cmd-queue 0.1.20__py3-none-any.whl → 0.2.1__py3-none-any.whl

cmd_queue-0.2.1.dist-info/METADATA

@@ -0,0 +1,746 @@
+Metadata-Version: 2.1
+Name: cmd_queue
+Version: 0.2.1
+Summary: The cmd_queue module for a DAG of bash commands
+Home-page: https://gitlab.kitware.com/computer-vision/cmd_queue
+Author: Kitware Inc., Jon Crall
+Author-email: kitware@kitware.com, jon.crall@kitware.com
+License: Apache 2
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Utilities
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
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+
+Command Queue - cmd_queue
+=========================
+
+.. ..  |Appveyor| |Codecov|
+
+|Pypi| |Downloads| |GitlabCIPipeline| |GitlabCICoverage| |ReadTheDocs|
+
+
++------------------+-------------------------------------------------------------------------------------+
+| Read the docs    | https://cmd-queue.readthedocs.io                                                    |
++------------------+-------------------------------------------------------------------------------------+
+| Gitlab           | https://gitlab.kitware.com/computer-vision/cmd_queue                                |
++------------------+-------------------------------------------------------------------------------------+
+| Pypi             | https://pypi.org/project/cmd_queue                                                  |
++------------------+-------------------------------------------------------------------------------------+
+| Slides           | https://docs.google.com/presentation/d/1BjJkjMx6bxu1uek-hAGpwj760u9rraVn7st8J5OsZME |
++------------------+-------------------------------------------------------------------------------------+
+
+
+This is a simple module for "generating" a bash script that schedules multiples
+jobs (in parallel if possible) on a single machine. There are 3 backends with
+increasing levels of complexity: serial, tmux, and slurm.
+
+In serial mode, a single bash script gets written that executes your jobs in
+sequence. There are no external dependencies
+
+In tmux mode, multiple tmux sessions get opened and each of them executes your
+independent parts of your jobs. Dependencies are handled.
+
+In slurm mode, a real heavy-weight scheduling algorithm is used. In this mode
+we simply convert your jobs to slurm commands and execute them.
+
+Under the hood we build a DAG based on your specified dependencies and use this
+to appropriately order jobs.
+
+By default, bash scripts that would execute your jobs print to the console.
+This gives the user fine-grained control if they only want to run a subset of a
+pipeline manually. But if asked to run, cmd_queue will execute the bash jobs.
+
+Features
+~~~~~~~~
+
+* Bash command scheduling
+
+* Execution is optional, can just print commands instead
+
+* No-parallelism always-available serial backend
+
+* Tmux based lightweight backend
+
+* Slurm based heavyweight backend
+
+* Python and Bash interface
+
+* Rich monitoring / live-control
+
+
+Installation
+============
+
+The cmd_queue package is available on pypi.
+
+.. code:: bash
+
+    pip install cmd_queue
+
+The serial queue backend will always work. To gain access other backends you
+must install their associated dependencies. The tmux backend is the easiest and
+simply requires that tmux is installed (e.g. ``sudo apt install tmux`` on
+Debian systems).
+
+Other backends require more complex setups. The slurm backend will require that
+`slurm is installed <https://slurm.schedmd.com/quickstart_admin.html>`_ and the
+daemon is running. The slurm backend is functional and tested, but improvements
+can still be made (help wanted). The airflow backend similarly requires a
+configured airflow server, but is not fully functional or tested (contributions
+to make airflow work / easier are wanted!).
+
+
+Tmux Queue Demo
+===============
+
+After installing, the following command runs a demo of the tmux queue:
+
+.. code:: bash
+
+   # Reproduce the
+   INTERACTIVE_TEST=1 xdoctest -m cmd_queue.tmux_queue TMUXMultiQueue.monitor:1
+
+
+This executes the following code, which creates two parallel tmux workers and
+submits several bash jobs with non-trivial dependencies.
