AMBER Archive (2000)

Subject: Re: parallel sander

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It is possiblly two reasons in my experiences: 1) your machine can not provide so much CPU as you rquired at that time.
2) you did not  setenv MP_SET_NUMTHREADS correctly.
I compiled in different systems, there should not be any problems.
Good luck.
Jianxin

Frank Yan wrote:

it's amber 5, and i used shared memory to compile it. thanks a lot... frank

>From: Carlos Simmerling <carlos@morita.chem.sunysb.edu>
>Reply-To: carlos.simmerling@sunysb.edu
>To: Frank Yan <siebenamber@hotmail.com>
>Subject: Re: parallel sander
>Date: Sat, 19 Feb 2000 09:47:29 -0500
>
>it would help if you told us what version of AMBER you are using,
>and how it was compiled (shared memory, MPI). also
>the version of the SGI Message Passng Toolkit (MPT).
>thanks
>
>Frank Yan wrote:
>
> > i'm running sander on a shared memory sgi 6.5 machine. for instance i
>use 2
> > cpus, but sometime sander cannot use both of them, only one is 99% used
>and
> > another is not used at all when using top to look at. for like 4 cpus,
> > sometime it shows like each is 25% used (at that time the machine is not
> > loaded heavily). is there any way to solve the imbalance problem between
>the
> > cpus? thanks a lot... frank
> >
> > ______________________________________________________
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>--
>===================================================================
>Carlos L. Simmerling, Ph.D.
>Assistant Professor           Phone: (631) 632-1336  NOTE NEW AREA CODE
>Department of Chemistry       Fax:   (631) 632-7960
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