Re: LDB questions/problems

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Dec 15 2003 - 15:41:32 CST

Interesting...so I assume you meant reduce the number of processors I was
using. I went from 64 to 32 cpus and it made it through the load
balancing step before the queue timedout. However, one stray pme error did
persist.
Now i am more perplexed. my system has >2 million atoms so I don't know
how to get this system minimized effeciently with any peace of mind...

Brian

 On Tue, 16 Dec 2003, himanshu chandola
wrote:

> I was getting the same kinda errors when i used to run it on a solaris box
> .Though in my case the namd would give ldb messages - stay there for a
> few minutes and then crash showing memory problems. Reducing the number of
> processes helped and removed this problem from reappearing.
>
> You can just try this perhaps!
>
>
> cheers
>
> himanshu
>
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.
>
>
> On Mon, 15 Dec 2003, Brian Bennion wrote:
>
> >
> > Hello,
> >
> > I am attempting to minimize a large system. I call for 100 steps of min,
> > however, at the 10th step the load distribution system kicks in, gives the
> > following message in the log and stays there for at least 20 minutes at
> > which point I get kicked out of the queue. I turn the balancer off, with
> > ldbstrategy none and things progress, but not without many stray pme grid
> > errors.
> >
> > Any insight?
> > Brian
> >
> > log snippet....
> >
> > ENERGY: 9 4446565.9422 815057.1233 0.0000
> > 0.0000 -8238197.7208 17559560.4307 0.0000 0.0000
> > 0.0000 14582985.7753 0.0000 14582985.7753 14582985.7753
> > 0.0000 228178.0317 226466.3996 35898114.1381 228178.0317
> > 226466.3996
> >
> > LDB: LOAD: AVG 17.6773 MAX 22.956 MSGS: TOTAL 17196 MAXC 336 MAXP 5
> > None
> > LDB: LOAD: AVG 17.6773 MAX 21.2128 MSGS: TOTAL 20029 MAXC 633 MAXP 6
> > Alg7
> >
> > --
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
> >
> >
> >
>

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 424-6605                 **
*****************************************************************

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