[Fwd: Re: [gmx-users] Coredump when using PME]

[David van der Spoel]

-------- Original Message --------
Subject: 	Re: [gmx-users] Coredump when using PME
Date: 	Tue, 27 Dec 2005 21:46:08 -0500
From: 	Robert Bjornson <rbjornson at gmail.com>
Reply-To: 	bjornson at aya.yale.edu
To: 	David van der Spoel <spoel at xray.bmc.uu.se>
CC: 	jsachs at mail.csb.yale.edu <jsachs at mail.csb.yale.edu>
References: 
<49ad48320512271422u2cc9c9few5363feb439ee769c at mail.gmail.com> 
<43B1D2F4.6060307 at xray.bmc.uu.se>



Hi David,

thanks for your reply to my question.
Am I right in assuming that you mean I should vary the parameters dt and emstep?

If so, here's what I've tried:

dt        emstep
.002      .01 (these were the original settings)
.001      .005
.001      .01
.002      .004
.001      .002

All of them coredump.  I'm hoping that I misunderstood your email, and
that I have varied the wrong parameters.

Thanks again, very much, for your help,

Rob Bjornson




On 12/27/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Robert Bjornson wrote:
> > Hi,
> >
> > I'm experiencing a coredump when running gromacs 3.3 on a system of
> > 72000 atoms.  The coredump only occurs when I use pme for
> > electrostatics.
>
> this is due to large forces. try using shorter timestep or do more
> energy minimization.
>
> >
> > Here is the stacktrace (no symbols compiled in unfortunately)
> > (gdb) where
> > #0  0x0000000000457877 in spread_q_bsplines ()
> > #1  0x000000000045b4f8 in do_pme ()
> > #2  0x0000000000437d81 in force ()
> > #3  0x000000000046bb6a in do_force ()
> > #4  0x000000000041d329 in do_md ()
> > #5  0x000000000041ba14 in mdrunner ()
> > #6  0x0000000000420057 in main ()
> >
> > I also noticed some odd behavior in stderr output.  No idea if they
> > are related, but the
> > non-ewald run doesn't show this behavior:
> >
> > ==================
> > Step 20, time 0.04 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 0.096362 (between atoms 523 and 524) rms 0.004632
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >     524    525   66.5    0.1431   0.1395      0.1430
> >     524    526   37.7    0.1502   0.1430      0.1500
> >
> > Back Off! I just backed up step19.pdb to ./#step19.pdb.1#
> > Wrote pdb files with previous and current coordinates
> >
> > Step 21, time 0.042 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 0.120046 (between atoms 524 and 526) rms 0.005158
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >     524    525   64.7    0.1398   0.1573      0.1430
> >     524    526   55.8    0.1433   0.1680      0.1500
> >
> > Back Off! I just backed up step20.pdb to ./#step20.pdb.1#
> > Sorry couldn't backup step20.pdb to ./#step20.pdb.1#
> >
> > Back Off! I just backed up step20.pdb to ./#step20.pdb.1#
> > Sorry couldn't backup step20.pdb to ./#step20.pdb.2#
> >
> > Back Off! I just backed up step21.pdb to ./#step21.pdb.1#
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> >
> > Back Off! I just backed up step21.pdb to ./#step21.pdb.2#
> > Sorry couldn't backup step21.pdb to ./#step21.pdb.2#
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > -----------------------------------------------------------------------------
> >
> >
> > Some background data:
> > I'm running on 8 processors using LAM-MPI and pbs-pro (although the
> > problem also occurs for sequential runs)
> >
> > The only difference between the two runs is the use of pme in the run
> > that fails.  PME failed in a similar way on a different input set, as
> > well.
> >
> > Does anyone have any idea why this might be happening?  I can provide
> > the input/output files or corefile, but didn't want to broadcast them
> > to everyone.
> >
> > Thanks very much for any assistance,
> >
> > Rob Bjornson
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++