[Swift-commit] r8197 - www/ATPESC_2014/swift-t
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Thu Aug 14 12:28:59 CDT 2014
Author: wozniak
Date: 2014-08-14 12:28:59 -0500 (Thu, 14 Aug 2014)
New Revision: 8197
Added:
www/ATPESC_2014/swift-t/tutorial.html
Log:
Adding swift-t/tutorial.html
Added: www/ATPESC_2014/swift-t/tutorial.html
===================================================================
--- www/ATPESC_2014/swift-t/tutorial.html (rev 0)
+++ www/ATPESC_2014/swift-t/tutorial.html 2014-08-14 17:28:59 UTC (rev 8197)
@@ -0,0 +1,1161 @@
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+<body class="article" style="max-width:750px">
+<div id="header">
+<h1>Tutorial: Swift/T</h1>
+<div id="toc">
+ <div id="toctitle">Table of Contents</div>
+ <noscript><p><b>JavaScript must be enabled in your browser to display the table of contents.</b></p></noscript>
+</div>
+</div>
+<div id="content">
+<div id="preamble">
+<div class="sectionbody">
+<div class="paragraph"><p>This tutorial will walk through 4 examples of the use of Swift/T, in
+addition to a molecular dynamics example.</p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_swift_t_materials">Swift/T materials</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>For more information on Swift/T, see:</p></div>
+<div class="ulist"><ul>
+<li>
+<p>
+<a href="http://swift-lang.org/Swift-T">Swift/T home</a>
+</p>
+</li>
+<li>
+<p>
+<a href="http://swift-lang.org/Swift-T/guide.html">Swift/T user guide</a>
+</p>
+</li>
+</ul></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_files">Files</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>The examples are in the <code>examples/</code> directory.</p></div>
+<div class="paragraph"><p>Each example directory is numbered from <code>01</code> to <code>05</code>.</p></div>
+<div class="paragraph"><p>Configuration files are in <code>cfg/</code>. These refer to public
+installations of Swift/T on Cetus/Mira.</p></div>
+<div class="paragraph"><p>Each example contains a <code>*.swift</code> Swift script that is the Swift
+program. The Swift/T compiler <code>stc</code> translates the Swift script into
+an MPI program encoded in a <code>*.tcl</code> file. This is launched by using
+the <code>turbine</code> program or a scheduler-specific script, such as the
+provided <code>turbine-cobalt-run.zsh</code> script.</p></div>
+<div class="paragraph"><p>There is also a <code>run-local</code> script to run the Swift script
+on the login node and a <code>run-compute</code> script to submit the Swift
+program to Cobalt. These scripts add <code>stc</code> and <code>turbine</code> entries to
+your <code>PATH</code> automatically.</p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_swift_t_installations">Swift/T installations</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>Two Swift/T installations are provided- one that runs on the login
+node and one that runs on the compute nodes (via Cobalt). The login
+node installation should be used with caution- expensive computation
+will impact other users on the login nodes.</p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_examples">Examples</h2>
+<div class="sectionbody">
+<div class="sect2">
+<h3 id="_01_hello_world">01 Hello world</h3>
+<div class="paragraph"><p>This is a very simple Swift/T program that illustrates Swift/T usage.</p></div>
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+<code>cd</code> into the directory <code>01-hello</code>
+</p>
+</li>
+<li>
+<p>
+Run:
+</p>
+<div class="listingblock">
+<div class="content">
+<pre><code>./run-local.sh</code></pre>
+</div></div>
+</li>
+<li>
+<p>
+This program is a simple Hello World example.