+
+.. code:: python
+
+     # xdoctest: +REQUIRES(env:INTERACTIVE_TEST)
+     from cmd_queue.tmux_queue import *  # NOQA
+     # Setup a lot of longer running jobs
+     n = 2
+     self = TMUXMultiQueue(size=n, name='demo_cmd_queue')
+     first_job = None
+     for i in range(n):
+         prev_job = None
+         for j in range(4):
+            command = f'sleep 1 && echo "This is job {i}.{j}"'
+            job = self.submit(command, depends=prev_job)
+            prev_job = job
+            first_job = first_job or job
+    command = f'sleep 1 && echo "this is the last job"'
+    job = self.submit(command, depends=[prev_job, first_job])
+    self.print_commands(style='rich')
+    self.print_graph()
+    if self.is_available():
+        self.run(block=True, other_session_handler='kill')
+
+
+When running the ``print_commands`` command will first display all of the submitted
+commands that will be distributed across multiple new tmux sessions. These are
+the commands will be executed. This is useful for spot checking that your bash
+command templating is correct before the queue is executed with ``run``.
+
+
+.. .. Screenshot of the print_commands output
+.. image:: https://i.imgur.com/rVbyHzM.png
+   :height: 300px
+   :align: left
+
+
+The ``print_graph`` command will render the DAG to be executed using
+`network text <https://networkx.org/documentation/stable/reference/readwrite/generated/networkx.readwrite.text.write_network_text.html#networkx.readwrite.text.write_network_text>`_.
+And finally ``run`` is called with ``block=True``, which starts executing the
+DAG and displays progress and job status in rich or textual monitor.
+
+.. .. image:: https://i.imgur.com/RbyTvP9.png
+..   :height: 300px
+..   :align: left
+
+.. .. Animated gif of the queue from dev/record_demo.sh
+.. image:: https://i.imgur.com/4mxFIMk.gif
+   :height: 300px
+   :align: left
+
+
+While this is running it is possible to simply attach to a tmux sessions (e.g.
+``tmux a``) and inspect a specific queue while it is running. (We recommend
+using ``<ctrl-b>s`` inside of a tmux session to view and navigate through the
+tmux sessions). Unlike the slurm backend, the entire execution of the DAG is
+entirely transparent to the developer! The following screenshot shows the tmux
+sessions spawned while running this demo.
+
+.. .. Screenshot of the tmux sessions
+.. image:: https://i.imgur.com/46LRK8M.png
+   :height: 300px
+   :align: left
+
+By default, if there are no errors, these sessions will exit after execution
+completes, but this is configurable. Likewise if there are errors, the tmux
+sessions will persist to allow for debugging.
+
+
+Modivation
+==========
+Recently, I needed to run several jobs on 4 jobs across 2 GPUs and then execute
+a script after all of them were done. What I should have done was use slurm or
+some other proper queuing system to schedule the jobs, but instead I wrote my
+own hacky scheduler using tmux. I opened N (number of parallel workers) tmux
+sessions and then I ran independent jobs in each different sessions.
+
+This worked unreasonably well for my use cases, and it was nice to be able to effectively schedule jobs without heavyweight software like slurm on my machine.
+
+Eventually I did get slurm on my machine, and I abstracted the API of my
+tmux_queue to be a general "command queue" that can use 1 of 3 backends:
+serial, tmux, or slurm.
+
+
+Niche
+=====
+There are many DAG schedulers out there:
+
+ * airflow
+ * luigi
+ * submitit
+ * rq_scheduler
+
+
+The the niche for this is when you have large pipelines of bash commands that
+depend on each other and you want to template out those parameters with logic
+that you define in Python.
+
+We plan on adding an airflow backend.
+
+
+Usage
+=====
+
+
+There are two ways to use ``cmd_queue``:
+
+1. In Python create a Queue object, and then call the .submit method to pass it
+   a shell invocation. It returns an object that you can use to specify
+   dependencies of any further calls to .submit. This simply organizes all of
+   your CLI invocations into a bash script, which can be inspected and then
+   run. There are different backends that enable parallel execution of jobs
+   when dependencies allow.
+
+2. There is a way to use it via the CLI, with details shown in cmd_queue
+   --help. Usage is basically the same.  You create a queue, submit jobs to it,
+   you can inspect it, and you can run it.
