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High Performance Computers

High Performance Computers

Relevant Machines

This page includes instructions and guidelines when deploying Dask on high performance supercomputers commonly found in scientific and industry research labs. These systems commonly have the following attributes:

  1. Some mechanism to launch MPI applications or use job schedulers like SLURM, SGE, TORQUE, LSF, DRMAA, PBS, or others

  2. A shared network file system visible to all machines in the cluster

  3. A high performance network interconnect, such as Infiniband

  4. Little or no node-local storage

Where to start

Most of this page documents various ways and best practices to use Dask on an HPC cluster. This is technical and aimed both at users with some experience deploying Dask and also system administrators.

The preferred and simplest way to run Dask on HPC systems today both for new, experienced users or administrator is to use dask-jobqueue.

However, dask-jobqueue is slightly oriented toward interactive analysis usage, and it might be better to use tools like dask-mpi in some routine batch production workloads.

Dask-jobqueue and Dask-drmaa

dask-jobqueue provides cluster managers for PBS, SLURM, LSF, SGE and other resource managers. You can launch a Dask cluster on these systems like this.

from dask_jobqueue import PBSCluster

cluster = PBSCluster(cores=36,
                     memory="100GB",
                     project='P48500028',
                     queue='premium',
                     interface='ib0',
                     walltime='02:00:00')

cluster.scale(100)  # Start 100 workers in 100 jobs that match the description above

from dask.distributed import Client
client = Client(cluster)    # Connect to that cluster

Dask-jobqueue provides a lot of possibilities like adaptive dynamic scaling of workers, we recommend reading the dask-jobqueue documentation first to get a basic system running and then returning to this documentation for fine-tuning if necessary.

Using MPI

You can launch a Dask cluster using mpirun or mpiexec and the dask-mpi command line tool.

mpirun --np 4 dask-mpi --scheduler-file /home/$USER/scheduler.json

from dask.distributed import Client
client = Client(scheduler_file='/path/to/scheduler.json')

This depends on the mpi4py library. It only uses MPI to start the Dask cluster and not for inter-node communication. MPI implementations differ: the use of mpirun --np 4 is specific to the mpich or open-mpi MPI implementation installed through conda and linked to mpi4py.

conda install mpi4py

It is not necessary to use exactly this implementation, but you may want to verify that your mpi4py Python library is linked against the proper mpirun/mpiexec executable and that the flags used (like --np 4) are correct for your system. The system administrator of your cluster should be very familiar with these concerns and able to help.

In some setups, MPI processes are not allowed to fork other processes. In this case, we recommend using --no-nanny option in order to prevent dask from using an additional nanny process to manage workers.

Run dask-mpi --help to see more options for the dask-mpi command.

Using a Shared Network File System and a Job Scheduler

Note

This section is not necessary if you use a tool like dask-jobqueue.

Some clusters benefit from a shared File System (NFS, GPFS, Lustre or alike), and can use this to communicate the scheduler location to the workers:

dask-scheduler --scheduler-file /path/to/scheduler.json  # writes address to file

dask-worker --scheduler-file /path/to/scheduler.json  # reads file for address
dask-worker --scheduler-file /path/to/scheduler.json  # reads file for address

>>> client = Client(scheduler_file='/path/to/scheduler.json')

This can be particularly useful when deploying dask-scheduler and dask-worker processes using a job scheduler like SGE/SLURM/Torque/etc. Here is an example using SGE’s qsub command:

# Start a dask-scheduler somewhere and write the connection information to a file
qsub -b y /path/to/dask-scheduler --scheduler-file /home/$USER/scheduler.json

# Start 100 dask-worker processes in an array job pointing to the same file
qsub -b y -t 1-100 /path/to/dask-worker --scheduler-file /home/$USER/scheduler.json

Note, the --scheduler-file option is only valuable if your scheduler and workers share a network file system.

