AMBER Archive (2008)

Subject: Re: AMBER: Optimal compiling of amber on XT3

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Oct 30 2008 - 00:31:49 CDT

Hello Patrick,
You probably want to run pmemd for most of your amber simulations on an xt3.
You could probably also configure and run the rest of amber, but I don't
have that information readily available, as my account on an xt3 is inactive
at the moment. However, for pmemd, just do:

cd $AMBERHOME/src/pmemd
./configure cray_xt3 pgf90 mpi pubfft
make install

The last time I checked, it was better to not use the binary trajectory file
capability (which would have been made available by adding "bintraj" at the
end of the configure line) on this type of machine, as the lustre file
system did not really do all that well in that mode (and you would have to
either find netcdf on the machine or get it built as part of amber). I'll
have to check into this again for you all if file i/o is an issue on
sapphire (I don't know this particular machine).

Let me know if you have any problems, and give my best to Ken!

Best Regards - Bob Duke

----- Original Message -----
From: "Patrick McCarren" <mccarren_at_chem.ucla.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, October 30, 2008 12:30 AM
Subject: AMBER: Optimal compiling of amber on XT3

> I'm trying to compile AMBER on a Cray XT3 at the ERDC MSRC (sapphire).
> What are the optimal settings for libraries, mpi/mpich/ mpich2, compiler,
> etc. for AMBER? Am I right that the test programs in the configure
> script will not run on the login node? I can switch to pathscale or
> whichever compiler is best I think. If I could get a configure script or
> configure diff from someone, I would be really happy. Thanks,
>
> Patrick
>
>
> Patrick McCarren
> Graduate Student Researcher
> Houk Research Group
> UCLA Dept of Chem and Biochem
> 607 Charles E Young Dr E
> Los Angeles, CA 90095-1569
>
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