[gmx-users] outputs from parallel jobs

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 8 08:53:52 CET 2005

Lubos Vrbka wrote:
>> If you are running under a batch queue manager (e.g. PBS) then there 
>> may well be commands to scatter/gather files to/from nodes 
>> appropriately, particularly if you are constrained to have all I/O in 
>> these local scratch spaces. I suggest you seek some more information 
>> from the people who support the machine. Distribution of files is a 
>> problem that isn't unique to gromacs (or MD) & thus the best tools to 
>> solve it won't be gromacs-specific. It'd also be silly for gromacs to 
>> be re-inventing that wheel. :-)
> yes, it is running under PBS. finally i found a solution using pbsdsh 
> that can be used to run a comand on all nodes, so i use for the 
> distribution.
> the thing that is not clear to me is, why gromacs prints separate output 
> for each processor. is it possible to disable it without recompiling the 
> code? it contains only lincs information anyway...
sometimes it contains more, e.g. in case of problems. If your simulation 
ends normally you might consider throwing the files away.

> thanks,

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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