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https://github.com/jupyterhub/batchspawner

Custom Spawner for Jupyterhub to start servers in batch scheduled systems
https://github.com/jupyterhub/batchspawner

batch-scheduler hpc jupyter jupyterhub spawner supercomputer

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Custom Spawner for Jupyterhub to start servers in batch scheduled systems

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README 

        
# batchspawner for Jupyterhub



[![Latest PyPI version](https://img.shields.io/pypi/v/batchspawner?logo=pypi)](https://pypi.python.org/pypi/batchspawner)

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This is a custom spawner for [Jupyterhub](https://jupyterhub.readthedocs.io/) that is designed for installations on clusters using batch scheduling software.



This began as a generalization of [mkgilbert's batchspawner](https://github.com/mkgilbert/slurmspawner) which in turn was inspired by [Andrea Zonca's blog post](http://zonca.github.io/2015/04/jupyterhub-hpc.html "Run jupyterhub on a Supercomputer") where he explains his implementation for a spawner that uses SSH and Torque. His github repo is found [here](http://www.github.com/zonca/remotespawner "RemoteSpawner").



This package formerly included WrapSpawner and ProfilesSpawner, which provide mechanisms for runtime configuration of spawners. These have been split out and moved to the [`wrapspawner`](https://github.com/jupyterhub/wrapspawner) package.



## Installation



1. from root directory of this repo (where setup.py is), run `pip install -e .`



   If you don't actually need an editable version, you can simply run

   `pip install batchspawner`



2. add lines in jupyterhub_config.py for the spawner you intend to use, e.g.



   ```python

      c = get_config()

      c.JupyterHub.spawner_class = 'batchspawner.TorqueSpawner'

      import batchspawner    # Even though not used, needed to register batchspawner interface

   ```



3. Depending on the spawner, additional configuration will likely be needed.



## Batch Spawners



For information on the specific spawners, see [SPAWNERS.md](SPAWNERS.md).



### Overview



This file contains an abstraction layer for batch job queueing systems (`BatchSpawnerBase`), and implements

Jupyterhub spawners for Torque, Moab, SLURM, SGE, HTCondor, LSF, and eventually others.

Common attributes of batch submission / resource manager environments will include notions of:



- queue names, resource manager addresses

- resource limits including runtime, number of processes, memory

- singleuser child process running on (usually remote) host not known until runtime

- job submission and monitoring via resource manager utilities

- remote execution via submission of templated scripts

- job names instead of PIDs



`BatchSpawnerBase` provides several general mechanisms:



- configurable traits `req_foo` that are exposed as `{foo}` in job template scripts. Templates (submit scripts in particular) may also use the full power of [jinja2](http://jinja.pocoo.org/). Templates are automatically detected if a `{{` or `{%` is present, otherwise str.format() used.

- configurable command templates for submitting/querying/cancelling jobs

- a generic concept of job-ID and ID-based job state tracking

- overrideable hooks for subclasses to plug in logic at numerous points



### Example



Every effort has been made to accommodate highly diverse systems through configuration

only. This example consists of the (lightly edited) configuration used by the author

to run Jupyter notebooks on an academic supercomputer cluster.



```python

# Select the Torque backend and increase the timeout since batch jobs may take time to start

import batchspawner

c.JupyterHub.spawner_class = 'batchspawner.TorqueSpawner'

c.Spawner.http_timeout = 120



#------------------------------------------------------------------------------

# BatchSpawnerBase configuration

#    These are simply setting parameters used in the job script template below

#------------------------------------------------------------------------------

c.BatchSpawnerBase.req_nprocs = '2'

c.BatchSpawnerBase.req_queue = 'mesabi'

c.BatchSpawnerBase.req_host = 'mesabi.xyz.edu'

c.BatchSpawnerBase.req_runtime = '12:00:00'

c.BatchSpawnerBase.req_memory = '4gb'

#------------------------------------------------------------------------------

# TorqueSpawner configuration

#    The script below is nearly identical to the default template, but we needed

#    to add a line for our local environment. For most sites the default templates

#    should be a good starting point.

#------------------------------------------------------------------------------

c.TorqueSpawner.batch_script = '''#!/bin/sh

#PBS -q {queue}@{host}

#PBS -l walltime={runtime}

#PBS -l nodes=1:ppn={nprocs}

#PBS -l mem={memory}

#PBS -N jupyterhub-singleuser

#PBS -v {keepvars}

module load python3

{cmd}

'''

# For our site we need to munge the execution hostname returned by qstat

c.TorqueSpawner.state_exechost_exp = r'int-\1.mesabi.xyz.edu'

```



### Security



Unless otherwise stated for a specific spawner, assume that spawners

_do_ evaluate shell environment for users and thus the [security

requirements of JupyterHub security for untrusted

users](https://jupyterhub.readthedocs.io/en/stable/reference/websecurity.html)

are not fulfilled because some (most?) spawners _do_ start a user

shell which will execute arbitrary user environment configuration

(`.profile`, `.bashrc` and the like) unless users do not have

access to their own cluster user account. This is something which we

are working on.