+</p>
+<div class="listingblock">
+<div class="content">
+<pre><code>/**
+ Example 1 - HELLO.SWIFT
+*/
+
+import io;
+
+main
+{
+ printf("Hello world!");
+}</code></pre>
+</div></div>
+</li>
+<li>
+<p>
+Run:
+</p>
+<div class="listingblock">
+<div class="content">
+<pre><code>./run-compute.sh</code></pre>
+</div></div>
+<div class="paragraph"><p>This will report something like:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>SETTINGS=../../cfg/settings-compute.sh
+TURBINE_OUTPUT=/home/user/turbine-output/2014/08/14/10/06/20
+SCRIPT_NAME=hello.tcl
+NODES=2
+project: ATPESC2014
+JOB_ID=312170</code></pre>
+</div></div>
+<div class="paragraph"><p>Turbine will copy <code>hello.tcl</code> to <code>TURBINE_OUTPUT</code> and run from that
+directory. The Cobalt log may be found there. Standard output is
+directed to <code>TURBINE_OUTPUT/output.txt</code>.</p></div>
+<div class="paragraph"><p>The contents of <code>output.txt</code> are the Blue Gene runtime output plus the
+Swift-generated line:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>stdout[0]: Hello world!</code></pre>
+</div></div>
+</li>
+</ol></div>
+</div>
+<div class="sect2">
+<h3 id="_02_loop">02 Loop</h3>
+<div class="paragraph"><p>This example shows one way to obtain concurrency from Swift/T.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>/**
+ Example 2 - LOOP.SWIFT
+*/
+
+import io;
+
+ at dispatch=WORKER
+(int j) compute(int i) "turbine" "0.0"
+[
+----
+ after [ expr <<i>> * 1000 ]
+ puts "compute: <<i>> [ expr [clock seconds] % 1000]"
+ set <<j>> [ expr <<i>> * 2 ]
+----
+];
+
+main
+{
+ printf("Running loop...");
+ foreach i in [0:9]
+ {
+ j = compute(i);
+ printf("compute(%i) = %i", i, j);
+ }
+}</code></pre>
+</div></div>
+<div class="paragraph"><p>The program executes <code>compute()</code> 10 times concurrently, because the
+Swift <code>foreach</code> loop is concurrent. The <code>compute()</code> function is
+implemented as a Tcl fragment that does 3 things:</p></div>
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+Delay progress with <code>after</code> (sleeps for <code>i*1000</code> milliseconds)
+</p>
+</li>
+<li>
+<p>
+Print a timestamp for reference
+</p>
+</li>
+<li>
+<p>
+Set a result value
+</p>
+</li>
+</ol></div>
+<div class="paragraph"><p>The result value is printed by Swift’s <code>printf()</code>.</p></div>
+<div class="paragraph"><p>Note the use of the <code><<<code>x</code>>></code> syntax, which maps Swift variable <code>x</code> to a
+Tcl variable.</p></div>
+<div class="paragraph"><p>This script may be run as the Hello World case, but the run scripts
+accept Turbine runtime arguments:</p></div>
+<div class="dlist"><dl>
+<dt class="hdlist1">
+<code>-l</code>
+</dt>
+<dd>
+<p>
+Prepend outputs with the MPI rank number (like <code>mpiexec -l</code>)
+</p>
+</dd>
+<dt class="hdlist1">
+<code>-n N</code>
+</dt>
+<dd>
+<p>
+Run <code>N</code> MPI processes (like <code>mpiexec -n N</code>). Note that one
+process is dedicated for Swift logic, so choose <code>N>1</code>.
+</p>
+</dd>
+</dl></div>
+<div class="paragraph"><p>Add more processes and see how that improves time to job
+completion. Check <code>output.txt</code> for the <code>ADLB Total Elapsed Time:</code>,
+which is a good measure of total execution time (discounts queue and
+allocation startup/shutdown time).</p></div>
+<div class="admonitionblock">
+<table><tr>
+<td class="icon">
+<div class="title">Note</div>
+</td>
+<td class="content">Ease of calling to Tcl makes for ease of calling to native code,
+as shown in the next example.</td>
+</tr></table>
+</div>
+</div>
+<div class="sect2">
+<h3 id="_03_blas">03 BLAS</h3>
+<div class="paragraph"><p>In this example, we use Swift to call a BLAS routine for dot product.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>/**
+ Example 3 - DOT.SWIFT
+*/
+
+// Swift/T libraries:
+import blob;
+import io;
+import matrix;
+
+// BLAS library for this example:
+import blas;
+
+main
+{
+ // Swift floats are 64-bit
+ float A[];
+ float B[];
+ int N = 3;
+ foreach i in [0:N-1]
+ {
+ A[i] = itof(i); // integer-to-float
+ B[i] = itof(i+1);
+ }
+
+ // Use => for output ordering
+ printf("A") =>
+ vector_print(A) =>
+ printf("\nB") =>
+ vector_print(B)
+ =>
+ float z = blas_ddot(N, A, B);
+
+ printf("\nA*B=%0.1f", z);
+}</code></pre>
+</div></div>
+<div class="paragraph"><p>In this example, we created a stub of a Swift BLAS library in
+<code>blas.swift</code>. This calls the CBLAS <code>cblas_ddot()</code> function through a
+Tcl interface.</p></div>
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+Run:
+</p>
+<div class="listingblock">
+<div class="content">
+<pre><code>./build.sh</code></pre>
+</div></div>
+<div class="paragraph"><p>This creates a Tcl package for BLAS (using a hand-coded method- we
+could also use <a href="http://swig.org">SWIG</a> to automate this).</p></div>
+</li>
+<li>
+<p>
+Run <code>./run-*.sh</code>.
