Re: [AMBER] Error with multiple GPU run: kCalculateMolecularVirial

From: Gould, Ian R <i.gould.imperial.ac.uk>
Date: Sun, 19 Dec 2010 13:20:08 +0000

Hi

I am running 2 x C2050 system for 10's of ns and not experiencing these issues. You need to make sure that you have applied all the bugfixes as stated on the web site.

Cheers
Ian


"Education: that which reveals to the wise, and conceals from the stupid, the vast limits of their knowledge."
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Dr Ian R Gould
Senior Lecturer Biological and Biophysical Chemistry
Imperial College London
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On 19/12/2010 11:05, "Andre Serobian" <serobian.a.student.unsw.edu.au> wrote:
Hi All,
On a 2X C2050 system a kCalculateMolecularVirial error terminates my md run when I execute the below run file looping it by 100 using the following mdcont.in file:
mdcont.in file:
# constant pressure dynamics 10ps
&cntrl
 imin = 0,
 ntx = 7, irest = 1,
 ntt = 1, temp0 = 288.0, tautp = 2.0,
 ntwr = 500, ntwx = 500, ntwv = 500,
 ntc = 2, tol = 0.00001,
 cut = 10.0,
 ntpr = 500,
 ntb = 2,
 ntp = 1,
 nstlim = 100000,
&end
run file:
#!/bin/bash
COUNT=0
until [ $COUNT -gt $1 ]; do
  let NJOB=COUNT+1
  let LJOB=COUNT
  mpirun -np 2 pmemd.cuda.MPI -O -i mdcont.in -o md$NJOB.out -c md$LJOB.restrt -p input.prmtop -r md$NJOB.restrt -x md$NJOB.mdcrd -v md$NJOB.mdvel -ref md$LJOB.restrt
        let COUNT=COUNT+1
done
Any ideas why this may be happening? Someone suggested a bugfix.9 issue.
Kind regards,
Andre
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Received on Sun Dec 19 2010 - 05:30:03 PST