Hi Andrew,
> mpirun -np 256 -maxtime 1500 "$AMBERHOME/exe/sander.MPI -O -i
> gb_md1_nocut.in -o fzd9_gb_md1_nocut.out -c fzd9_gb_init_min.rst -p
> fzd9.prmtop -r fzd9_md1_nocut.rst -x fzd9_gb_md1_nocut.mdcrd </dev/null
> "
I would also think very carefully about whether you want to run on 256 cpus
here. I don't think sander.MPI even runs on this many, I think the limit is
128 and even then you will be lucky to get scaling to that. You might here
since you are doing GB if you have an infinite cut off and your system is
very large >5000 atoms at least for GB. Note you need to have more residues
than processors to run anyway. I assume this is NOT a gigiabit ethernet
cluster otherwise all bets are off.
You might also want to consider using PMEMD v10.0 which supports GB and will
give better performance and scaling than sander.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 04 2009 - 01:31:41 PST
