[gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED
Baofu Qiao
qiaobf at gmail.com
Fri Nov 26 21:17:10 CET 2010
Hi all,
What Roland said is right! the lustre system causes the problem of
"lock". Now I copy all the files to a folder of /tmp, then run the
continuation. It works!
Thanks!
regards,
$于 2010-11-26 22:53, Florian Dommert 写道:
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> 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)
>> 172.31.100.222 at o2ib,172.30.100.222 at tcp:172.31.100.221 at o2ib,172.30.100.221 at tcp:/lprod
>> on /lustre/ws1 type lustre (rw,noatime,nodiratime)
>> 172.31.100.222 at o2ib,172.30.100.222 at tcp:172.31.100.221 at o2ib,172.30.100.221 at 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<qiaobf at 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<qiaobf at 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
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>>>>>>
>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>> Please search the archive at
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>>>>
>>>>
>>>>
>>>
>>
>
> - --
> 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: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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