Readthedocs documentation

docs/.gitignore

@@ -0,0 +1,3 @@
+build
+_static
+_templates

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = SmartDispatch
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/autoresume.rst

@@ -0,0 +1,14 @@
+====================
+Automatic resumption
+====================
+
+Oftentimes, there is a hard limit on maximum amount of time you can run your
+job for on the cluster (we refer to it as **walltime**). Smart Dispatch allows you
+to partially overcome that and run your tasks for longer periods. This is done
+by enchancing generated PBS files with additional code that reschedules your
+tasks as soon as they hit the walltime. The caveat here is that your tasks
+**must be resumable**, i.e. be capable of restoring their state after being
+killed and rerun.
+
+You can engage the autoresumption by passing ``-m`` or ``--autoresume`` during
+``smart-dispatch`` execution. See :doc:`usage` for details. 

docs/source/conf.py

@@ -0,0 +1,156 @@
+# -*- coding: utf-8 -*-
+#
+# Smart Dispatch documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb 17 15:44:10 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinxcontrib.autoprogram']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Smart Dispatch'
+copyright = u'2017, Stanislas Lauly, Marc-Alexandre Côté, Mathieu Germain'
+author = u'Stanislas Lauly, Marc-Alexandre Côté, Mathieu Germain'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'2.0'
+# The full version, including alpha/beta/rc tags.
+release = u'2.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SmartDispatchdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'SmartDispatch.tex', u'Smart Dispatch Documentation',
+     u'Stanislas Lauly, Marc-Alexandre Côté, Mathieu Germain', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'smartdispatch', u'Smart Dispatch Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'SmartDispatch', u'Smart Dispatch Documentation',
+     author, 'SmartDispatch', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/source/examples.rst

@@ -0,0 +1,62 @@
+========
+Examples
+========
+
+Launch job
+----------
+
+::
+
+  smart-dispatch -q qtest@mp2 launch python my_script.py 2 80 tanh 0.1
+
+Will launch ``python my_script.py 2 80 tanh 0.1`` on the queue ``qtest@mp2``.
+
+
+Launch batch of jobs
+--------------------
+
+Automatically generate commands from combinations of arguments. ::
+
+  smart-dispatch -q qtest@mp2 launch python my_script.py [1 2] 80 [tanh sigmoid] 0.1
+
+Will generate 4 different commands and launch them on the queue ``qtest@mp2``: ::
+
+  python my_script.py 1 80 sigmoid 0.1
+  python my_script.py 1 80 tanh 0.1
+  python my_script.py 2 80 sigmoid 0.1
+  python my_script.py 2 80 tanh 0.1
+
+
+Another possiblility is to generate argument from a range. ::
+
+  smart-dispatch -q qtest@mp2 launch python my_script.py [1:4]
+
+Will generate: ::
+
+  python my_script.py 1
+  python my_script.py 2
+  python my_script.py 3
+
+You can also add a step size to the range as the 3rd argument. ::
+
+  smart-dispatch -q qtest@mp2 launch python my_script.py [1:10:2]
+
+Will generate: ::
+
+  python my_script.py 1
+  python my_script.py 3
+  python my_script.py 5
+  python my_script.py 7
+  python my_script.py 9
+
+
+Resuming job/batch
+------------------
+
+::
+
+  smart-dispatch -q qtest@mp2 resume {batch_id}
+
+Jobs that did not terminate properly, for example, it exceeded the walltime, can be resumed using the ``{batch_id}`` given to you upon launch. Of course, all this assuming your script is resumable.
+
+*Note: Jobs are always in a batch, even if it's a batch of one.*

docs/source/index.rst

@@ -0,0 +1,40 @@
+Welcome to Smart Dispatch's documentation!
+==========================================
+
+Smart Dispatch is an easy to use job launcher for supercomputers with PBS compatible job manager.
+
+Features
+--------
+  * Launch multiple jobs with a single line.
+  * Automatically generate combinations of arguments. See :doc:`examples`.
+  * Automatic resources management. Determine for you the optimal fit for your commands on nodes.
+  * Resume batch of commands.
+  * Easily manage logs.
+  * Advanced mode for complete control.
+  * Use automatic rescheduling of jobs that hit the walltime. See :doc:`autoresume`.
+
+
+Installing
+----------
+
+Use ``pip`` package manager: ::
+
+  pip install git+https://github.com/SMART-Lab/smartdispatch
+
+
+Contents
+--------
+
+.. toctree::
+  :maxdepth: 2
+
+  usage
+  examples
+  autoresume
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

