[gmx-users] GROMACS with SGI native compliers

[Nathan Moore]

With best intentions, I'd suggest you start by reading the Man pages for
the SGI IRIX compiler that's installed on your Origin.  These man pages
generally have the best description of how to compile a binary for a
specific MIPS processor (I think optimization goes all the way down to the
chipset - ie not all R12k processors are optimized with the same flag).

Also, if you're doing a bunch of PME stuff you might want to either (1)
replace FFTW with the SGI-specific LAPACK routine (I think has name
similar to "complib.sgimath" or else (2) talk to the FFTW developers to
see if there's a version of FFTW that's optimized for your R14k
architecture.

regards,

NT



> Hello All,
>
> We've been successfully running GROMACS on an SGI supercomputer using
> the gcc complier. However, we'd really like to realize the speed
> increases that should be possible using the MIPSpro 7.4 IRIX native
> compliers.
>
> This what we're running on:
>
> SGI Origin 3800, 128 processor R14000 500 MHz
> SGI Message Passing Toolkit 1.6 (this is SGI's tuned MPI libraries)
> FFTW version 2.1.3 (single-precision, shared libraries, MPI-enabled)
> GCC 3.3 (SGI supplied) and SGI MIPSpro 7.4 compilers
> Latest GROMACS config flags: --enable-shared --enable-mpi CC=gcc
> CFLAGS=-L/usr/lib32 CPPFLAGS=-I/usr/local/include
> LDFLAGS=-L/usr/local/lib
>
> I'd love to hear from anyone who's running GROMACS on a similar
> system... especially the kind individual at SGI that offered to help
> the last time I posted w/SGI issues, whose e-mail I've apparently
> misplaced/lost.
>
> thanks in advance,
>
> Ken
>
> K.S. Rotondi Ph.D.
> Research Fellow
> The Gierasch Laboratory
> Department of Biochemistry and Molecular Biology
> University of Massachusetts-Amherst
> Phone: 413-545-1250
> Fax;      413-545-3291
>
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