[gmx-developers] How to distribute charges over parallel nodes

Roland Schulz roland at utk.edu
Wed May 4 11:07:35 CEST 2011

On Wed, May 4, 2011 at 4:46 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> On 04/05/11, *Igor Leontyev * <ileontyev at ucdavis.edu> wrote:
> To make partial charges be adjustable according to acting field I have
> introduced modifications to gromacs 4.0.7. The serial (single thread)
> version seems to be ready and I want to implement parallelization (with
> particle decomposition). In my current implementation:
> - values of mdatoms->chargeA for local atoms are updated in "do_md" at the
> begininig of each timestep;
> - 'MPI_Sendrecv' + 'gmx_wait' are used in "do_force" (right after the call
> "move_cgcm") to distribute the new charges over parallel nodes.
> After this the array mdatoms->chargeA have updated values on all nodes. But
> some problem arises later in "gmx_pme_do" (modification free routine)
> hanging up execution and even PC.
> Standard procedure is to use a debugger to see which memory access from
> where is problematic. I'm not aware of a free parallel debugger, however.
> Bisecting with printf() calls can work...

As free parallel debuggers you can use:
- gdb/xterm trick. See section Debugging:
- Eclipse/PTP: http://www.eclipse.org/ptp/


ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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