[gmx-users] Long trajectory split

[Justin Lemkul]

On 2/23/14, 12:10 PM, Marcelo Depólo wrote:
> Pretty sure. I ran other simulations in the same system and worked just
> fine.
>
> About the frames, each file contains different number of frames, apparently
> random numbers (one file contains 400ns of data and other contains 10ns)
>

What are the starting and ending points of those data?  Is the run re-starting 
or just writing successive time intervals to new files when it shouldn't be?  Do 
you have some limitation on file size that is being reached, causing the new 
files to be generated?

-Justin

>
> 2014-02-23 17:54 GMT+01:00 Dr. Vitaly Chaban <vvchaban at gmail.com>:
>
>> are you sure that your binary is parallel?
>>
>> how many frames do those trajectory files contain?
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo <marcelodepolo at gmail.com>
>> 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.
>>>
>>>
>>> 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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>>>
>>>
>>>
>>> --
>>> Marcelo Depólo Polêto
>>> Uppsala Universitet - Sweden
>>> Science without Borders - CAPES
>>> Phone: +46 76 581 67 49
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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

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