3.4. Job runners¶

Class representing local job runner.

The goal of JobRunner is to take care of two important things – parallelization and runscript execution:

• When the method run() of any Job instance is executed, this method, after some preparations, passes control to a JobRunner instance. This JobRunner instance decides if a separate thread should be spawned for this job or if the execution should proceed in the main thread. This decision is based on parallel attribute which can be set on JobRunner creation. There are no separate classes for serial and parallel job runner, both cases are covered by JobRunner depending on one bool parameter.
• If the executed job is an instance of SingleJob, it creates a shell script (called runscript) which contains most of the actual computational work (usually it is just an execution of some external binary). The runscript is then submitted to a JobRunner instance using its method call(). This method executes the runscript in a separate subprocess and takes care of setting proper working directory, output and error stream handling etc.

The number of simultaneously running call() methods can be limited using maxjobs parameter. If maxjobs is 0, no limit is enforced. If parallel is False, maxjobs is ignored. If parallel is True and maxjobs is a positive integer, a BoundedSemaphore of that size is used to limit the number of concurrently running call() methods.

A JobRunner instance can be passed to run() with a keyword argument jobrunner. If this argument is omitted, the instance stored in config.default_jobrunner is used.

call(runscript, workdir, out, err, **kwargs)[source]¶

Execute the runscript in the folder workdir. Redirect output and error streams to out and err, respectively.

Arguments mentioned above should be strings containing paths to corresponding files or folders

Other keyword arguments are ignored here but they can be useful in JobRunner subclasses (see GridRunner.call()).

Returns integer value indicating the exit code returned by execution of runscript.

This method can be safely overridden in JobRunner subclasses. For example, in GridRunner it submits the runscript to a job scheduler instead of executing it locally.

Note

This method is used automatically during run() and should never be explicitly called in your script.

_run_job(job, jobmanager)[source]¶

This method aggregates these parts of run() that are supposed to be run in a separate thread in case of parallel job execution. It is wrapped with _in_thread() decorator.

This method should not be overridden.

Subclass of JobRunner that submits the runscript to a job scheduler instead of executing it locally. Besides two new keyword arguments (grid and sleepstep) and different call() method it behaves and is meant to be used just like regular JobRunner.

There are many different job schedulers that are popular and widely used nowadays (for example TORQUE, SLURM, OGE). Usually they use different commands for submitting jobs or checking queue status. This class tries to build a common and flexible interface for all those tools. The idea is that commands used to communicate with job scheduler are not rigidly hard-coded but dynamically taken from a Settings instance instead. Thanks to that user has almost full control over the behavior of GridRunner.

So the behavior of GridRunner is determined by the contents of Settings instance stored in its settings attribute. This Settings instance can be manually supplied by the user or taken from a collection of predefined behaviors stored as branches of config.gridrunner. The adjustment is done via grid parameter that should be either string or Settings. If string, it has to be a key occurring in config.gridrunner (or 'auto' for autodetection). For example, if grid='slurm' is passed, config.gridrunner.slurm is linked as settings. If grid is 'auto', entries in config.gridrunner are tested one by one and the first one that works (its submit command is present on your system) is chosen. When a Settings instance is passed it gets plugged directly as settings.

Currently two predefined job schedulers are available (see plams_defaults.py): slurm for SLURM and pbs for job schedulers following PBS syntax (PBS, TORQUE, Oracle Grid Engine etc.).

The Settings instance used for GridRunner should have the following structure:

• .output – flag for specifying output file path.
• .error – flag for specifying error file path.
• .workdir – flag for specifying path to working directory.
• .commands.submit – submit command.
• .commands.check – queue status check command.
• .commands.getid – function extracting submitted job’s ID from output of submit command.
• .commands.finished – function checking if submitted job is finished. It should take a single string (job’s ID) and return boolean.
• .commands.special. – branch storing definitions of special run() keyword arguments.

See call() for more technical details and examples.

The sleepstep parameter defines how often the job is checked for being finished. It should be an integer value telling how many seconds should the interval between two checks last. If None, the global default from config.sleepstep is copied.

call(runscript, workdir, out, err, runflags, **kwargs)[source]¶

Submit runscript to the job scheduler with workdir as the working directory. Redirect output and error streams to out and err, respectively. runflags stores submit command options.

The submit command has the following structure. Underscores denote spaces, parts in pointy brackets correspond to settings entries, parts in curly brackets to call() arguments, square brackets contain optional parts:

<.commands.submit>_<.workdir>_{workdir}_<.error>_{err}[_<.output>_{out}][FLAGS]_{runscript}

Output part is added if out is not None. This is handled automatically based on .runscript.stdout_redirect value in job’s settings.

FLAGS part is built based on runflags argument, which is a dictionary storing run() keyword arguments. For every (key,value) pair in runflags the string _-key_value is appended unless key is a special key occurring in .commands.special.. In that case _<.commands.special.key>value is used (mind the lack of space in between!). For example, a Settings instance defining interaction with SLURM job scheduler stored in config.gridrunner.slurm has the following entries:

.workdir = '-D'
.output  = '-o'
.error   = '-e'
.special.nodes    = '-N '
.special.walltime = '-t '
.special.queue    = '-p '
.commands.submit  = 'sbatch'
.commands.check   = 'squeue -j '

The submit command produced in such case:

>>> gr = GridRunner(parallel=True, maxjobs=4, grid='slurm')
>>> j.run(jobrunner=gr, queue='short', nodes=2, J='something', O='')

will be:

sbatch -D {workdir} -e {err} -o {out} -p short -N 2 -J something -O  {runscript}

In some job schedulers some flags don’t have a short form with semantics -key value. For example, in SLURM the flag --nodefile=value have a short form -F value, but the flag --export=value does not. One can still use such a flag using special keys mechanism:

>>> gr = GridRunner(parallel=True, maxjobs=4, grid='slurm')
>>> gr.settings.special.export = '--export='
>>> j.run(jobrunner=gr, queue='short', export='value')
sbatch -D {workdir} -e {err} -o {out} -p short --export=value {runscript}

The submit command produced in the way explained above is then executed and returned output is used to determine submitted job’s ID. Function stored in .commands.getid is used for that purpose, it should take one string (whole output) and return a string with job’s ID.

Now the method waits for the job to finish. Every sleepstep seconds it queries the job scheduler using following algorithm:

• if a key finished exists in .commands. it is used. It should be a function taking job’s ID and returning True or False.
• otherwise a string stored in .commands.check is concatenated with job’s ID (with no space between) and such command is executed. Nonzero exit status indicates that job is no longer in job scheduler hence it is finished.

Since it is difficult (on some systems even impossible) to automatically obtain job’s exit code, the returned value is always 0. From run() perspective it means that a job executed with GridRunner is never crashed.

Note

This method is used automatically during run() and should never be explicitly called in your script.

_autodetect()[source]¶

Try to autodetect the type of job scheduler.

The autodetection mechanism is very simple. For each entry in config.gridrunner the submit command followed by --version is executed (for example qsub --version). If the execution was successful (which is indicated by exit code 0) the job scheduler of corresponding type is present on the system and it is chosen. So if there are multiple different job schedulers installed, only one is picked – the one which “name” (indicated by a key in config.gridrunner) is first in the lexicographical order.

Returned value is one of config.gridrunner branches. If autodetection was not successful, an exception is raised.