On Fri, Sep 04, 2009, Ross Walker wrote:
>
> I just want to bring your attention to some recent changes to ptraj in the
> AMBER11 CVS Tree. Thanks to Paul Frybarger, an undergraduate at Hope
> College, MI who spent the summer working with me there is now a parallel
> version (MPI) of ptraj.
Can I ask what version of MPI you are using? The lam MPI that we ship with
Amber fails at the pnetcdf configure step, with the error message that it
does not support MPI-IO. I'm still fiddling with the configuration scripts
and Makefiles to recover from this (so that one could compile the rest of
AmberTools with MPI turned on, even though ptraj.MPI will fail.
Some thoughts:
1. Could we have a parallel version of ptraj without netcdf support? (i.e.
make that an option).
2. Is there an MPI whose source we could supply with Amber that does support
MPI-IO?
> cleaned up a lot of the ptraj output as well as massively improving the way
> ptraj handles random file access. While this does not have a huge impact on
> NetCDF for ASCII files ptraj can now do true random access of the files.
If parallelization would not have a "huge impact on NetCDF", maybe that is
another argument for making that optional(?)
Thanks to Paul and Ross for getting this going.
....dac
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Received on Mon Sep 14 2009 - 11:52:04 PDT
