After examining my restart files and carefully checking the Amber 12
manual, I concluded that it is several lines in specific restart files that
are the problem and that turning "iwrap" on could potentially solve the
problem. The Amber 12 manual says that turning this tag on doesn't
influence the forces and velocities, but I am concerned it could influence
my analysis, especially since I will be turning on the tag mid-simulation.
Could someone provide a comprehensive explanation of "iwrap"?
Thanks,
David
On Mon, May 6, 2013 at 3:49 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, May 06, 2013, David Winogradoff wrote:
>
> > ... due to Open MPI failures.
>
> OK: *my* favorite answer: build your own MPI installation, by using the
> configure_openmpi or configure_mpich scripts in AMBERHOME/AmberTools/src.
> That way, you know you are getting the right compiler, nothing outside the
> Amber tree is referenced (so you don't need to worry about what MPI
> installations might or might not be on your computer), etc. Also, this
> more
> or less automatically gets you an up to date version.
>
> Also, if you build MPI using our scripts, we have a reasonable shot at
> debugging errors. If you are using something from
> "/cell_root/software/openmpi/1.4.3/gnu/sys/lib" (your example), we have
> only
> very indirect knowledge to go on.
>
> ...dac
>
>
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Received on Tue May 07 2013 - 09:30:02 PDT
