Draft slide decks for parts 1 and 2.

docs/programmers/tutorials/bottom-up/gc3.sty

@@ -71,7 +71,7 @@
     procnamestyle=\bfseries\color{BrickRed},%
     procnamekeys={def},%
     stringstyle=\color{MidnightBlue},%
-    showstringspaces=true,%
+    showstringspaces=false,%
     emph={self},%
     emphstyle=\bfseries\color{gray},%
     % --- escaping and special displays ---

docs/programmers/tutorials/index.rst

@@ -32,6 +32,17 @@ to extend and adapt the examples provided.
   A presentation of the training material and outline of the course.
   Probably not much useful unless you're actually sitting in class.
 
+`Overview of GC3Pie use cases <https://github.com/uzh/gc3pie/tree/training-july-2016/docs/programmers/tutorials/workflows/part01.pdf>`_
+
+  A quick overview of the kind of computational use cases that GC3Pie
+  can easily solve.
+
+`GC3Pie basics <https://github.com/uzh/gc3pie/tree/training-july-2016/docs/programmers/tutorials/workflows/part02.pdf>`_
+
+  The basics needed to write simple GC3Pie scripts: the minimal
+  session-based script scaffolding, and the properties and features of
+  the `Application`:class: object.
+
 
 A bottom-up introduction to programming with GC3Pie
 ---------------------------------------------------

docs/programmers/tutorials/workflows/day1.py

@@ -0,0 +1,19 @@
+#! /usr/bin/env python
+
+import os
+import sys
+
+from gc3libs.cmdline import SessionBasedScript
+
+if __name__ == '__main__':
+    from day1 import AScript
+    AScript().run()
+
+class AScript(SessionBasedScript):
+    """
+    Minimal workflow scaffolding.
+    """
+    def __init__(self):
+      super(AScript, self).__init__(version='1.0')
+    def new_tasks(self, extra):
+      return []

docs/programmers/tutorials/workflows/gc3.sty

@@ -71,7 +71,7 @@
     procnamestyle=\bfseries\color{BrickRed},%
     procnamekeys={def},%
     stringstyle=\color{MidnightBlue},%
-    showstringspaces=true,%
+    showstringspaces=false,%
     emph={self},%
     emphstyle=\bfseries\color{gray},%
     % --- escaping and special displays ---

docs/programmers/tutorials/workflows/grayscale_app.py

@@ -0,0 +1,16 @@
+from gc3libs import Application
+
+class GrayscaleApp(Application):
+  """Convert an image file to grayscale."""
+  def __init__(self, img):
+    inp = basename(img)
+    out = "gray-" + inp
+    Application.__init__(
+      self,
+      arguments=[
+        "convert", inp, "-colorspace", "gray", out],
+      inputs=[img],
+      outputs=[out],
+      output_dir="grayscale.d",
+      stdout="stdout.txt",
+      stderr="stderr.txt")

docs/programmers/tutorials/workflows/make_state_graph.py

@@ -0,0 +1,31 @@
+#! /usr/bin/env python
+
+from graphviz import Digraph
+
+desc = [#('UNKNOWN',       ()),
+        ('NEW',           ('SUBMITTED', 'RUNNING')),
+        ('SUBMITTED',     ('RUNNING',)),
+        ('RUNNING',       ('TERMINATING', 'STOPPED',)),
+        ('TERMINATING',   ('TERMINATED',)),
+        ('TERMINATED',    ()),
+        ('STOPPED',       ())]
+
+for n in range(len(desc)):
+    refstate = desc[n][0]
+    g = Digraph(comment='GC3Pie Application states: ' + refstate)
+    for k, (state, transitions) in enumerate(desc):
+        attrs = { 'shape': 'box' }
+        if not transitions and state != 'UNKNOWN':
+            attrs['rank'] = 'max'
+            attrs['shape'] = 'house'
+        if n == k:
+            attrs['style'] = 'filled'
+            attrs['fillcolor'] = 'antiquewhite'
+        g.node(state, **attrs)
+        for next_state in transitions:
+            g.edge(state, next_state)
+            #if state != 'UNKNOWN':
+            #    g.edge(state, 'UNKNOWN', constraint='false')
+
+    out = 'states-' + refstate
+    g.render(out, view=False, cleanup=True)

