The Interaction between Modules, MPI and Parallel Filesystems

Many sites that use modules have hundred to thousands of nodes connected to large parallel filesystems. Some care has to be taken when a user’s job scripts start a parallel mpi execution to avoid problems with the parallel filesystem. Module commands in a user’s ~/.bashrc or ~/.cshrc can overload or cause timeouts in a parallel filesystem.

At TACC, we do a couple of things to avoid this problem. We have seen this timeout problem for mpi programs that execute more than 1000 nodes, but when this problem occurs will depend on relative speeds of the network and the parallel filesystem.

It is helpful to outline the proceedure that we use at TACC to start a job on a compute node for a user

  1. The bash user submits a job to the scheduler.
  2. The current environment is captured
  3. That environment passed to the shell script that starts on a compute node.
  4. The user’s job script starts an mpi execution.
  5. The mpi execution starts an interactive non-login (and not prompt) shell on every node.
  6. This non-login interactive shell sources the user’s ~/.bashrc
  7. Then the environment found at the start of mpi execution is passed to all nodes.

It is the sixth step that causes the problem. If there are any module load commands in ~/.bashrc, these module commands will be started on every node at about the same time. The module command has to walk the directories listed in $MODULEPATH to find the modules. This hits the parallel filesystem hard when there are thousands of nodes.

At TACC we define an environment variable call ENVIRONMENT (a clever name, no?) to be BATCH when a job is started on a compute node. We provide every user with a default ~/.bashrc that has the following section:

if [ -z "$__BASHRC_SOURCED__" -a "$ENVIRONMENT" != BATCH ]; then
  export __BASHRC_SOURCED__=1

  ##########################################################
  # **** PLACE MODULE COMMANDS HERE and ONLY HERE.      ****
  ##########################################################

  # module load git

fi

This way modules are only loaded once on the initial shell and not reloaded on subshells or on compute nodes during job submission.

Some users won’t follow our guidelines so as an extra layer of protection we make the module be a no-op for bash users.

The module command for bash is defined to be:

module () {
   eval $( $LMOD_CMD bash "[email protected]" ) ...
}

Normally, $LMOD_CMD points the lmod command but on compute nodes we have the following startup behavior for bash users:

# Compute notes set the ENVIRONMENT var to BATCH for non-interactive shells.
if [ -z "$PS1" ]; then
  export ENVIRONMENT=BATCH

  # If we are in BATCH mode then turn off the module command.
  if [ -z "$TACC_DEBUG" ]; then
    export LMOD_CMD=':'
    export LMOD_SETTARG_CMD=':'
  fi
fi

By making $LMOD_CMD be a colon, we make the module command silently do nothing. Unfortunately, this only works for bash and not tcsh or zsh users. We want module command to work in a user’s job submission script:

#!/bin/bash
#SBATCH ...

module load intel mvapich2
ibrun ./my_mpi_program        # start parallel executation.

Note that the total environment is passed by our parallel job starter ibrun. So there is no need for a user’s ~/bashrc or similar file to load modules. In fact it can lead to problems if the user’s current module environment loads modules that don’t match the environment that ibrun pushes to the compute nodes.

Tcsh and Zsh source the startup scripts sourced in /etc/profile.d/ for shell script startup. This is how the module command is defined there. If we redefined $LMOD_CMD for those shell, module command would not work in tcsh or zsh scripts.

Bash uses a different technique. It only uses the value of $BASH_ENV. If that variable points to a file then that file is source. Lmod defines that variable to point to a file that defines the module command. So re-defining $LMOD_CMD in the startup scripts won’t affect the module commands in the job submission script, just in the parallel execution when ~/.bashrc is sourced.

One drawback to redefining $LMOD_CMD is that if bash user tries to invoke a shell script to run in parallel any module command will silently do nothing.