Qsubmit

Wrapper for batch engine submission commands (a Python remake of Ondrej Bojar's Perl qsubmit).

This script attempts to abstract away from local batch engine quirks and create a unified job submission interface, wherever you run it. It also allows you to send commands instead of scripts into the queue, and you can easily request an interactive shell using the same set of options.

It's a work-in-progress, now only supporting the local settings at Charles University/UFAL (SLURM with local specific settings), with some (not up-to-date) support for the Son of Grid Engine (SGE) system and Grun as well as local execution (so you can run your script without a cluster engine and don't have to change your workflow much).

Usage

You can install the script using pip:

pip3 install git+https://github.com/ufal/qsubmit

Run the script to see the available options:

qsubmit -h

The basic command for executing a job is this:

qsubmit [modifiers] [-n job-name] [resources] command

As resources, you can specify:

--cpus/--cores -- the required number of CPUs
--gpus -- the required number of GPUs
--queue -- the target queue name
--mem -- the required CPU memory
--gpu-mem -- the required GPU memory

There are a few additional modifiers to qsubmit's behavior:

--hold/--wait <jobid> -- waits for a specified other job(s)
--logdir -- sets a target logfile directory (defaults to current directory)
--location/--engine -- setting for the cluster engine (location defaults to ufal, engine defaults to slurm). You can set the --engine to console to run locally.

In order to get an interactive shell instead of running a batch job, use

qsubmit --interactive [modifiers] [-n job-name] [resources]

Note that the command is empty in this case.

Qruncmd

Runs the line processing command (one input line for one output line) on SIZE-sized sections of stdin in parallel qsubmit jobs, and prints the outputs to stdout. It goes through the input only once and uses constant working disk space. It gives the original

It is a remake of the old perl qruncmd that got obsolete when ÚFAL cluster moved to slurm.

It is still work in progress. Only the case of non-failing jobs is implemented and tested.

Also, the case when the command does not produce the same number of lines as on input is not implemented. The assumption of the expected number of output lines is hard-coded in the current version.

Usage:

It has all the qsubmit parameters that define the parallel jobs, plus:

  --workdir WORKDIR     workdir, default is qruncmd-workdir-XXXXXXXXX where X stands for random a letter
  --jobs JOBS, --workers JOBS
                        How many workers to start. The workers concurrently wait for jobs (stdin sections saved to workdir), 
                        claim them, process and return the outputs.
  -s SIZE, --size SIZE  How many lines in one job section.

The basic usage command is like this:

cat large-train-data.txt | qruncmd "./slow-line-processing-tool" --jobs 50 -size 50000 > out

If anything fails, you can inspect the logs in workdir.

Contribution

If you like the idea and would like to add your own local settings to the mix, please do. Edit the code accordingly and send us a pull request!

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.