docs/programmers/tutorials/workflows/part01.tex

@@ -0,0 +1,146 @@
+\documentclass[english,serif,mathserif,xcolor=pdftex,dvipsnames,table]{beamer}
+\usetheme{gc3}
+
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage{babel}
+
+\usepackage{gc3}
+
+\title[Introduction]{%
+  Overview of common GC3Pie use cases
+}
+\author[R. Murri, S3IT UZH]{%
+  Riccardo Murri \texttt{<riccardo.murri@uzh.ch>}
+  \\[1ex]
+  \emph{S3IT: Services and Support for Science IT}
+  \\[1ex]
+  University of Zurich
+}
+\date{July~11--14, 2016}
+
+\begin{document}
+
+% title frame
+\maketitle
+
+\begin{frame}
+  \frametitle{What is GC3Pie?}
+  GC3Pie is \ldots
+  \begin{enumerate}
+  \item \alert<1>{An \emph{opinionated} Python framework for defining and running computational workflows;}
+  \item A \emph{rapid development toolkit} for running user applications on clusters and IaaS cloud resources;
+  \item The worst name ever given to a middleware piece\ldots
+  \end{enumerate}
+
+  \+
+  As \emph{developers}, \alert<1>{you're mostly interested in this part.}
+\end{frame}
+
+
+\begin{frame}[fragile]
+  \frametitle{Uses of GC3Pie: parameter sweep}
+
+  You have a simulation code that is dependent on a number of parameters.
+
+  \+
+  Run the code for all possible combinations of parameters.
+
+  \+
+  Then collect all the outputs and post-process to get a
+  statistical overview.
+\end{frame}
+
+
+\begin{frame}[fragile]
+  \frametitle{Uses of GC3Pie: model calibration}
+
+  You have a simulation code that is dependent on a number of parameters.
+
+  \+
+  Run the code for all possible combinations of parameters, and
+  find the ones that ``best'' approximate a given experimental result.
+\end{frame}
+
+
+\begin{frame}[fragile]
+  \frametitle{Uses of GC3Pie: parallel processing}
+
+  Run the same program over and over again,
+  feeding it different input files each time.
+
+  \+
+  Then collect all the outputs and post-process to get a
+  statistical overview.
+\end{frame}
+
+
+\begin{frame}[fragile]
+  \frametitle{Uses of GC3Pie: parallel processing}
+  (At times, you chop a large input file into pieces and process each one separately instead.)
+
+  \+
+  \begin{quote}
+    ``For example, say we have a de novo assembly of 100,000
+    contigs. If we run 1 BLAST job against NR it could take as long as
+    50,000 minutes/35 days!! (30sec/query sequence), however if we
+    split this job into subsets of 5,000 sequences and ran 20 jobs in
+    "parallel" on a cluster, our total run-time is reduced to only 41
+    hours.''
+  \end{quote}
+  \begin{references}
+    \url{http://sfg.stanford.edu/BLAST.html}
+  \end{references}
+\end{frame}
+
+
+\begin{frame}
+  \frametitle{Uses of GC3Pie: workflows}
+
+  \begin{center}
+    Orchestrate execution of several applications:
+    some steps may run in parallel, some might need to be sequenced.
+
+    \+
+    \includegraphics[width=0.70\textwidth]{fig/warholize-wkf}
+  \end{center}
+\end{frame}
+
+
+\begin{frame}
+  \frametitle{A typical high-throughput script structure}
+
+  \begin{enumerate}
+  \item Initialize computational resources
+  \item Prepare programs and inputs for submission
+  \item Submit tasks
+  \item Monitor task status (loop)
+  \item Retrieve results
+  \item Postprocess and display
+  \end{enumerate}
+\end{frame}
+
+
+\begin{frame}
+  \frametitle{What GC3Pie handles for you}
+
+  \begin{enumerate}\small
+  \item Resource allocation (e.g. starting new instances on
+    ScienceCloud)
+  \item Selection of resources for each application in the session
+  \item Data transfer (e.g. copying input files in the new instances)
+  \item Remote execution of the application
+  \item Retrieval of results (e.g. copying output files from the
+    running instance)
+  \item De-allocation of resources
+  \end{enumerate}
+
+\end{frame}
+
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End: