Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL

From: Francesco Pietra <>
Date: Thu, 2 Oct 2008 23:35:45 +0200

Thanks indeed. However, for shared-memory amd machine, is there an
advantage with respect to the recipe furnished previously by Ross

From: Francesco Pietra <>
Date: Sun Jun 01 2008 - 00:12:12 PDT

 If advantageous, I'll try to implement the new recipe.


On Thu, Oct 2, 2008 at 10:56 PM, Robert Duke <> wrote:
> Folks,
> I have finally gotten around to checking out modifications to support Intel
> MPI for pmemd 10 and generating a patch. These mods also are supposed to
> better support configuration for the Intel MKL, though I have not checked
> out the plusses and minuses compared to my last code. These changes were
> first generated by Klaus-Dieter Oertel of Intel (thanks much,
> Klaus-Dieter!), and I have tweaked them a bit, mostly for cosmetic issues. I
> will have the patch posted to the amber website, (not sure how
> you "patch" a new file yet). Why use this stuff? At least as far as I
> know, Intel MPI offers superior performance on Infiniband, and possibly
> other interconnects. I have not done extensive testing myself, as I only
> had an evaluation license for a little while and was wrapped up doing other
> stuff, and did not see much difference for gigabit ethernet, but I also did
> not work on performance tuning - my goal was to insure that the patch
> worked. For Infiniband, I have seen quite impressive numbers on benchmarks
> run by Klaus-Dieter, and I believe Ross Walker is going to make this info
> available.
> So, anyway, what's here and what to do?
> Attached is:
> pmemd10.patch2
> interconnect.intelmpi
> Take interconnect.intelmpi and move it to $AMBERHOME/src/pmemd/config_data.
> Take pmemd10.patch2 and move it to $AMBERHOME. Then execute the command
> "patch -p0 -N < pmemd10.patch2" from $AMBERHOME. You can then build for
> intel mpi by specifying intelmpi as the interconnect to configure.
> The interconnect file should also work for pmemd 9, though the patch file
> certainly won't (but is not necessary for the interconnect fix).
> Best Regards - Bob Duke
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Received on Fri Oct 03 2008 - 05:11:34 PDT
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