[gmx-users] GROMACS with SGI native compliers

[Ken Rotondi]

Haruna,

manymanymanyMANY thanks!

We'll work with this and let you know if it succeeds, or report probs.

Ken

On Aug 4, 2005, at 9:30 AM, Haruna Cofer wrote:

> Hello again, Ken!
>
> I haven't built the latest CVS version of GROMACS on IRIX yet, but here
> are my notes on building GROMACS 3.2.1 on IRIX.
>
> -- Haruna @ SGI
>
> =====
>
> Porting Notes for GROMACS 3.2.1 to SGI IRIX
> -------------------------------------------
>
> 1. Download GROMACS 3.2.1 source code via anonymous ftp:
>
>    % ftp ftp.gromacs.org
>    ftp> cd pub/gromacs
>    ftp> get gromacs-3.2.1.tar.gz
>    ftp> quit
>    %
>
>   or via your web browser:
>
>    ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.2.1.tar.gz
>
>   Uncompress and unarchive the distribution, and it will be
>   put in a directory called gromacs-3.2.1/.  For example:
>
>    uncompress gromacs-3.2.1.tar.gz
>    tar xvf gromacs-3.2.1.tar
>
> 2. Download FFTW 2.1.5 (not 3.0.1) source code via anonymous ftp:
>
>    % ftp ftp.fftw.org
>    ftp> cd pub/fftw
>    ftp> get fftw-2.1.5.tar.gz
>    ftp> quit
>
>   or via your web browser:
>
>    ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz
>
>   Uncompress and unarchive the distribution, and it will be
>   put in a directory called fftw-2.1.5.  For example:
>
>    uncompress fftw-2.1.5.tar.gz
>    tar xvf fftw-2.1.5.tar
>
>   NOTE: We have to use the older FFTW 2.1.5 instead of the latest
>   FFTW 3.0.1 because GROMACS has not been ported to use FFTW 3.x yet.
>
> 3. Make sure automake (from SGI Freeware) is installed and
>    set your PATH to include /usr/freeware/bin:
>
>     setenv PATH "${PATH}:/usr/freeware/bin"
>
>    The SGI Freeware web site is http://freeware.sgi.com/.
>
> 4. For best performance, make sure you have SGI's Message Passing
>    Toolkit (MPT) installed:
>
>     http://www.sgi.com/products/software/mpt/
>
> 5. Build FFTW 2.1.5:
>
>    a. Specify the compilers to use:
>
>        setenv CC cc
>        setenv F77 f77
>        setenv MPICC cc
>
>    b. Specify the location of the MPI header and library files,
>       substituting the SGI MPT directory for $SGI_MPT_DIR below:
>
>        setenv CPPFLAGS "$SGI_MPT_DIR/include"
>        setenv LDFLAGS "-L$SGI_MPT_DIR/lib"
>
>    c. Now build FFTW, substituting your target FFTW installation
>       directory (i.e., where you would like the FFTW include/ and lib/
>       files to be installed) for $FFTW_DIR below:
>
>        cd fftw-2.1.5
>        ./configure --enable-float --enable-mpi --prefix=$FFTW_DIR
>        make
>        make install
>        cd ../
>
> 7. Build GROMACS 3.2.1:
>
>    a. First download the three patch files from:
>
>
> http://www.gromacs.org/pipermail/gmx-developers/2004-March/000797.html
>
>       Then apply the patches:
>
>        cd gromacs-3.2.1
>        patch -p0 < gromacs-3.2.1-acinclude.patch
>        patch -p0 < gromacs-3.2.1-gmx_sgangle.patch
>        patch -p0 < gromacs-3.2.1-make_edi.patch
>
>    b. Set the compilers to use:
>
>        setenv CC cc
>        setenv F77 f77
>        setenv MPICC cc
>
>    c. Specify the location of the FFTW and MPI header and library
>       files, substituting your FFTW installation directory for
>       $FFTW_DIR and your SGI MPT installation directory for
>       $SGI_MPT_DIR below:
>
>        setenv CPPFLAGS "-I$FFTW_DIR/include $SGI_MPT_DIR/include"
>        setenv LDFLAGS "-L$FFTW_DIR/lib
> -L$SGI_MPT_DIR/lib"
>
>    d. Now build GROMACS, substituting your target GROMACS installation
>       directory (i.e., where you would like the GROMACS binaries to be
>       installed under) for $GROMACS_DIR below:
>
>        setenv LIBS "-lmpi"
>        ./configure --enable-mpi --prefix=$GROMACS_DIR
>        make
>        make install
>
>       The GROMACS binaries and libraries will be installed under the
>       $GROMACS_DIR/mips-sgi-irix6.5 directory.
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