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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