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Mympirun#

mympirun is a tool to make it easier for users of HPC clusters to run MPI programs with good performance. We strongly recommend to use mympirun instead of impirun.

In this chapter, we give a high-level overview. For a more detailed description of all options, see the vsc-mympirun README.

Basic usage#

Before using mympirun, we first need to load its module:

module load vsc-mympirun

As an exception, we don't specify a version here. The reason is that we want to ensure that the latest version of the mympirun script is always used, since it may include important bug fixes or improvements.

The most basic form of using mympirun is mympirun [mympirun options] your_program [your_program options].

For example, to run a program named example and give it a single argument (5), we can run it with mympirun example 5.

Controlling number of processes#

There are four options you can choose from to control the number of processes mympirun will start. In the following example, the program mpi_hello prints a single line: Hello world from processor <node> ... (the sourcecode of mpi_hello is available in the vsc-mympirun repository).

By default, mympirun starts one process per core on every node you assigned. So if you assigned 2 nodes with 16 cores each, mympirun will start 2 . 16 = 32 test processes in total.

--hybrid/-h#

This is the most commonly used option for controlling the number of processing.

The --hybrid option requires a positive number. This number specifies the number of processes started on each available physical node. It will ignore the number of available cores per node.

$ echo $PBS_NUM_NODES
2
$ mympirun --hybrid 2 ./mpihello
Hello world from processor node3400.doduo.os, rank 1 out of 4 processors 
Hello world from processor node3401.doduo.os, rank 3 out of 4 processors 
Hello world from processor node3401.doduo.os, rank 2 out of 4 processors 
Hello world from processor node3400.doduo.os, rank 0 out of 4 processors

Other options#

There's also --universe, which sets the exact amount of processes started by mympirun; --double, which uses double the amount of processes it normally would; and --multi that does the same as --double, but takes a multiplier (instead of the implied factor 2 with --double).

See vsc-mympirun README for a detailed explanation of these options.

Dry run#

You can do a so-called "dry run", which doesn't have any side-effects, but just prints the command that mympirun would execute. You enable this with the --dry-run flag:

$ mympirun --dry-run ./mpi_hello
mpirun ... -genv I_MPI_FABRICS shm:dapl ... -np 16 ... ./mpi_hello