Installation of ANUGA parallel



Installation of ANUGA parallel

Platform:

Linux 64-bit AMD Quad-core Ubuntu server (kernel 2.6.24-23-server)

Checkout from svn repository:

– pypar_numeric

– pymetis

– anuga_parallel

Prerequisite:

– Anuga being installed successfully (here: anuga-1.0beta_5638.tgz)

– mpi

o check if mpi is already installed: mpicc --showme should show the package being installed in e.g. /usr/lib/openmpi

o if nothing shows up install openmpi-bin, libopenmpi-dev

o ll /usr/bin/m* yields for my machine

lrwxrwxrwx 1 root root 24 2009-02-23 16:00 /usr/bin/mpic++ -> /etc/alternatives/mpic++

lrwxrwxrwx 1 root root 23 2009-02-23 15:54 /usr/bin/mpicc -> /etc/alternatives/mpicc

lrwxrwxrwx 1 root root 23 2009-02-23 15:54 /usr/bin/mpiCC -> /etc/alternatives/mpiCC

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpicc.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpiCC.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 30 2009-02-23 15:23 /usr/bin/mpichversion -> /etc/alternatives/mpichversion

lrwxrwxrwx 1 root root 35 2009-02-23 15:28 /usr/bin/mpichversion.mpich-shmem -> ../lib/mpich-shmem/bin/mpichversion

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpic++.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 24 2009-02-23 15:54 /usr/bin/mpicxx -> /etc/alternatives/mpicxx

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpicxx.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 25 2009-02-23 14:28 /usr/bin/mpiexec -> /etc/alternatives/mpiexec

lrwxrwxrwx 1 root root 7 2009-02-23 14:28 /usr/bin/mpiexec.openmpi -> orterun

lrwxrwxrwx 1 root root 24 2009-02-23 15:54 /usr/bin/mpif77 -> /etc/alternatives/mpif77

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpif77.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 24 2009-02-23 15:54 /usr/bin/mpif90 -> /etc/alternatives/mpif90

lrwxrwxrwx 1 root root 12 2009-02-23 15:54 /usr/bin/mpif90.openmpi -> opal_wrapper

lrwxrwxrwx 1 root root 24 2009-02-23 15:23 /usr/bin/mpiman -> /etc/alternatives/mpiman

lrwxrwxrwx 1 root root 29 2009-02-23 15:28 /usr/bin/mpiman.mpich-shmem -> ../lib/mpich-shmem/bin/mpiman

lrwxrwxrwx 1 root root 27 2009-02-23 15:28 /usr/bin/mpipython -> /etc/alternatives/mpipython

-rwxr-xr-x 1 root root 389064 2008-03-25 20:04 /usr/bin/mpipython.mpich

lrwxrwxrwx 1 root root 24 2009-02-23 14:28 /usr/bin/mpirun -> /etc/alternatives/mpirun

lrwxrwxrwx 1 root root 29 2009-02-23 15:28 /usr/bin/mpirun.mpich-shmem -> ../lib/mpich-shmem/bin/mpirun

lrwxrwxrwx 1 root root 7 2009-02-23 14:28 /usr/bin/mpirun.openmpi -> orterun

o install libg2c0, libg2c0-dev (when compiler complains about "cannot find -lg2c"

o (doing a lamboot -v to invoke the mpi environment)

o a line you can add or remove uncomment symbol (#) to /etc/openmpi/openmpi-mca-params.conf to prevent using of infiniband_network:

btl=^openib

o check if which mpicc points to the binaries

Installation steps

– Copy the svn folders to your /usr/lib/python2.x/site-packages directory

o Change to pypar_numeric

o type sudo python2.x setup.py install

o check if a directory pypar is being created including a mpiext.so library and check out whether all test scripts are running without errors by

orterun --np python2.x script.py

– Build pymetis

o Type: sudo make clean in the beginning

o Now change to pymetis directory and closely look at the Makefile and you might alter the lines where python is called to your appropriate python call (e.g. python2.x setup.py install)

o change to the pymetis directory and check if get_module is executable otherwise do a chmod +x get_module

o save the file and type: sudo make (32bit) or sudo make COPTIONS="-fPIC" (64bit)

o check if metis.so is present in the pymetis directory

– Some of the tests delivered with anuga_parallel still fail but if you copy the okushiri_2005 example from anuga_validation to your home folder and after having executed python2.x create_okushiri.py and python2.x create_okushiri_orginal.py the line: orterun --np python2.x run_okushiri_parallel.py should invoke the run in parallel

– Copy anuga_parallel into the site-packages folder of your local python2.x distribution

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