+
+
+Example usage in Python:
+
+.. code:: python
+
+   import cmd_queue
+
+   # Create a Queue object
+   self = cmd_queue.Queue.create(name='demo_queue', backend='serial')
+
+   # Submit bash invocations that you want to run, and mark dependencies.
+   job1 = self.submit('echo hello')
+   job2 = self.submit('echo world', depends=[job1])
+   job3 = self.submit('echo foo')
+   job4 = self.submit('echo bar', depends=[job2, job3])
+   job5 = self.submit('echo spam', depends=[job1])
+
+   # Print a graph of job dependencies
+   self.print_graph()
+
+   # Display the simplified bash script to be executed.
+   self.print_commands()
+
+   # Execute the jobs
+   self.run()
+
+
+Example usage in the CLI:
+
+.. code:: bash
+
+    # Create a Queue
+    cmd_queue new "demo_cli_queue"
+
+    # Submit bash invocations that you want to run, and mark dependencies.
+    cmd_queue submit --jobname job1 "demo_cli_queue" -- echo hello
+    cmd_queue submit --jobname job2 --depends job1 "demo_cli_queue" -- echo world
+    cmd_queue submit --jobname job3 "demo_cli_queue" -- echo foo
+    cmd_queue submit --jobname job4 --depends job1,job2 "demo_cli_queue" -- echo bar
+    cmd_queue submit --jobname job5 --depends job1  "demo_cli_queue" -- echo spam
+
+    # Display the simplified bash script to be executed.
+    cmd_queue show "demo_cli_queue" --backend=serial
+
+    # Execute the jobs
+    cmd_queue run "demo_cli_queue" --backend=serial
+
+
+
+
+Examples
+========
+
+
+All of the dependency checking and book keeping logic is handled in bash
+itself. Write (or better yet template) your bash scripts in Python, and then
+use cmd_queue to "transpile" these sequences of commands to pure bash.
+
+
+.. code:: python
+
+   import cmd_queue
+
+   # Create a Queue object
+   self = cmd_queue.Queue.create(name='demo_queue', backend='serial')
+
+   # Submit bash invocations that you want to run, and mark dependencies.
+   job1 = self.submit('echo hello && sleep 0.5')
+   job2 = self.submit('echo world && sleep 0.5', depends=[job1])
+   job3 = self.submit('echo foo && sleep 0.5')
+   job4 = self.submit('echo bar && sleep 0.5')
+   job5 = self.submit('echo spam && sleep 0.5', depends=[job1])
+   job6 = self.submit('echo spam && sleep 0.5')
+   job7 = self.submit('echo err && false')
+   job8 = self.submit('echo spam && sleep 0.5')
+   job9 = self.submit('echo eggs && sleep 0.5', depends=[job8])
+   job10 = self.submit('echo bazbiz && sleep 0.5', depends=[job9])
+
+   # Display the simplified bash script to be executed.
+   self.print_commands()
+
+   # Execute the jobs
+   self.run()
+
+
+This prints the bash commands in an appropriate order to resolve dependencies.
+
+
+.. code:: bash
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_cc9d551e/demo_queue_2022-04-08_cc9d551e.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 10 - demo_queue-job-0
+    echo hello && sleep 0.5
+    #
+    ### Command 2 / 10 - demo_queue-job-1
+    echo world && sleep 0.5
+    #
+    ### Command 3 / 10 - demo_queue-job-2
+    echo foo && sleep 0.5
+    #
+    ### Command 4 / 10 - demo_queue-job-3
+    echo bar && sleep 0.5
+    #
+    ### Command 5 / 10 - demo_queue-job-4
+    echo spam && sleep 0.5
+    #
+    ### Command 6 / 10 - demo_queue-job-5
+    echo spam && sleep 0.5
+    #
+    ### Command 7 / 10 - demo_queue-job-6
+    echo err && false
+    #
+    ### Command 8 / 10 - demo_queue-job-7
+    echo spam && sleep 0.5
+    #
+    ### Command 9 / 10 - demo_queue-job-8
+    echo eggs && sleep 0.5
+    #
+    ### Command 10 / 10 - demo_queue-job-9
+    echo bazbiz && sleep 0.5
+
+
+The same code can be run in parallel by chosing a more powerful backend.
