[gmx-users] outputs from parallel jobs

Lubos Vrbka lubos.vrbka at gmail.com
Thu Dec 8 07:39:02 CET 2005

> 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 

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...


_ at _"

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