AMBER Archive (2008)

Subject: Fw: Re: AMBER: AMD Opteron: compiler recommendations?

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Apr 26 2008 - 02:05:18 CDT

Sorry, I forgot. As to Amber, I mean sander.MPI. I was unable to compile pmend. Hope one day Bob Duke will find the time to provide a configuration to compile pmend on OpenMPI.

--- On Sat, 4/26/08, Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Re: AMBER: AMD Opteron: compiler recommendations?
> To: amber_at_scripps.edu
> Date: Saturday, April 26, 2008, 12:01 AM
> There must be the comparison you are looking for on the
> Amber archives. I remember that a comparison of Intel with
> other compilers for dual-opteron was posted, and Intel was
> scored very high. As Intel is free for non commercial use,
> I choose Intel for Amber and OpenMPI and found Amber
> running very fast. As I am no expert, I guess I have no
> particular settings. On request I can show my settings for
> a NUMA system of 8 logical opterons. Tell me what you want,
> unless some other guy can provide the settings far better
> than I can.
> francesco
>
>
> --- On Fri, 4/25/08, Robert Duke
> <rduke_at_email.unc.edu> wrote:
>
> > From: Robert Duke <rduke_at_email.unc.edu>
> > Subject: Re: AMBER: AMD Opteron: compiler
> recommendations?
> > To: amber_at_scripps.edu
> > Date: Friday, April 25, 2008, 3:04 PM
> > The pathscale compilers are pretty good for opterons;
> the
> > pgi compilers are used for cray machines running
> opterons,
> > so they must not be too bad on performance either,
> though
> > there has been grief with pgi from time to time (in
> > fairness, they have tried to fix their problems, so I
> > should give them credit for responding to the past
> > problems). With intel, it may be a specific switches
> > problem; I last tried running them on opterons a
> couple of
> > years ago. I preferred pathscale for the opteron, but
> > there was not a 30% performance differential at that
> point
> > in time (things could have changed). It is completely
> > possible that my default ifort settings for the
> opteron are
> > no longer the best choice (sorry, I just didn't
> get
> > around to trying this combination in the current
> release
> > cycle).
> > Regards - Bob Duke
> > ----- Original Message -----
> > From: Sasha Buzko
> > To: amber_at_scripps.edu
> > Sent: Friday, April 25, 2008 5:54 PM
> > Subject: AMBER: AMD Opteron: compiler
> recommendations?
> >
> >
> > Hi all,
> > I've compiled sander.MPI and pmemd using Intel
> > compilers and tested them with no apparent errors on
> AMD
> > processors. However, the executables seem to be
> > considerably faster on Intel chips (while the hardware
> is a
> > bit better in that case, it shouldn't account for
> a 30%
> > performance increase).
> >
> > Has anyone had any experience with comparing
> performance
> > of binaries built using different compilers on AMD
> > hardware? For instance, how do Pathscale compilers
> compare
> > to Intel on Opterons? I've read reports about the
> evil
> > Intel intentionally under-optimizing code on non-Intel
> > chips, but hope it's not the issue here :).
> >
> > Any recommendations and/or benchmark results would
> be
> > very much appreciated.
> >
> > Thanks in advance
> >
> > Sasha
>
>
>
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