Hi Baofu,<div><br></div><div>could you provide more information about the file system? </div><div>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.</div>
<div><br></div><div>Roland<br><br><div class="gmail_quote">On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao <span dir="ltr"><<a href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Roland,<br>
<br>
Thanks a lot!<br>
<br>
OS: Scientific Linux 5.5. But the system to store data is called as<br>
WORKSPACE, different from the regular hardware system. Maybe this is the<br>
reason.<br>
<br>
I'll try what you suggest!<br>
<br>
regards,<br>
<font color="#888888">Baofu Qiao<br>
</font><div><div></div><div class="h5"><br>
<br>
On 11/26/2010 04:07 PM, Roland Schulz wrote:<br>
> Baofu,<br>
><br>
> what operating system are you using? On what file system do you try to store<br>
> the log file? The error (should) mean that the file system you use doesn't<br>
> support locking of files.<br>
> Try to store the log file on some other file system. If you want you can<br>
> still store the (large) trajectory files on the same file system.<br>
><br>
> Roland<br>
><br>
> On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao <<a href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>> wrote:<br>
><br>
><br>
>> Hi Carsten,<br>
>><br>
>> Thanks for your suggestion! But because my simulation will be run for<br>
>> about 200ns, 10ns per day(24 hours is the maximum duration for one<br>
>> single job on the Cluster I am using), which will generate about 20<br>
>> trajectories!<br>
>><br>
>> Can anyone find the reason causing such error?<br>
>><br>
>> regards,<br>
>> Baofu Qiao<br>
>><br>
>><br>
>> On 11/26/2010 09:07 AM, Carsten Kutzner wrote:<br>
>><br>
>>> Hi,<br>
>>><br>
>>> as a workaround you could run with -noappend and later<br>
>>> concatenate the output files. Then you should have no<br>
>>> problems with locking.<br>
>>><br>
>>> Carsten<br>
>>><br>
>>><br>
>>> On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote:<br>
>>><br>
>>><br>
>>><br>
>>>> Hi all,<br>
>>>><br>
>>>> I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about<br>
>>>><br>
>> 30% slower than 4.5.3. So I really appreciate if anyone can help me with it!<br>
>><br>
>>>> best regards,<br>
>>>> Baofu Qiao<br>
>>>><br>
>>>><br>
>>>> 于 2010-11-25 20:17, Baofu Qiao 写道:<br>
>>>><br>
>>>><br>
>>>>> Hi all,<br>
>>>>><br>
>>>>> I got the error message when I am extending the simulation using the<br>
>>>>><br>
>> following command:<br>
>><br>
>>>>> mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi<br>
>>>>><br>
>> pre.cpt -append<br>
>><br>
>>>>> The previous simuluation is succeeded. I wonder why pre.log is locked,<br>
>>>>><br>
>> and the strange warning of "Function not implemented"?<br>
>><br>
>>>>> Any suggestion is appreciated!<br>
>>>>><br>
>>>>> *********************************************************************<br>
>>>>> Getting Loaded...<br>
>>>>> Reading file pre.tpr, VERSION 4.5.3 (single precision)<br>
>>>>><br>
>>>>> Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010<br>
>>>>><br>
>>>>> -------------------------------------------------------<br>
>>>>> Program mdrun, VERSION 4.5.3<br>
>>>>> Source code file: checkpoint.c, line: 1750<br>
>>>>><br>
>>>>> Fatal error:<br>
>>>>> Failed to lock: pre.log. Function not implemented.<br>
>>>>> For more information and tips for troubleshooting, please check the<br>
>>>>><br>
>> GROMACS<br>
>><br>
>>>>> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
>>>>> -------------------------------------------------------<br>
>>>>><br>
>>>>> "It Doesn't Have to Be Tip Top" (Pulp Fiction)<br>
>>>>><br>
>>>>> Error on node 0, will try to stop all the nodes<br>
>>>>> Halting parallel program mdrun on CPU 0 out of 64<br>
>>>>><br>
>>>>> gcq#147: "It Doesn't Have to Be Tip Top" (Pulp Fiction)<br>
>>>>><br>
>>>>><br>
>>>>><br>
>> --------------------------------------------------------------------------<br>
>><br>
>>>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>
>>>>> with errorcode -1.<br>
>>>>><br>
>>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
>>>>> You may or may not see output from other processes, depending on<br>
>>>>> exactly when Open MPI kills them.<br>
>>>>><br>
>>>>><br>
>> --------------------------------------------------------------------------<br>
>><br>
>>>>><br>
>> --------------------------------------------------------------------------<br>
>><br>
>>>>> mpiexec has exited due to process rank 0 with PID 32758 on<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>> --<br>
>>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>>>> Please search the archive at<br>
>>>><br>
>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>><br>
>>>> Please don't post (un)subscribe requests to the list. Use the<br>
>>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>>>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>>>><br>
>>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
</div>