AMBER Archive (2008)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Oct 03 2008 - 10:43:22 CDT

Folks,
Please hold off in applying this patch/installing the new file. I have
realized that the patch is diff'd against a May 16th version of configure,
which is post-release. I am puzzled as to why this file is in my amber 10
cvs tree, and need to sort out exactly what went out with the release (but
can't at the moment, as the cvs tree has moved and I am not plugged in yet
with a new account). I'll probably also release a patch that includes
creation of the new intel mpi interconnect file as part of the patch. Sorry
for the confusion.
Regards - Bob Duke
----- Original Message -----
From: "Robert Duke" <rduke_at_email.unc.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, October 02, 2008 4:56 PM
Subject: AMBER: Support for intel mpi in pmemd 10; better support for intel
MKL

> 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, ambermd.org (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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