High Performance Network

Many HPC systems have both standard Ethernet networks as well as high-performance networks capable of increased bandwidth. You can instruct Dask to use the high-performance network interface by using the --interface keyword with the dask-worker, dask-scheduler, or dask-mpi commands or the interface= keyword with the dask-jobqueue Cluster objects:

mpirun --np 4 dask-mpi --scheduler-file /home/$USER/scheduler.json --interface ib0

In the code example above, we have assumed that your cluster has an Infiniband network interface called ib0. You can check this by asking your system administrator or by inspecting the output of ifconfig

$ ifconfig
lo          Link encap:Local Loopback                       # Localhost
                        inet addr:127.0.0.1  Mask:255.0.0.0
                        inet6 addr: ::1/128 Scope:Host
eth0        Link encap:Ethernet  HWaddr XX:XX:XX:XX:XX:XX   # Ethernet
                        inet addr:192.168.0.101
                        ...
ib0         Link encap:Infiniband                           # Fast InfiniBand
                        inet addr:172.42.0.101

https://stackoverflow.com/questions/43881157/how-do-i-use-an-infiniband-network-with-dask

Local Storage

Users often exceed memory limits available to a specific Dask deployment. In normal operation, Dask spills excess data to disk, often to the default temporary directory.

However, in HPC systems this default temporary directory may point to an network file system (NFS) mount which can cause problems as Dask tries to read and write many small files. Beware, reading and writing many tiny files from many distributed processes is a good way to shut down a national supercomputer.

If available, it’s good practice to point Dask workers to local storage, or hard drives that are physically on each node. Your IT administrators will be able to point you to these locations. You can do this with the --local-directory or local_directory= keyword in the dask-worker command:

dask-mpi ... --local-directory /path/to/local/storage

or any of the other Dask Setup utilities, or by specifying the following configuration value:

temporary-directory: /path/to/local/storage

However, not all HPC systems have local storage. If this is the case then you may want to turn off Dask’s ability to spill to disk altogether. See this page for more information on Dask’s memory policies. Consider changing the following values in your ~/.config/dask/distributed.yaml file to disable spilling data to disk:

distributed:
  worker:
    memory:
      target: false  # don't spill to disk
      spill: false  # don't spill to disk
      pause: 0.80  # pause execution at 80% memory use
      terminate: 0.95  # restart the worker at 95% use

This stops Dask workers from spilling to disk, and instead relies entirely on mechanisms to stop them from processing when they reach memory limits.

As a reminder, you can set the memory limit for a worker using the --memory-limit keyword:

dask-mpi ... --memory-limit 10GB

Launch Many Small Jobs

Note

This section is not necessary if you use a tool like dask-jobqueue.

HPC job schedulers are optimized for large monolithic jobs with many nodes that all need to run as a group at the same time. Dask jobs can be quite a bit more flexible: workers can come and go without strongly affecting the job. If we split our job into many smaller jobs, we can often get through the job scheduling queue much more quickly than a typical job. This is particularly valuable when we want to get started right away and interact with a Jupyter notebook session rather than waiting for hours for a suitable allocation block to become free.

So, to get a large cluster quickly, we recommend allocating a dask-scheduler process on one node with a modest wall time (the intended time of your session) and then allocating many small single-node dask-worker jobs with shorter wall times (perhaps 30 minutes) that can easily squeeze into extra space in the job scheduler. As you need more computation, you can add more of these single-node jobs or let them expire.

Use Dask to co-launch a Jupyter server

Dask can help you by launching other services alongside it. For example, you can run a Jupyter notebook server on the machine running the dask-scheduler process with the following commands

from dask.distributed import Client
client = Client(scheduler_file='scheduler.json')

import socket
host = client.run_on_scheduler(socket.gethostname)

def start_jlab(dask_scheduler):
    import subprocess
    proc = subprocess.Popen(['/path/to/jupyter', 'lab', '--ip', host, '--no-browser'])
    dask_scheduler.jlab_proc = proc

client.run_on_scheduler(start_jlab)

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