[gmx-users] Gromacs 4.0.2 hangs?
gmx3 at hotmail.com
Mon Jan 5 15:05:33 CET 2009
There could be a bug in Gromacs 4.0.2 which causes problems
when running in parallel.
We are investigating this.
A much simpler way to run shorter simulations for the moment is
the -maxh option of mdrun.
You don't need tpbconv either, you can directly read a checkpoint
file with the -cpi option.
PS you might want to use mdrun -deffnm dppc_01
> From: ydubief at uvm.edu
> To: gmx-users at gromacs.org
> Date: Mon, 5 Jan 2009 08:10:49 -0500
> Subject: [gmx-users] Gromacs 4.0.2 hangs?
> Dear all,
> I have some difficulties running mdrun_mpi for large number of
> iterations, typically > 40000. The code hangs, not necessarily at a
> fixed iteration, for all configurations I run and this behavior shows
> up under linux and mac OS. The simulations range from 10^4 to 10^6
> coarse-grained atoms and I try to keep the amount of data generated
> per much smaller than 1Gb. I have worked around this issue by running
> 25000-iteration similations with tpbconv-restarts, as follows:
> mpiexec -np 256 mdrun_mpi -nosum -v -s dppc0_1.tpr -o dppc0_1.trr -c
> dppc0_1.gro -e dppc0_1.edr -x dppc0_1.xtc
> tpbconv -s dppc0_1.tpr -f dppc0_1.trr -e dppc0_1.edr -o dppc0_2.tpr -
> extend 250.0
> With such scripts, I have been able to generate 10^5 to 10^6
> iterations without any problem. I was wondering if anyone has
> experienced similar problems and if I am missing something.
> I have pretty much ruled out a problem with mpi, since I have
> thoroughly tested these computers with other mpi codes. I am now
> wondering if there might be a problem with output files.
> I run Gromacs 4.0.2 on a linux cluster (quad core processors, myrinet
> and mpich, compiled with gcc, single precision) up to 256 processors,
> on a macpro 2 quad and on a macbook dual core using the Fink package
> for openmpi. All these computers have enough available disk space for
> any simulation I run. A typical simulation is a coarse grained MD
> using martini with .mdp files obtained from Marrink's website.
> Yves Dubief, Ph.D., Assistant Professor
> Graduate program coordinator
> University of Vermont, School of Engineering
> Mechanical Engineering Program
> 201 D Votey Bldg, 33 Colchester Ave, Burlington, VT 05405
> Tel: (1) 802 656 1930 Fax: (1) 802 656 3358
> Vermont Advanced Computing Center
> 206 Farrell Hall, 210 Colchester Ave, Burlington, VT 05405
> Tel: (1) 802 656 9830 Fax: (1) 802 656 9892
> email: ydubief at uvm.edu
> web: http://www.uvm.edu/~ydubief/
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