mympirun is a tool to facilitate running MPI programs on an HPC cluster
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README.md

Description

mympirun is a tool to make it easier for users of HPC clusters to run MPI programs with good performance.

It wraps around the mpiexec/mpirun/... commands that are provided by the different MPI implementations (OpenMPI, Intel MPI, ...).

mympirun will determine the mpirun command to use, sets up the environment, and takes into account the available resources to configure it.

Originally created by the HPC team of Ghent University.

License

vsc-mympirun is made available under the GNU General Public License (GPL) version 2.

Basic usage

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

Mympirun parses options until it runs into something it doesn't recognize as an option and assumes this is the executable, and everything after it are options for the program. To separate mympirun options from program options manually, use -- in between both.

Setup

The vsc-mympirun installation provides 'fake' mpirun commands to try and ensure that mympirun is always used. These fake mpirun commands basically wrap around mympirun (which in turn wraps around the real mpirun command).

Therefore, you should make sure that the location of the mympirun command and the fake mpirun is prepended to $PATH. If mympirun is provided via a module, you should load it after any other modules.

Detection of MPI and job scheduler

mympirun detects which MPI implementation (OpenMPI, Intel MPI, ...) is being used, to figure out which mpirun command it should be using. This can be overridden using the --setmpi or -M option. An overview of known MPI implementations is available via -m or --showmpi.

In addition, the job scheduler (e.g., Torque) is also detected automatically, and can be overridden via --schedtype or -S. If no job scheduler could be detected, local execution is assumed.

An overview of known job schedulers is available via -s or --showsched.

Available resources

mympirun will detect the available resources, and pass options to the mpirun command being used accordingly.

By default, it will use all available cores, i.e.:

  • all cores on the current system, if the local scheduler is used
  • all cores assigned to the current job, if the pbs scheduler is used

This can be changed if needed using the --hybrid, --universe, --double or --multi options, see below.

Pinning of MPI processes to cores is also enabled by default (can be disabled using --disable-pinmpi).

It will also leverage the Torque integration of the MPI library being used by default, by launching MPI processes using pbsdsh rather than ssh. (See also: Controlling launcher)

Configuring mympirun

To get a full overview of available mympirun options, run mympirun --help.

For each command line option, there is a corresponding environment variable $MYMPIRUN_* (for example, --basepath corresponds to $MPI_BASEPATH) and configuration file entry. Command line options override environment variables, and environment variables override configuration files.

Controlling number of processes

--hybrid / -h

The --hybrid or -h option requires one integer. This integer specifies the number of processes started on each available physical node.

$ echo $PBS_NUM_NODES
2

$ mympirun --hybrid 2 ./mpi_hello
Hello world from processor node2157.delcatty.os, rank 1 out of 4 processors
Hello world from processor node2158.delcatty.os, rank 3 out of 4 processors
Hello world from processor node2158.delcatty.os, rank 2 out of 4 processors
Hello world from processor node2157.delcatty.os, rank 0 out of 4 processors

--universe

The --universeoption also requires one integer. This integer will be the exact number of processes started by mympirun (independent of the number of nodes).

$ echo $PBS_NUM_NODES
2

$ mympirun --universe 1 ./mpi_hello
Hello world from processor node2157.delcatty.os, rank 0 out of 1 processors

$ echo $PBS_NUM_NODES
3

$ mympirun --universe 2 ./mpi_hello
Hello world from processor node2157.delcatty.os, rank 1 out of 2 processors
Hello world from processor node2157.delcatty.os, rank 0 out of 2 processors

--double and --multi

As the name suggests, when using the --double option, mympirun will start double the amount of processes as it normally would. The --multi option works the same but it requires an integer, indicating the multiplier, for example, --multi 3 will start triple the amount of processes. This means --double and --multi 2 will have the exact same effect.

