[gmx-users] outputs from parallel jobs

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 6 13:55:09 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?

You can end your script with an scp copy command from the client to the 
master. For this you have to save the ssh keys from the nodes on the 
master in your .ssh/authorized_hosts file.

mdrun can not do it for you.

> thanks for any hints. regards,

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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