## Provide different configurations of BatchSpawner



### Overview



`ProfilesSpawner`, available as part of the [`wrapspawner`](https://github.com/jupyterhub/wrapspawner)

package, allows the Jupyterhub administrator to define a set of different spawning configurations,

both different spawners and different configurations of the same spawner.

The user is then presented a dropdown menu for choosing the most suitable configuration for their needs.



This method provides an easy and safe way to provide different configurations of `BatchSpawner` to the

users, see an example below.



### Example



The following is based on the author's configuration (at the same site as the example above)

showing how to give users access to multiple job configurations on the batch scheduled

clusters, as well as an option to run a local notebook directly on the jupyterhub server.



```python

# Same initial setup as the previous example

import batchspawner

c.JupyterHub.spawner_class = 'wrapspawner.ProfilesSpawner'

c.Spawner.http_timeout = 120

#------------------------------------------------------------------------------

# BatchSpawnerBase configuration

#   Providing default values that we may omit in the profiles

#------------------------------------------------------------------------------

c.BatchSpawnerBase.req_host = 'mesabi.xyz.edu'

c.BatchSpawnerBase.req_runtime = '12:00:00'

c.TorqueSpawner.state_exechost_exp = r'in-\1.mesabi.xyz.edu'

#------------------------------------------------------------------------------

# ProfilesSpawner configuration

#------------------------------------------------------------------------------

# List of profiles to offer for selection. Signature is:

#   List(Tuple( Unicode, Unicode, Type(Spawner), Dict ))

# corresponding to profile display name, unique key, Spawner class,

# dictionary of spawner config options.

#

# The first three values will be exposed in the input_template as {display},

# {key}, and {type}

#

c.ProfilesSpawner.profiles = [

   ( "Local server", 'local', 'jupyterhub.spawner.LocalProcessSpawner', {'ip':'0.0.0.0'} ),

   ('Mesabi - 2 cores, 4 GB, 8 hours', 'mesabi2c4g12h', 'batchspawner.TorqueSpawner',

      dict(req_nprocs='2', req_queue='mesabi', req_runtime='8:00:00', req_memory='4gb')),

   ('Mesabi - 12 cores, 128 GB, 4 hours', 'mesabi128gb', 'batchspawner.TorqueSpawner',

      dict(req_nprocs='12', req_queue='ram256g', req_runtime='4:00:00', req_memory='125gb')),

   ('Mesabi - 2 cores, 4 GB, 24 hours', 'mesabi2c4gb24h', 'batchspawner.TorqueSpawner',

      dict(req_nprocs='2', req_queue='mesabi', req_runtime='24:00:00', req_memory='4gb')),

   ('Interactive Cluster - 2 cores, 4 GB, 8 hours', 'lab', 'batchspawner.TorqueSpawner',

      dict(req_nprocs='2', req_host='labhost.xyz.edu', req_queue='lab',

          req_runtime='8:00:00', req_memory='4gb', state_exechost_exp='')),

   ]

c.ProfilesSpawner.ip = '0.0.0.0'

```



## Debugging batchspawner



Sometimes it can be hard to debug batchspawner, but it's not really

once you know how the pieces interact. Check the following places for

error messages:



- Check the JupyterHub logs for errors.



- Check the JupyterHub logs for the batch script that got submitted

  and the command used to submit it. Are these correct? (Note that

  there are submission environment variables too, which aren't

  displayed.)



- At this point, it's a matter of checking the batch system. Is the

  job ever scheduled? Does it run? Does it succeed? Check the batch

  system status and output of the job. The most comon failure

  patterns are a) job never starting due to bad scheduler options, b)

  job waiting in the queue beyond the `start_timeout`, causing

  JupyterHub to kill the job.



- At this point the job starts. Does it fail immediately, or before

  Jupyter starts? Check the scheduler output files (stdout/stderr of

  the job), wherever it is stored. To debug the job script, you can

  add debugging into the batch script, such as an `env` or `set -x`.



- At this point Jupyter itself starts - check its error messages. Is

  it starting with the right options? Can it communicate with the

  hub? At this point there usually isn't anything

  batchspawner-specific, with the one exception below. The error log

  would be in the batch script output (same file as above). There may

  also be clues in the JupyterHub logfile.

- Are you running on an NFS filesystem? It's possible for Jupyter to

  experience issues due to varying implementations of the fcntl() system

  call. (See also [Jupyterhub-Notes and Tips: SQLite](https://jupyterhub.readthedocs.io/en/latest/reference/database.html?highlight=NFS#sqlite))



Common problems:



- Did you `import batchspawner` in the `jupyterhub_config.py` file?

  This is needed in order to activate the batchspawer API in

  JupyterHub.



## Changelog



See [CHANGELOG.md](CHANGELOG.md).