[gmx-users] mdrun -multi
feenstra at chem.vu.nl
Tue Dec 2 08:53:00 CET 2003
Nguyen Hoang Phuong wrote:
> thanks Anton. Here we have a linux cluster with many queues but each
> queues has only 2 cpus. If I use mdrun -np 4 -multi then four jobs will be
> submitted to one queue and running on 2cpus. Are there possibilities
> (some trick or modify the code) to distribute these 4 jobs on 4
> cpus (2 queues)? Of course without starting multiple separate
> instances of mdrun.
No - in principle at least you are restricted to the nodes that the
queue assignes to you. In practice it is sometimes possible to 'steal'
other nodes as well, but then you have a big chance that somebody else
will also be running on those nodes. Please take due note, however,
that this is not recommended procedure, it can severely compromise the
performance of the cluster as a whole and also your job(s) in
particular, and is usually frowned upon severely (or worse) by the
If this is a 'public' (i.e., national, institutional or departmental)
cluster, I guess you are out of luck. If it is 'private' (i.e., e.g.
only your own group), you may convince the appropriate people that
the queuing system may be set up differently. If all you can use is
two cpu's at a time, what is the use of clustering...?
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users