+The tmux backend is the lightest weight parallel backend.
+
+.. code:: python
+
+   # Need to tell the tmux queue how many processes can run at the same time
+   import cmd_queue
+   self = cmd_queue.Queue.create(size=4, name='demo_queue', backend='tmux')
+   job1 = self.submit('echo hello && sleep 0.5')
+   job2 = self.submit('echo world && sleep 0.5', depends=[job1])
+   job3 = self.submit('echo foo && sleep 0.5')
+   job4 = self.submit('echo bar && sleep 0.5')
+   job5 = self.submit('echo spam && sleep 0.5', depends=[job1])
+   job6 = self.submit('echo spam && sleep 0.5')
+   job7 = self.submit('echo err && false')
+   job8 = self.submit('echo spam && sleep 0.5')
+   job9 = self.submit('echo eggs && sleep 0.5', depends=[job8])
+   job10 = self.submit('echo bazbiz && sleep 0.5', depends=[job9])
+
+   # Display the "user-friendly" pure bash
+   self.print_commands()
+
+   # Display the real bash that gets executed under the hood
+   # that is independencly executable, tracks the success / failure of each job,
+   # and manages dependencies.
+   self.print_commands(1, 1)
+
+   # Blocking will display a job monitor while it waits for everything to
+   # complete
+   self.run(block=True)
+
+
+This prints the sequence of bash commands that will be executed in each tmux session.
+
+.. code:: bash
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_0_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 3 - demo_queue-job-7
+    echo spam && sleep 0.5
+    #
+    ### Command 2 / 3 - demo_queue-job-8
+    echo eggs && sleep 0.5
+    #
+    ### Command 3 / 3 - demo_queue-job-9
+    echo bazbiz && sleep 0.5
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_1_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 2 - demo_queue-job-2
+    echo foo && sleep 0.5
+    #
+    ### Command 2 / 2 - demo_queue-job-6
+    echo err && false
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_2_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 2 - demo_queue-job-0
+    echo hello && sleep 0.5
+    #
+    ### Command 2 / 2 - demo_queue-job-5
+    echo spam && sleep 0.5
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_3_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 1 - demo_queue-job-3
+    echo bar && sleep 0.5
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_4_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 1 - demo_queue-job-4
+    echo spam && sleep 0.5
+
+    # --- /home/joncrall/.cache/base_queue/demo_queue_2022-04-08_a1ef7600/queue_demo_queue_5_2022-04-08_a1ef7600.sh
+
+    #!/bin/bash
+    #
+    # Jobs
+    #
+    ### Command 1 / 1 - demo_queue-job-1
+    echo world && sleep 0.5
+
+
+
+Slurm mode is the real deal. But you need slurm installed on your machint to
+use it. Asking for tmux is a might ligher weight tool. We can specify slurm
+options here
+
+.. code:: python
+
+   import cmd_queue
+   self = cmd_queue.Queue.create(name='demo_queue', backend='slurm')
+   job1 = self.submit('echo hello && sleep 0.5', cpus=4, mem='8GB')
+   job2 = self.submit('echo world && sleep 0.5', depends=[job1], parition='default')
+   job3 = self.submit('echo foo && sleep 0.5')
+   job4 = self.submit('echo bar && sleep 0.5')
+   job5 = self.submit('echo spam && sleep 0.5', depends=[job1])
+   job6 = self.submit('echo spam && sleep 0.5')
+   job7 = self.submit('echo err && false')
+   job8 = self.submit('echo spam && sleep 0.5')
+   job9 = self.submit('echo eggs && sleep 0.5', depends=[job8])
+   job10 = self.submit('echo bazbiz && sleep 0.5', depends=[job9])
+
+   # Display the "user-friendly" pure bash
+   self.print_commands()
+
+   # Display the real bash that gets executed under the hood
+   # that is independencly executable, tracks the success / failure of each job,
+   # and manages dependencies.
