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Although it is not stated anywhere, an installation of MPICH (or MVAPICH worked for me) is required for this to run. I found this posting online which was very helpful in installing this module:
From vanallsburg at hope.edu Tue Aug 7 08:12:29 2007
From: vanallsburg at hope.edu (Paul Van Allsburg)
Date: Fri Dec 4 01:06:18 2009
Subject: [Beowulf] recompile with -fPIC
I've been asked to port a Mandelbrot example written in c to perl - to
prepare an exercise to get students familiar with the
ideas of writing parallel/distributed code. Perl is what the students will
be learning in the course.
I have:
installed MPICH release (1.2.7p1) required by the Perl
Parallel:MPI module
installed mpiexec-0.82 from OSC, required interface to PBS
compiled the mandelbrot c code with the MPICH mpicc wrapper and
successfully ran it using PBS.
Next steps:
(fail) install the Parallel:MPI code & test,
begin porting the Mandelbrot example...
chop
Success!
I found the problem in an earlier install(2006) of lam-mpi had placed mpi.h files in /usr/include that caused the Parallel::MPI install script to fail. I changed a few lines in Makefile.PL for parallel:MPI from:
$MPIDIR = "/usr/local/mpich/include";
foreach (qw(/usr/mpich/include /usr/local/mpich/include
/usr/include/mpi /usr/local/include/mpi
/usr/lib/mpich/include /usr/local/lib/mpich/include))
to:
$MPIDIR = "/usr/local/mpich/include";
foreach (qw(/usr/local/mpich/include))
In brief- I did this:
- INSTALL MPICH
get MPICH current release (1.2.7p1) from http://www-unix.mcs.anl.gov/mpi/mpich1/download.html
wget http://www-unix.mcs.anl.gov/mpi/mpich1/downloads/mpich.tar.gz
gunzip mpich.tar.gz
tar -xf mpich.tar
cd /home/vanallp/mpich-1.2.7p1
make clean
CFLAGS="-fPIC";export CFLAGS
./configure --with-device=ch_p4 --prefix=/usr/local/mpich --enable-sharedlib | tee config.out
make | tee make.out
su - root
cd /home/vanallp/mpich-1.2.7p1
make install | tee make-install.out
- now get the correct mpicc in my path
PATH="/usr/local/mpich/bin:$PATH";export PATH
- INSTALL MPIEXEC
PATH="/usr/local/mpich/bin:$PATH";export PATH
wget http://www.osc.edu/%7Epw/mpiexec/mpiexec-0.82.tgz
gunzip mpiexec-0.82.tgz
tar -xf mpiexec-0.82.tar
cd /home/vanallp/mpiexec-0.82
make clean
rm test*
CFLAGS="-fPIC";export CFLAGS
./configure --with-pbs=/usr/local --with-default-comm=mpich-p4 --disable-p4-shmem --prefix=/usr/lo
+cal/osc | tee config.out
make | tee make.out
make hello | tee make-hello.out
./runtests.pl
su - root
cd /home/vanallp/mpiexec-0.82
make install | tee make-install.out
- TESTING Parallel - Mendelbrot - Master / Slave:
test mpich and mpiexec with an example in c
cp -R /usr/local/lam-7.1.3/examples/mandelbrot .
cd mandelbrot
mpicc -o master master.c
mpicc -o slave slave.c
- my PBS ms.sh script:
#!/bin/sh
#PBS -N ms
#PBS -l nodes=4
#PBS -j oe
PATH="/usr/local/mpich/bin:$PATH";export PATH
alias mpiexec='/usr/local/osc/bin/mpiexec -verbose'
mpiexec -config /home/vanallp/mpi/mpich/ms.config
- my mpiexec config file: ms.config
-n 1 : /home/vanallp/mpi/mpich/mandelbrot/master
curie* : /home/vanallp/mpi/mpich/mandelbrot/slave
- submit job to cluster:
qsub ms.sh
produces: /home/vanallp/mandel.out Sun rasterfile formatted file. Try viewing it with eog or xloadimage:
start Xming or CygwinXsvr on windows desktop,
$ eog
$ xloadimage mandel.out
- INSTALL Perl Parallel::MPI module
wget http://search.cpan.org/CPAN/authors/id/J/JO/JOSH/Parallel-MPI-0.03.tar.gz
tar -zxf Parallel-MPI-0.03.tar.gz
cd Parallel-MPI-0.03
perl Makecurie.PL | tee makecurie.out <-THIS IS THE MODIFIED Makefile.PL
make | tee make.out
make test | tee make-test.out
su - root
cd /home/vanallp/Parallel-MPI-0.03
make install | tee make-install.out
I also came across a perl parallel example for this specific port by Josh Wilmes and Chris Stevens,
https://bioinformatics.ccr.buffalo.edu/workshop/bioinformatics/Powerpoint/All/Intro_MPI.ppt
that runs successfully.
Thanks!
--
Paul Van Allsburg
Computational Science & Modeling Facilitator
Natural Sciences Division, Hope College
35 East 12th Street
Holland, Michigan 49423
616-395-7292
http://www.hope.edu/academic/csm/
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