[gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Florian Dommert dommert at icp.uni-stuttgart.de
Fri Nov 26 21:53:29 CET 2010 

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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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>>>>>>>
>>>>>>>             
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>           
>>> --
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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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