[gmx-users] MD PME in paralle

[David van der Spoel]

On Mon, 2003-03-10 at 13:03, e.akhmatskaya at fle.fujitsu.com wrote:
> Hi David, 
> 
> Thanks for your reply.
> 
> >Could you give some more detail?
> >size of simulation system, how the problem comes about?
> I've tried two systems of very different sizes: 23558 and 141154.
> Smaller system seems to be more stable. I've managed to finish the
> calculations for several times. 
> 
> The most typical outcome is:
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Getting Loaded...
> Reading file topol.tpr, VERSION 3.1.4 (double precision)
> Reading file topol.tpr, VERSION 3.1.4 (double precision)
> Loaded with Money
> 
> starting mdrun 'Protein in water'
> 100 steps,      0.1 ps.
> 
> step 0
> [PRIMEPOWER]aprun: parallel process 1 abnormally terminated.
> [Blade server]: MPI process rank 0 (n0, p14255) caught a SIGSEGV.
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
> PID 14255 failed on node n0 with exit status 1.

I have run it using LAM and SCALI networks, in both cases it crashes at
the end when writing the coordinates (confout.gro). It writes roughly
6000 lines out of 23000.

I do however use a development version of the code...

You implied somehow that the problem only occurs when you have no water
on node 0. There is a workaround for that, the -load option of grompp
allows you to modify the division over nodes, e.g.:

grompp -load "1.1 1.0 1.0 1.0 1.0"

grompp will normalize the numbers, so you (with trial and error) just
increase the first number until your processor 0 has a water.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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