AMBER Archive (2009)

Subject: Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 04 2009 - 05:16:34 CST

just for the purposes of future people with similar problems looking
at the archives for help:

it is not likely that the problem was the number of processors. the
error message that you sent to the list was
" Unit 5 Error on OPEN:mdin"
changing the number of processors should not change that- you probably
fixed something else without realizing it.

On Wed, Feb 4, 2009 at 12:46 AM, drugdesign <drugdesign_at_yandex.ru> wrote:
> Looks like the problem was in the number of processors. It's a protein with 250 amino acid residues so as I understand 128 is maximum number of processors for it. I've made a run with 64 processors - works fine.
>
> Best regards,
> Andrew
>
>
> 03.02.09, 20:21, "Ross Walker" <ross_at_rosswalker.co.uk>:
>
>> 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_at_rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
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