Install and configure MPI

This article explains how to install and configure MPI to be able to run the ESTEL model in parallel on a network of computers. Note that this article is merely a quick run through the MPI Installer's Guide at http://www-unix.mcs.anl.gov/mpi/mpich2/.

Pre-requesites

ssh key authentication

To use MPI on a network of computers, you need to be able to log in any of the computer without user interaction (password etc...) This is easily achieved using secure shell key authentication. The methodology to setup ssh to use key authentication is described in the article entitled " Configure ssh for MPI".

Fortran 90 compiler

You need a Fortran90 compiler to compile and run the TELEMAC system. When running simulations in parallel mode, MPI use a wrapper to your existing compiler, usually called mpif90. This wrapper is built when MPI is compiled and therefore, you need to have a Fortran 90 compiler installed before you attempt to compile MPI.

Download MPI

You can download from http://www-unix.mcs.anl.gov/mpi/mpich2/. You will end up with a gzipped tarball called something like mpich2.tar.gz with a version number in the name as well. Note that the TELEMAC system uses MPI-1 statements but we encourage you to install MPICH-2 (which is backward compatible) as TELEMAC will probably move towards MPI 2 at some point in the future.

For the sake of this article, we assume that you have extracted the tarball into a directory called /path/to/mpi-download/.

Compilation

The compilation of MPI is fairly straightforward but beforehand, you need to create an install folder (called /path/to/mpi/ here) and a build folder (called /path/to/mpi-build/ here):

$ mkdir /path/to/mpi
$ mkdir /tmp/mpi-build

To configure the MPI build, the only required step is to assign to the environment variable F90 the name of your Fortran 90 compiler. This name needs to be in your PATH or you have to give the full path to the Fortran 90- compiler if not. Then the configure command will automatically configure the build for you:

cd /tmp/mpi-build
export F90=f90compiler
/path/to/mpi-download/configure --prefix=/path/to/mpi 2>&1 | tee configure.log

This will test many factors on your machine and configure the build. If the configure command finished without problem, you are ready to build MPI. Note that you can inspect configure.log for problems. In particular, you want to make sure that the Fortran 90 compiler is OK for the build.

To compile and install MPI, just issue the standard make and make install commands:

make
make install

This will install MPI in /path/tp/mpi/.

Note that you will need to install MPI on all the nodes in your network that will be used for MPI jobs. As they probably have the same computer architecture, you could just copy the /path/to/mpi accross.

Configuration of MPI

PATH

Add /path/to/mpi/bin to PATH. This often means adding the following lines to your .bashrc file:

PATH=/path/to/mpi/bin:$PATH
export PATH

In particular, you should be able to run the MPI Fortran 90 wrapper mpif90 now:

which mpif90
/path/to/mpi/bin/mpif90

This needs to be done on each node in the network. This is straightforward if your home directory is shared for all the nodes or you need to do it manually othwerwise.

Password in .mpd.conf

MPI requires a file in your home directory called .mpd.conf (yes, there are two dots) which contains the line:

secretword=something_secret_but_don't_use_your_real_password

This file should be readable and writable only by you.

Check if this needs to be done on all nodes.... and if the secret thing needs to be the same. Probably yes.

Hosts in mpd.hosts

Create a file in your home directory called mpd.hosts which contain a list of the nodes to be used by MPI, one per line. This file should theoretically be created on the master node, i.e. the one that you will use to launch MPI jobs.

master.full.domain
slave1.full.domain
slave2.full.domain

This is only required on the master node if you use this node only to start your MPI jobs.

Using an MPI ring

Start the ring

master $ mpd -n 3 -f ~/mpd.hosts

Where 3 is the number of nodes to include in the ring. By default, the master is always included in the ring.

Test the ring

the command mpdtrace can be used to test which machines are in the ring:

master $ mpdtrace
master
slave1
slave2

You can also send a command in parallel using mpiexec. The option -l will append the node number before the outoput of the command. The option -n 5 request the job to be sent to 5 processors, as we only have 3, it will wrap around as shown in the listing below where master and slave2 have been used twice:

master $ mpiexec -l -n 5 hostname
2: slave1
1: master
4: master
0: slave2
3: slave2

Close the ring

The command mpdallexit is used to close the MPI ring:

master $ mpdallexit

Trouble shooting

/etc/hosts