ParallelHowTo

Portland Compiler

It is possible to run CLaMS on multi-processor machines using MPI or OpenMP.

On the Ubuntu machines the PGF compiler suite is installed that has MPICH implemented.

In the following a short How to:

First it is necessary to make the path of the MPI libraries public by executing:

for 64bit machines:

. /opt/pgi/linux86-64/10.4/mpi.sh

for 32bit machines:

. /opt/pgi/linux86/10.4/mpi.sh

Then compile the needed programs by executing:

make useMPI=true

Before running the CLaMS script or a single program you have to execute:

> ssh-agent
> SSH_AUTH_SOCK=/tmp/ssh-arHtY17224/agent.17224; export SSH_AUTH_SOCK;
> SSH_AGENT_PID=17225; export SSH_AGENT_PID;
> echo Agent pid 17225;
> ssh-add .ssh/id_rsa

This is necessary, because the processes communicate per ssh.

The programs must be called as following:

mpirun -np # [ --all-local ] program

# - number of processors
use the option --all-local for running it on the CPUs of the local machine only.

Intel Compiler

The MPICH2 Library (1.3.2p1) is installed in directory /usr/nfs/local/local/mpich2-intel (for Intel C and Fortran compilers).

Add the bin subdirectory of the installation directory to your path:

PATH=/usr/nfs/local/local/mpich2-intel/bin:$PATH
export PATH

To read the man pages set MANPATH to the following:

MANPATH=/usr/nfs/local/local/mpich2-intel/share/man:$MANPATH
export MANPATH

The programs can be compiled with:

make useComp=ifc useMPI=true <progname>

Execute on <n> CPUs:

mpiexec -np <n> <progname>

It may be necessary to unset the memory limit:

ulimit -s unlimited

-  ⇤ ← Revision 2 as of 2011-05-02 12:25:48 → 
  Size: 839
  Editor: GebhardGuenther
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+   ← Revision 11 as of 2013-11-11 08:41:50 → ⇥
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  Editor: NicoleThomas
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+#acl ClamsUserGroup:read,write,delete,revert All:read
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-= HowToParallel =
+<<TableOfContents>>
= ParallelHowTo =

=== Portland Compiler ===
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-On the Ubuntu machines is the PGF compiler suite installed that has MPICH implemented.
+On the Ubuntu machines the PGF compiler suite is installed that has MPICH implemented.
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+Line 21:
-. /opt/pgi/linux86-64/8.0-2/mpi.sh
+. /opt/pgi/linux86-64/10.4/mpi.sh
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+Line 27:
-. /opt/pgi/linux86/8.0-2/mpi.sh
+. /opt/pgi/linux86/10.4/mpi.sh
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+Line 39:
-ssh-add
+> ssh-agent
> SSH_AUTH_SOCK=/tmp/ssh-arHtY17224/agent.17224; export SSH_AUTH_SOCK;
> SSH_AGENT_PID=17225; export SSH_AGENT_PID;
> echo Agent pid 17225;
> ssh-add .ssh/id_rsa
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+Line 51:
-mpirun -np # program
+mpirun -np # [ --all-local ] program
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+Line 54:
+use the option --all-local for running it on the CPUs of the local machine only.
}}}
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+Line 57:
+=== Intel Compiler ===

The MPICH2 Library (1.3.2p1) is installed in directory ''/usr/nfs/local/local/mpich2-intel'' (for Intel C and Fortran compilers).

Add the bin subdirectory of the installation directory to your path:
{{{
PATH=/usr/nfs/local/local/mpich2-intel/bin:$PATH
export PATH
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+Line 67:
+To read the man pages set MANPATH to the following:
{{{
MANPATH=/usr/nfs/local/local/mpich2-intel/share/man:$MANPATH
export MANPATH
}}}

The programs can be compiled with:
{{{
make useComp=ifc useMPI=true <progname>
}}}

Execute on <n> CPUs:
{{{
mpiexec -np <n> <progname>
}}}

It may be necessary to unset the memory limit:
{{{
ulimit -s unlimited
}}}