[gmx-users] Strange assignment of atoms to processors with pd

Thu May 28 11:17:49 CEST 2009

Well, David is the person who should fix this.
You can submit a bugzilla or bug him directly.

Berk

> Date: Thu, 28 May 2009 10:41:12 +0200
> From: erikm at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Strange assignment of atoms to processors with pd
> 
> Berk Hess skrev:
> > Hi,
> >
> > This is plain 4.0 code is presume?
> > This problem should be fixed then.
> Should I commit a buzilla?
> >
> > But I now also made vacuum without cut-off working with domain 
> > decomposition in CVS head.
> > Compared to a not-unbalanced PD (for instance only a protein, no 
> > water) DD is slightly slower.
> > But DD will be faster than a badly balanced PD system.
> >
> > Berk
> >
> > > Date: Wed, 27 May 2009 11:04:49 +0200
> > > From: spoel at xray.bmc.uu.se
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] Strange assignment of atoms to processors 
> > with pd
> > >
> > > Erik Marklund wrote:
> > > > David van der Spoel skrev:
> > > >> Erik Marklund wrote:
> > > >>> I should add that this problem only seem to arise when the 
> > analyte is
> > > >>> covered with a thin sheet of water. When simulating a dry analyte I
> > > >>> get good scaling. In the latter case the charges, and therefore the
> > > >>> topology, is slightly different.
> > > >> How about vsites? Did you happen to turn them off as well in the
> > > >> vacuum case?
> > > > Turned off in all cases. The VSites mentioned in the log file is the
> > > > 4:th particle on the tip4p-water molecules.
> > > OK. Did you try a one step run with -debug?
> > > It may give more info on the partitioning.
> > >
> > > >>>
> > > >>> /Erik
> > > >>>
> > > >>> Erik Marklund skrev:
> > > >>>> Hi,
> > > >>>>
> > > >>>> I'm simulating non-periodic systems in vacuo, using constrained
> > > >>>> h-bonds and particle decomposition. For some of my simulations the
> > > >>>> cpu-usage seem far from optimal. The first cpu gets no atoms, 
> > while
> > > >>>> the second one gets plenty and the remaining cpus get less than I
> > > >>>> expected. Is this a bug?
> > > >>>>
> > > >>>>
> > > >>>> An excerpt from the log file:
> > > >>>>
> > > >>>> There are: 2911 Atoms
> > > >>>> There are: 317 VSites
> > > >>>> splitting topology...
> > > >>>> There are 999 charge group borders and 318 shake borders
> > > >>>> There are 318 total borders
> > > >>>> Division over nodes in atoms:
> > > >>>> 0 1960 212 212 212 212 212 208
> > > >>>> Walking down the molecule graph to make constraint-blocks
> > > >>>> CPU= 0, lastcg= -1, targetcg= 499, myshift= 1
> > > >>>> CPU= 1, lastcg= 681, targetcg= 182, myshift= 0
> > > >>>> CPU= 2, lastcg= 734, targetcg= 235, myshift= 7
> > > >>>> CPU= 3, lastcg= 787, targetcg= 288, myshift= 6
> > > >>>> CPU= 4, lastcg= 840, targetcg= 341, myshift= 5
> > > >>>> CPU= 5, lastcg= 893, targetcg= 394, myshift= 4
> > > >>>> CPU= 6, lastcg= 946, targetcg= 447, myshift= 3
> > > >>>> CPU= 7, lastcg= 998, targetcg= 499, myshift= 2
> > > >>>> pd->shift = 7, pd->bshift= 0
> > > >>>> Division of bonded forces over processors
> > > >>>> CPU 0 1 2 3 4 5 6 7
> > > >>>> Workload division
> > > >>>> nnodes: 8
> > > >>>> pd->shift: 7
> > > >>>> pd->bshift: 0
> > > >>>> Nodeid atom0 #atom cg0 #cg
> > > >>>> 0 0 0 0 0
> > > >>>> 1 0 1960 0 682
> > > >>>> 2 1960 212 682 53
> > > >>>> 3 2172 212 735 53
> > > >>>> 4 2384 212 788 53
> > > >>>> 5 2596 212 841 53
> > > >>>> 6 2808 212 894 53
> > > >>>> 7 3020 208 947 52
> > > >>>>
> > > >>>> …
> > > >>>> Total Scaling: 18% of max performance
> > > >>>>
> > > >>>
> > > >>>
> > > >>
> > > >>
> > > >
> > > >
> > >
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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> 
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
> 
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