmle3HfamNtrsYlh =oYjI -----END PGP SIGNATURE----- -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