+   self.print_commands(1, 1)
+
+   # Blocking will display a job monitor while it waits for everything to
+   # complete
+   self.run(block=True)
+
+
+This prints the very simple slurm submission script:
+
+.. code:: bash
+
+    # --- /home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/demo_queue-20220408T170615-a9e238b5.sh
+
+    mkdir -p "$HOME/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs"
+    JOB_000=$(sbatch --job-name="J0000-demo_queue-20220408T170615-a9e238b5" --cpus-per-task=4 --mem=8000 --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0000-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo hello && sleep 0.5' --parsable)
+    JOB_001=$(sbatch --job-name="J0002-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0002-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo foo && sleep 0.5' --parsable)
+    JOB_002=$(sbatch --job-name="J0003-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0003-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo bar && sleep 0.5' --parsable)
+    JOB_003=$(sbatch --job-name="J0005-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0005-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo spam && sleep 0.5' --parsable)
+    JOB_004=$(sbatch --job-name="J0006-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0006-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo err && false' --parsable)
+    JOB_005=$(sbatch --job-name="J0007-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0007-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo spam && sleep 0.5' --parsable)
+    JOB_006=$(sbatch --job-name="J0001-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0001-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo world && sleep 0.5' "--dependency=afterok:${JOB_000}" --parsable)
+    JOB_007=$(sbatch --job-name="J0004-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0004-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo spam && sleep 0.5' "--dependency=afterok:${JOB_000}" --parsable)
+    JOB_008=$(sbatch --job-name="J0008-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0008-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo eggs && sleep 0.5' "--dependency=afterok:${JOB_005}" --parsable)
+    JOB_009=$(sbatch --job-name="J0009-demo_queue-20220408T170615-a9e238b5" --output="/home/joncrall/.cache/slurm_queue/demo_queue-20220408T170615-a9e238b5/logs/J0009-demo_queue-20220408T170615-a9e238b5.sh" --wrap 'echo bazbiz && sleep 0.5' "--dependency=afterok:${JOB_008}" --parsable)
+
+
+
+.. |Pypi| image:: https://img.shields.io/pypi/v/cmd_queue.svg
+   :target: https://pypi.python.org/pypi/cmd_queue
+
+.. |Downloads| image:: https://img.shields.io/pypi/dm/cmd_queue.svg
+   :target: https://pypistats.org/packages/cmd_queue
+
+.. |ReadTheDocs| image:: https://readthedocs.org/projects/cmd-queue/badge/?version=release
+    :target: https://cmd-queue.readthedocs.io/en/release/
+
+.. # See: https://ci.appveyor.com/project/jon.crall/cmd_queue/settings/badges
+.. |Appveyor| image:: https://ci.appveyor.com/api/projects/status/py3s2d6tyfjc8lm3/branch/main?svg=true
+   :target: https://ci.appveyor.com/project/jon.crall/cmd_queue/branch/main
+
+.. |GitlabCIPipeline| image:: https://gitlab.kitware.com/computer-vision/cmd_queue/badges/main/pipeline.svg
+   :target: https://gitlab.kitware.com/computer-vision/cmd_queue/-/jobs
+
+.. |GitlabCICoverage| image:: https://gitlab.kitware.com/computer-vision/cmd_queue/badges/main/coverage.svg?job=coverage
+    :target: https://gitlab.kitware.com/computer-vision/cmd_queue/commits/main
+
+.. |CircleCI| image:: https://circleci.com/gh/Erotemic/cmd_queue.svg?style=svg
+    :target: https://circleci.com/gh/Erotemic/cmd_queue
+
+.. |Travis| image:: https://img.shields.io/travis/Erotemic/cmd_queue/main.svg?label=Travis%20CI
+   :target: https://travis-ci.org/Erotemic/cmd_queue
+
+.. |Codecov| image:: https://codecov.io/github/Erotemic/cmd_queue/badge.svg?branch=main&service=github
+   :target: https://codecov.io/github/Erotemic/cmd_queue?branch=main