[gmx-developers] Bug with continuation from checkpoint with gromacs 4.0.7
roland at utk.edu
Mon Mar 15 22:58:50 CET 2010
your not giving enough information.
What exactly is the error? What happens? Does it hang or does it crash with
On Fri, Mar 12, 2010 at 7:01 PM, Alexey Shvetsov <alexxyum at gmail.com> wrote:
> Hi all
> Seem like there is bug with continuation from checkpoint for gromacs 4.0.7
> Steps to reproduce
> 1. submit parrallel job to pbs
> 2. kill job
> 3. try to resume from checkpoint
> relevant output from mdrun
> Reading checkpoint file md.cpt generated: Thu Mar 11 12:20:46 2010
> Loaded with Money
> Making 2D domain decomposition 16 x 7 x 1
> WARNING: This run will generate roughly 20607979313638129664 Mb of data
> starting mdrun 'Protein in water'
> 500000 steps, 1000.0 ps (continuing from step 3377000, 6754.0 ps).
> nodetime = 0! Infinite Giga flopses!
> Parallel run - timing based on wallclock.
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
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