docs/source/usage.rst

@@ -0,0 +1,76 @@
+=====
+Usage
+=====
+
+.. autoprogram:: scripts/smart-dispatch:get_parser()
+  :prog: smart-dispatch
+
+
+Hierarchy of generated files
+----------------------------
+
+In order to understand the contents of the generated folders/files, it's good to know how ``smart-dispatch`` deals with **commands** that a user requests to launch on the cluster:
+
+* Each invokation of ``smart-dispatch`` creates a so-called **batch** of **jobs**. Smart Dispatch will do its best to create as many simultaneous jobs so as to effecitvely utilze the allocated resources.
+* Each job is basically a single PBS file that is run by the queue management system on the cluster (either ``msub`` or ``qsub``).
+* A job spawns mulitple concurrent **workers** that all cooperate to execute the requested commands.
+* Each worker (basically, a python script) is executing commands sequentially.
+
+A typical hierarchy of ``./SMART_DISPATCH_LOGS/{batch_id}/`` should look like this: ::
+
+  commands/
+      job_commands_0.sh
+      job_commands_1.sh
+      ...
+      commands.txt
+      running_commands.txt
+      failed_commands.txt
+  logs/
+      job/
+          150472.gpu-srv1.helios.err
+          150472.gpu-srv1.helios.out
+          ...
+      worker/
+          150472.gpu-srv1.helios_worker_0.e
+          150472.gpu-srv1.helios_worker_0.o
+          150472.gpu-srv1.helios_worker_1.e
+          150472.gpu-srv1.helios_worker_1.o
+          ...
+      4d501b8b9805796ee913153e2493d7069a8bfb1aa469a50279940752bf26c935.err
+      4d501b8b9805796ee913153e2493d7069a8bfb1aa469a50279940752bf26c935.out
+      ...
+  command_line.log
+  jobs_id.txt
+
+The root directory contains two files:
+
+``command_line.log``:
+    A full command that was used to invoke ``smart-dispatch``.
+``jobs_id.txt``:
+    A list of job IDs being run.
+
+Now let's go through the subdirectories.
+
+
+``commands/``
+^^^^^^^^^^^^^
+
+This directory holds generated PBS files (``job_commands_{pbs_index}.sh``) as well as three command lists:
+
+``commands.txt``:
+    A list pending commands (this is where the workers are taking their next commands to execute from).
+``running_commands.txt``:
+    A list of currently running commands.
+``failed_commands.txt``:
+    A list of failed commands.
+
+
+``logs/``
+^^^^^^^^^
+
+Output and error logs in are saved in this directory. The root level contains logs for actual commands. There are also two additional subfolder:
+
+``job/``:
+    Holds logs for the PBS files.
+``worker/``:
+    Holds logs for workers.

scripts/smart-dispatch

@@ -185,7 +185,7 @@ def main():
     print "\nLogs, command, and jobs id related to this batch will be in:\n {smartdispatch_folder}".format(smartdispatch_folder=path_job)
 
 
-def parse_arguments():
+def get_parser():
     parser = argparse.ArgumentParser()
     parser.add_argument('-q', '--queueName', required=True, help='Queue used (ex: qwork@mp2, qfat256@mp2, gpu_1)')
     parser.add_argument('-n', '--batchName', required=False, help='The name of the batch. Default: The commands launched.')
@@ -215,6 +215,11 @@ def parse_arguments():
     resume_parser.add_argument('--expandPool', type=int, nargs='?', const=sys.maxsize, help='Add workers to the given batch. Default: # pending jobs.')
     resume_parser.add_argument("batch_uid", help="Batch UID of the jobs to resume.")
 
+    return parser
+
+
+def parse_arguments():
+    parser = get_parser()
     args = parser.parse_args()
 
     # Check for invalid arguments in