Re: LDB questions/problems

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Dec 16 2003 - 15:32:51 CST

I am running on a linux cluster, using an in house rh 7.3 kernel with elan
quadrics switches. So I don't think the solaris info applies. It may be
just to big for psfgen to do correctly.
I have also had several elan buffering errors which I worked around by
increasing the mpi buffers from 200MB to 400MB
Brian
 

 On Tue, 16 Dec 2003, Gengbin Zheng
wrote:

>
> Hi,
>
> I think I'v heard this before - there is some weird memory usage
> behavior with the Solaris-Sparc-SMP-CC version of Charm++
> built upon net-sol-smp version of Charm++.
> You may try the latest version of NAMD, but you have to build every thing
> from source out of the CVS - Charm++ and NAMD (they have separate CVS
> servers).
>
> Gengbin
>
> On Mon, 15 Dec 2003, Brian Bennion wrote:
>
> >
> > 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 **
> > *****************************************************************
> >
> >
>
>

-- 
*****************************************************************
**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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