[gmx-users] outputs from parallel jobs

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 6 14:13:30 CET 2005

Lubos Vrbka wrote:
> hi guys,
> i want to run parallel gromacs on a cluster with myrinet interconnection 
> (dual processor nodes). i have to have all inputs/outputs on /scratch 
> that is separate for every node. the problem is that gromacs writes 
> separate log files for every processor on its node. this brings the 
> problem how to populate the directories to every node of my calculation 
> and then how to gather them together.
> it can be done, but... is there any way how to avoid this? i.e., how to 
> put all logfiles into the same directory on the master node, or to 
> single file?

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. :-)


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