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 <vvcha...@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 <marcelodep...@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 <jalem...@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
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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