Using Chapel with InfiniBand ¶

This document describes how to run Chapel across multiple nodes of an InfiniBand cluster, including Cray CS and HPE Apollo systems. Multilocale Chapel Execution describes general information about running Chapel in a multilocale configuration.

Contents

Using Chapel with InfiniBand

Configuring for InfiniBand ¶

Due to the wide variety of InfiniBand clusters and potential for false-positives, Chapel does not currently auto-detect InfiniBand configurations or platforms that commonly use InfiniBand. To build Chapel with InfiniBand support, set:

export CHPL_COMM=gasnet
export CHPL_COMM_SUBSTRATE=ibv

Alternatively, when running on a Cray CS or HPE Apollo system CHPL_HOST_PLATFORM can instead be set, in which case the comm and substrate settings will be inferred.

For Cray CS:

export CHPL_HOST_PLATFORM=cray-cs

For HPE Apollo:

export CHPL_HOST_PLATFORM=hpe-apollo

Configuring a Launcher ¶

A gasnetrun_ibv based launcher should be used to launch jobs and generally speaking native launchers like srun will not work. Most InfiniBand clusters use a workload manager or queueing system such a Slurm, LSF, or PBS. To select an appropriate Chapel launcher you can set CHPL_LAUNCHER to one of the following values:

Launcher Name	Description
gasnetrun_ibv	run jobs interactively on your system
slurm-gasnetrun_ibv	queue jobs using Slurm (srun/sbatch)
pbs-gasnetrun_ibv	queue jobs using PBS (qsub)
lsf-gasnetrun_ibv	queue jobs using LSF (bsub)

CHPL_LAUNCHER will typically default to gasnetrun_ibv unless CHPL_HOST_PLATFORM is cray-cs or hpe-apollo and srun is in your path, in which case it will default to slurm-gasnetrun_ibv

By default Slurm, PBS, and LSF versions launch in an interactive mode. For batch submission with Slurm CHPL_LAUNCHER_USE_SBATCH can be used as described in Using Slurm. For other launchers and as an alternative for Slurm, users can write batch submission scripts and use gasnetrun_ibv to launch their jobs.

Setting Registration Limits ¶

On most high performance networks, including InfiniBand, memory has to be registered with the network in order for Chapel to take advantage of fast one-sided communication. On InfiniBand networks there may be limits placed on how much memory can be registered so GASNet will probe at startup to detect this value. This probing can be slow, so GASNet will recommend setting GASNET_PHYSMEM_MAX to avoid probing every time. On nodes with homogeneous amounts of memory this message usually looks something like:

WARNING: Beginning a potentially slow probe of max pinnable memory...
WARNING: Probe of max pinnable memory completed in 45s.
WARNING:   Probe of max pinnable memory has yielded '335 GB'.
WARNING:   If you have the same memory configuration on all nodes, then
WARNING:   to avoid this probe in the future either reconfigure using
WARNING:      --with-ibv-physmem-max='335 GB'
WARNING:   or run with environment variable
WARNING:      GASNET_PHYSMEM_MAX='335 GB'.

Where setting GASNET_PHYSMEM_MAX='335 GB' will quiet the warning and skip the startup probe. On nodes with non-homogeneous amounts of memory GASNet may recommend using a fraction of memory instead of an absolute value with something like GASNET_PHYSMEM_MAX='0.667'.

Setting GASNET_PHYSMEM_MAX to a small value can limit communication performance so it is highly recommend to use the value GASNet suggests.

Selecting a Spawner ¶

Under the covers gasnetrun_ibv based launchers must figure out how to spawn jobs and get them up and running on the compute nodes. GASNet’s two primary means of doing this on InfiniBand clusters are ssh and mpi. GASNet will default to mpi if MPI support is detected at configure time, otherwise it will default to ssh. Using mpi will likely incur a performance penalty because MPI will be running concurrently with GASNet. Running with ssh is recommended, but not all systems support ssh’ing to compute nodes so it is not always the default.

Using SSH for Job Launch ¶

To launch InfiniBand jobs with SSH, use the following:

# Specify ssh spawner
export GASNET_IBV_SPAWNER=ssh

# Specify the nodes to run on (only required when using plain
# gasnetrun_ibv outside a Slurm/PBS/LSF reservation)
export GASNET_SSH_SERVERS="nid00001 nid00002 nid00003 ..."

If you receive an error message like:

*** Failed to start processes on nid00001, possibly due to an inability to establish an ssh connection from login-node without interactive authentication.

This indicates passwordless SSH is not set up. You can try copying existing SSH keys or generating new ones with the following:

ssh-keygen -t rsa # use default location and empty passphrase
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys

If you see the same error message this may indicate ssh connections to compute nodes are not allowed, in which case using the MPI spawner may be your only option.

Using MPI for Job Launch ¶

To launch InfiniBand jobs with mpirun, first make sure that mpicc is available and that MPI programs launch appropriately with mpirun. Then use the following. You’ll want to make sure that GASNet detects MPI in its configuration output.

export GASNET_IBV_SPAWNER=mpi

Verifing Job Launch ¶

Once the above configuration has been done, checking that job launching is happening properly is recommended. The following Chapel program will print out the locale names and how much parallelism is available per locale. Ideally each locale is running on a unique node (not oversubscribed) and the amount of parallelism matches the number of physical cores on each node.

for loc in Locales do on loc do
  writeln((here.name, here.maxTaskPar));

An example run may look something like the following:

(nid00001, 28)
(nid00002, 28)

If nodes are oversubscribed or the amount of parallelism is far less than expected see Selecting a Spawner and if that does not help consider opening a bug as described in Reporting Chapel Issues.