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

[Baofu Qiao]

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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>>>
>>>
>>>
>>>
>>>