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README.md

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sparkhpc: Spark on HPC clusters made easy

This package tries to greatly simplify deploying and managing Apache Spark clusters on HPC resources.

Installation

From pypi

$ pip install sparkhpc

From source

$ python setup.py install

This will install the python package to your default package directory as well as the sparkcluster and hpcnotebook command-line scripts.

Usage

There are two options for using this library: from the command line or directly from python code.

Command line

Get usage info

Usage: sparkcluster [OPTIONS] COMMAND [ARGS]...

Options:
  --scheduler [lsf|slurm]  Which scheduler to use
  --help                   Show this message and exit.

Commands:
  info    Get info about currently running clusters
  launch  Launch the Spark master and workers within a...
  start   Start the spark cluster as a batch job
  stop    Kill a currently running cluster ('all' to...

$ sparkcluster start --help
Usage: sparkcluster start [OPTIONS] NCORES

  Start the spark cluster as a batch job

Options:
  --walltime TEXT                Walltime in HH:MM format
  --jobname TEXT                 Name to use for the job
  --template TEXT                Job template path
  --memory-per-executor INTEGER  Memory to reserve for each executor (i.e. the
                                 JVM) in MB
  --memory-per-core INTEGER      Memory per core to request from scheduler in
                                 MB
  --cores-per-executor INTEGER   Cores per executor
  --spark-home TEXT              Location of the Spark distribution
  --wait                         Wait until the job starts
  --help                         Show this message and exit.

Start a cluster

$ sparkcluster start 10

Get information about currently running clusters

$ sparkcluster info
----- Cluster 0 -----
Job 31454252 not yet started

$ sparkcluster info
----- Cluster 0 -----
Number of cores: 10
master URL: spark://10.11.12.13:7077
Spark UI: http://10.11.12.13:8080

Stop running clusters

$ sparkcluster stop 0
Job <31463649> is being terminated

Python code

from sparkhpc import sparkjob
import findspark 
findspark.init() # this sets up the paths required to find spark libraries
import pyspark

sj = sparkjob.sparkjob(ncores=10)

sj.wait_to_start()

sc = sj.start_spark()

sc.parallelize(...)

Jupyter notebook

sparkhpc gives you nicely formatted info about your jobs and clusters in the jupyter notebook - see the example notebook.

Dependencies

Python

These are installable via pip install.

System configuration

  • Spark installation in ~/spark OR wherever SPARK_HOME points to
  • java distribution (set JAVA_HOME)
  • mpirun in your path

Job templates

Simple job templates for the currently supported schedulers are included in the distribution. If you want to use your own template, you can specify the path using the --template flag to start. See the included templates for an example. Note that the variable names in curly braces, e.g. {jobname} will be used to inject runtime parameters. Currently you must specify walltime, ncores, memory, jobname, and spark_home. If you want to significantly alter the job submission, the best would be to subclass the relevant scheduler class (e.g. LSFSparkCluster) and override the submit method.

Using other schedulers

The LSF and SLURM schedulers are currently supported. However, adding support for other schedulers is rather straightforward (see the LSFSparkJob and SLURMSparkJob implementations as examples). Please submit a pull request if you implement a new scheduler or get in touch if you need help!

To implement support for a new scheduler you should subclass SparkCluster. You must define the following class variables:

  • _peek() (function to get stdout of the current job)
  • _submit_command (command to submit a job to the scheduler)
  • _job_regex (regex to get the job ID from return string of submit command)
  • _kill_command (scheduler command to kill a job)
  • _get_current_jobs (scheduler command to return jobid, status, jobname one job per line)

Note that _get_current_jobs should return a custom formatted string where the output looks like this:

JOB_NAME STAT JOBID
sparkcluster PEND 31610738
sparkcluster PEND 31610739
sparkcluster PEND 31610740

Depending on the scheduler's behavior, you may need to override some of the other methods as well.

Jupyter notebook

Running Spark applications, especially with python, is really nice from the comforts of a Jupyter notebook. This package includes the hpcnotebook script, which will setup and launch a secure, password-protected notebook for you.

$ hpcnotebook
Usage: hpcnotebook [OPTIONS] COMMAND [ARGS]...

Options:
  --port INTEGER  Port for the notebook server
  --help          Show this message and exit.

Commands:
  launch  Launch the notebook
  setup   Setup the notebook

Setup

Before launching the notebook, it needs to be configured. The script will first ask for a password for the notebook and generate a self-signed ssh certificate - this is done to prevent other users of your cluster to stumble into your notebook by chance.

Launching

On a computer cluster, you would normally either obtain an interactive job and issue the command below, or use this as a part of a batch submission script.

$ hpcnotebook launch
To access the notebook, inspect the output below for the port number, then point your browser to https://1.2.3.4:<port_number>
[TerminalIPythonApp] WARNING | Subcommand `ipython notebook` is deprecated and will be removed in future versions.
[TerminalIPythonApp] WARNING | You likely want to use `jupyter notebook` in the future
[I 15:43:12.022 NotebookApp] Serving notebooks from local directory: /cluster/home/roskarr
[I 15:43:12.022 NotebookApp] 0 active kernels
[I 15:43:12.022 NotebookApp] The Jupyter Notebook is running at: https://[all ip addresses on your system]:8889/
[I 15:43:12.022 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

In this case, you could set up a port forward to host 1.2.3.4 and instruct your browser to connect to https://1.2.3.4:8889.

Inside the notebook, it is straightforward to set up the SparkContext using the sparkhpc package (see above).

Contributing

Please submit an issue if you discover a bug or have a feature request! Pull requests also very welcome.

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