[gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)
Baofu Qiao
qiaobf at gmail.com
Fri Nov 26 17:49:53 CET 2010
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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>
>
--
************************************
Dr. Baofu Qiao
Institute for Computational Physics
Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Tel: +49(0)711 68563607
Fax: +49(0)711 68563658
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