MPI Cluster

Dynamo can be run on a cluster of CPUs.

Compilation

Compiling Dynamo on your cluster requires a cc compiler that links the MPI libraries.

In most systems, you can run the command:

module avail

on the shell of your login node to check the available modules. Modules for parallel computation typically will include an mpi-enabled compiler. You need to load one of them, for instance:.

module load mpiCC

This should add some compilers to your path. They are typically called mpiCC, mpicc... It is a good idea to check the availability and syntax of the compiler provided by the module just loaded.

which mpicc

should give you a complete path to a compiler called mpicc on your path. If this is not the case, try with alternative syntax.

If you are fortunate enough, your cluster environment should have some information system (like a webpage) that tells you the modules that you are expected to use for compilation, and the attached compilers.

Once you know the name of the compiler that you are going to use (say, mpicc), you can proceed compile the MPI executables:

cd <DYNAMO_ROOT>/mpi source dynamo_compile_mpi.sh mpicc

If you get an error during compilation, try with a different module of a different compiler inside the same module.

Preparing a project

You need first to pass

GUI

• You need to make certain that you are dialing the cluster MPI option on the Computing Environment GUI.
• Select the number of cores in CPU Cores. Each one will be handled by a separate MPI task.
• Make certain that the Parallelized averaging step in the bottom panel is set to zero. This option only applies to Matlab based computations.
• Pass the path to the cluster header file.

Using a cluster under Matlab

If your cluster supports