$ echo $PBS_NUM_NODES
2

$ echo $PBS_NUM_PPN
2

$ mympirun --double ./mpi_hello
Hello world from processor node2157.delcatty.os, rank 1 out of 8 processors
Hello world from processor node2158.delcatty.os, rank 3 out of 8 processors
Hello world from processor node2157.delcatty.os, rank 0 out of 8 processors
Hello world from processor node2158.delcatty.os, rank 2 out of 8 processors

Controlling output

Use --output to redirect the output of the (MPI) program being run to a file instead of stdout/stderr.

$ mympirun --output out.txt hostname

$ cat out.txt
node2157.delcatty.os
node2157.delcatty.os

Passing down environment variables

The environment variables that mympirun passes down into the environment of the MPI processes include CLASSPATH, LD_LIBRARY_PATH, LD_PRELOAD, PATH, PYTHONPATH, PYTHONUNBUFFERED and all environment variables that are prefixed with DAPL, IPATH, KMP, MKL, O64, OMP, PSC, PSM, TMI, and VSMP.

To add other variables to this list, you can use the mympirun option --variablesprefix. This option requires a comma-seperated list of strings. Mympirun will pass the exact string and every environment variable that starts with the string followed by an underscore. For example, --variablesprefix MPI will pass on the environment variables $MPI, $MPI_FOO, $MPI_BAR etc.

$ cat echo_my_env_var
echo ${MY_ENV_VAR:-default_value}

$ export MYENV_VAR="myenv_var"

$ mympirun ./echo_my_env_var
default_value
default_value

$ mympirun --variablesprefix MYENV ./echo_my_env_var
myenv_var
myenv_var

Controlling launcher

In recent Intel MPI versions (> 4.1), mpirun uses Hydra as its process manager. It is possible to change the launcher Hydra uses using the --launcher option. (see Bootstrap Options)

By default, mympirun will use pbsdsh as launcher, which is provided by the Torque/PBS resource manager. It enables distributing tasks under control of Torque, ensuring that the processes are properly pinned to the resources available in the job.

This is a better alternative to using ssh as launcher.

Passing options to mpirun

To pass options directly to the mpirun command, use --mpirunoptions. This option is used with a string of options, which is then appended to the mpirun command generated by mympirun.

Options to be used with Intel MPI can be found in the Command Reference section of the Intel MPI documentation. For options with OpenMPI, check the mpirun man page.

Hang detection

If your MPI program doesn't have any output for a long time, mympirun will assume something is wrong and will interrupt your job as a safety measure (we wouldn't want your program to "hang" for hours, or even days, without really doing anything). The default time mympirun waits for output is one hour (3600 seconds).

You can change the amount of time mympirun waits for output by using the option output-check-timeout with a number of seconds, or you can make the warning non-fatal by using the option --disable-output-check-fatal. In this case a warning will be printed, but the program will not be interrupted.

Debugging

To get all debugging info from mympirun itself, use the option --debug or simply -d. This will print to stdout by default.

For debugging on MPI level, use --debugmpi.

Redirecting the logger output of a mympirun script to a file is done with the option --logtofile.

Internal Workflow

The first step of mympirun is making sure that every mpirun command passes through mympirun. This is accomplished by prepending a fake mpirun path to $PATH, which will catch the attempt to execute mpirun and forward it to mympirun.

Next, the script will import every MPI flavor implementation from lib/vsc/mympirun/mpi. This way it is possible to deduce the MPI flavor that is requested by observing the path of the executable that called mympirun.

It will follow the same process for determining the scheduler. Both MPI flavor and scheduler flavor can be overwritten by using the --setmpi/-M and --schedtype/-S options respectively.

Once both flavors have been set, the script will get some standard MPI configuration variables, such as usable nodes, netmask,... It will handle CPU pinning if enabled.

After setting up, it will transform the command line arguments and other global environment variables to a dict with options that the chosen MPI flavor can understand.

Finally, it passes these options to the correct mpirun executable of the selected MPI flavor.