[gmx-users] compiling Gromacs on Sun cluster

[Choon Peng]

Hi Chris,

  Thanks! I got it to work now! The single-precision Gromacs
is now on our cluster.
However, there's some changes needed:

FFTw
Need to edit /mpi/Makefile for CPPFLAGS and LIBS
before we run 'make'.

Gromacs
During 'make install', you may get a complaint with regards
to '!'. It's because /bin/sh is /bin/bash on Linux but not on Solaris.
We have to edit the Makefile under /share/template manually.

Your method for mdrun_mpi works perfectly.
Initially I forgot and do 'make' after I've installed
the standalone version, instead of 'make mdrun' and
'make install' instead of 'make install-mdrun'.
Well, if someone encountered this, don't worry.
Simple remove all files with suffix mpi that got added
except mdrun_mpi.

I've ran the single-precision benchmark for Villin and gotten around
1.4GFlops with 4 CPUs on our Sun Fire 880 cluster.

Thank you again! You helped me solve this problem that has been
boggling me for weeks!

regards,
choon peng

On Fri, 27 Sep 2002, Christoph Freudenberger wrote:

> Choon Peng wrote:
> > Dear all,
> >
> >   Wonder if anyone successfully installed Gromacs on a Sun cluster using
> > Sun's MPI?
> Yepp.
>
> We succeded following this scheme:
>
> -----------------------------------
> #unpack the sources for fftw and gromacs
>
> #in the fftw dir do:
>
> host> export MPICC=mpcc
>
> host> export MPILIBS=-L/opt/SUNWhpc/lib
>
> host> ./configure --enable-float --enable-type-prefix
> --prefix=/some/place/where/you/can/write/fftw/ --enable-mpi
>
> #Check output for errors
>
> host> export CFLAGS="-fast -xtarget=ultra3 -xarch=v8plusb"
>
> host> gmake -j 8
>
> host> make install
>
> #fttw-intallation complete if no errors
>
> #cd to the gromacs dir:
>
> host> export CPPFLAGS=-I/path/to/fftw/include
>
> host> export LDFLAGS=-L/path/to/fftw/lib
>
> host> ./configure --prefix=/some/place/where/you/can/write/gmx
> --enable-shared
>
> host> make -e
>
> host> make install
>
>
> #Now the tools are installed as non-mpi programms
> #mpi is only needed for mdrun:
>
> host> make distclean
>
> host> export LIBS=-lmpi
> host> export CPPFLAGS="-I/opt/SUNWhpc/include -I/path/to/fftw/include"
> host> export CFLAGS="-fast -xtarget=ultra3 -xarch=v8plusb"
> host> export LDFLAGS="-fast -xtarget=ultra3 -xarch=v8plusb \
>                  -L/opt/SUNWhpc/lib -R/opt/SUNWhpc/lib \
>                  -L/path/to/fftw/lib -R/path/to/fftw"
> host> ./configure --prefix=/some/place/where/you/can/write/gmx \
>                  --enable-shared --enable-mpi --program-suffix=_mpi
>
> host> gmake -j 8 mdrun
>
> host> make install-mdrun
> ---------------------------
> The path to the mpi includes and libs may be system specific. Adopt it
> if necceary. there were a few more problems about the correct
> installation of the html and template dirs, but at least you should get
> all programs working.
>
> I have not yet tested the mpi-installation totally, but I'm planning to
> work out an howto as soon as i got data about stablilty and scaling.
>
> Please post, if you succeed.
>
> regards
> --
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
>
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