[gmx-users] Coredump when using PME

[David van der Spoel]

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
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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
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