Re: Stray PME grid charges

From: Vani Krishna (vakri2002_at_yahoo.com)
Date: Tue Sep 07 2004 - 21:16:35 CDT

Hi!
I had this problem earlier, and that was because my
PME grid sizes were less than the box size. May be you
want to check that..

PME grid size >= box size and a multiple of 2,3 or 5
in each direction

Hope that helps
Vani
--- Harindar Keer <hkeer_at_uci.edu> wrote:

> Hi,
>
> I am trying to equilibrate a system containing
> around 150,000 atoms,
> After several attempt I am still not able to
> successfully run
> simulation, but I am able to minimize the system
> without any problem.
> Following is snippet of the error:
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Stray PME grid charges detected: 20 sending
> to 28 for planes 100
> 101
> ERROR: Stray PME grid charges detected: 20 sending
> to 1 for planes 0
> ERROR: Stray PME grid charges detected: 20 sending
> to 27 for planes 99
>
>
> I have also tried something described in the mail
> attached below by Jim,
> although I don't understand much. It would be great
> to hear from people
> who were able to resolve this problem.
> Just to mention, I need to 40 Sodium ions to
> neutralize the system.
>
>
> Many thanks,
> Harindar
>
>
>
>
>
>
>
> On Tue, 2003-12-16 at 20:44, Jim Phillips wrote:
> > I don't understand the psfgen reference, but
> system size shouldn't be a
> > problem for psfgen. I'm guessing the load
> balancer is either running out
> > of memory or choking in the face of too many
> options (2M atoms is a lot).
> > I can definitely say it's getting stuck in
> Rebalancer::multirefine().
> >
> > Try setting "maxSelfPart 1" and "maxPairPart 1",
> which eliminates the
> > partitional of intra- and inter-patch interactions
> into multiple objects.
> > This should reduce the number of choices the load
> balancer has to make.
> >
> > Here's what these look like in SimParameters.C:
> >
> > // Maximum Partition options
> > opts.optional("main", "maxSelfPart",
> > "maximum number of self partitions in one
> patch", &maxSelfPart, 50);
> > opts.range("maxSelfPart",POSITIVE);
> > opts.optional("main", "maxPairPart",
> > "maximum number of pair partitions in one
> patch", &maxPairPart, 20);
> > opts.range("maxPairPart",POSITIVE);
> > opts.optional("main", "numAtomsSelf",
> > "maximum number of atoms in one
> self compute distribution",
> > &numAtomsSelf, 125);
> > opts.range("numAtomsSelf",NOT_NEGATIVE);
> > opts.optional("main", "numAtomsPair",
> > "maximum number of atoms in one
> pair compute distribution",
> > &numAtomsPair, 200);
> > opts.range("numAtomsPair",NOT_NEGATIVE);
> > opts.optional("main", "numAtomsPair2",
> > "maximum number of atoms in one
> pair compute distribution",
> > &numAtomsPair2, 400);
> > opts.range("numAtomsPair2",NOT_NEGATIVE);
> >
> > -Jim
> >
> >
> > On Tue, 16 Dec 2003, Brian Bennion wrote:
> >
> > > 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
>
=== message truncated ===

                
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