[gmx-users] Long trajectory split

[Justin Lemkul]

On 2/23/14, 11:32 AM, Marcelo Depólo wrote:
> Maybe I should explain it better.
>
> I am using "*mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*", pretty
> much a standard line. This job in a batch creates the outputs and, after
> some (random) time, a back up is done and new files are written, but the
> job itself do not finish.
>

It would help if you can post the .log file from one of the runs to see the 
information regarding mdrun's parallel capabilities.  This still sounds like a 
case of an incorrectly compiled binary.  Do other runs with the same binary 
produce the same problem?

-Justin

>
> 2014-02-23 17:12 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 2/23/14, 11:00 AM, Marcelo Depólo wrote:
>>
>>> But it is not quite happening simultaneously, Justin.
>>>
>>> It is producing one after another and, consequently, backing up the files.
>>>
>>>
>> You'll have to provide the exact commands you're issuing.  Likely you're
>> leaving the output names to the default, which causes them to be backed up
>> rather than overwritten.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================