[gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3) Neither of 4.5.1, 4.5.2 and 4.5.3 works

[Baofu Qiao]

Hi all,

I just made some tests by using gmx 4.5.1, 4.5.2 and 4.5.3. Neither of
them works on the continuation.
-------------------------------------------------------
Program mdrun, VERSION 4.5.1
Source code file: checkpoint.c, line: 1727

Fatal error:
Failed to lock: pre.log. Already running simulation?
-------------------------------------------------------
Program mdrun, VERSION 4.5.2
Source code file: checkpoint.c, line: 1748

Fatal error:
Failed to lock: pre.log. Already running simulation?
-------------------------------------------------------
Program mdrun, VERSION 4.5.3
Source code file: checkpoint.c, line: 1750

Fatal error:
Failed to lock: pre.log. Function not implemented.
=====================================================================

The system to test is 895 SPC/E water,box size of 3nm, (genbox -box 3
-cs). The pre.mdp is attached.

I have tested two clusters:
Cluster A: 1)compiler/gnu/4.3 2) mpi/openmpi/1.2.8-gnu-4.3 3)FFTW 3.3.2
4) GMX 4.5.1/4.5.2/4.5.3
Cluster B: 1)compiler/gnu/4.3 2) mpi/openmpi/1.4.2-gnu-4.3 3)FFTW 3.3.2
4) GMX 4.5.3

GMX command:
mpiexec -np 8 mdrun -deffnm pre -npme 2 -maxh 0.15 -cpt 5 -cpi pre.cpt
-append

Can anyone provide further help? Thanks a lot!

best regards,



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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