+</p>
+</li>
+</ol></div>
+<div class="paragraph"><p>In <code>dot.swift</code>, the Swift statement <code>import blas;</code> brings <code>blas.swift</code>
+into the program. The Swift call to <code>blas_ddot()</code> operates on the
+Swift arrays <code>A</code> and <code>B</code>. In <code>blas.swift</code>, the Swift arrays are
+converted to C-compatible arrays of <code>double</code>, which are represented in
+Swift/T with the <code>blob</code> type. These are passed to the BLAS package.</p></div>
+<div class="paragraph"><p>Thus, calling native code from Swift/T is comparable in complexity to
+calling native code from other scripting languages such as Tcl or
+Python.</p></div>
+</div>
+<div class="sect2">
+<h3 id="_04_python">04 Python</h3>
+<div class="paragraph"><p>Another good way to call native code and bind it together in a script
+is through Python. Swift/T has convenient interfaces for Python, Tcl,
+R, Julia, and Qt Script (and the shell). In this example, we call
+into Python and its numerical package Numpy, which uses BLAS
+internally for numerical operations.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>/**
+ Example 4 - ADD.SWIFT
+*/
+
+// Swift/T libraries:
+import io;
+import python;
+import string;
+
+// This example: See ./numpy.swift
+import numpy;
+
+f()
+{
+ python(
+----
+print("Python works!")
+repr(0)
+----);
+}
+
+main
+{
+ f();
+ matrix A1 = eye(3);
+ matrix A2 = eye(3);
+ matrix sum = add(A1, A2);
+ printf("2*eye(3)=%s", sum);
+}</code></pre>
+</div></div>
+<div class="paragraph"><p>In this example, we also created a stub Swift numerical library in
+<code>numpy.swift</code>. This is imported into the main Swift script
+<code>add.swift</code>.</p></div>
+<div class="paragraph"><p>First, this program calls <code>f()</code>, which is a simple use of the
+Swift/T-Python interface. The Python code fragment must return a
+value in its last line as a string- in this case, we return <code>"0"</code>.</p></div>
+<div class="paragraph"><p>Second, we use the <code>numpy.swift</code> features. We allocate 2 Numpy arrays
+<em>I<sub>3</sub></em> and add them together, producing <em>2I<sub>3</sub></em>.</p></div>
+<div class="paragraph"><p>Swift/T can call into arbitrary Python modules, just set <code>PYTHONPATH</code>.
+C/C++ code can be easily wrapped for Python with
+<a href="http://swig.org">SWIG</a>, Fortran code with SciPy’s
+<a href="http://wiki.scipy.org/Cookbook/F2Py">F2PY</a>.</p></div>
+<div class="paragraph"><p><strong><span class="red">★</span></strong> Thus, a variety of scripts and
+libraries can be easily integrated with Swift/T and run concurrently
+on massive computers like the Blue Gene/Q!</p></div>
+</div>
+<div class="sect2">
+<h3 id="_05_molecular_dynamics">05 Molecular dynamics</h3>
+<div class="paragraph"><p>In our most realistic example, we bundle a small molecular dynamics
+simulator <a href="http://people.sc.fsu.edu/~jburkardt/c_src/md/md.html">MD</a> for
+Swift/T and call it concurrently.</p></div>
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+<code>cd</code> to <code>examples/md-src/</code> and run:
+</p>
+<div class="listingblock">
+<div class="content">
+<pre><code>make</code></pre>
+</div></div>
+<div class="paragraph"><p>This builds the stand-alone <code>md</code> program. You can test it with
+<code>test-md-*.sh</code>.
+2. Run:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>make swift-pkg</code></pre>
+</div></div>
+<div class="paragraph"><p>This builds the Tcl package by:</p></div>
+<div class="olist loweralpha"><ol class="loweralpha">
+<li>
+<p>
+Running SWIG to expose the core <code>simulate()</code> function to Tcl;
+</p>
+</li>
+<li>
+<p>
+Compiling the SWIG-generated wrapper code and linking it as a Tcl
+package.
+</p>
+<div class="paragraph"><p>You can test the Tcl function with <code>./test-md.tcl</code>, which simply loads
+the package and calls <code>simulate</code> once.</p></div>
+</li>
+</ol></div>
+</li>
+<li>
+<p>
+<code>cd</code> back to <code>examples/05-md/</code>.
+</p>
+</li>
+<li>
+<p>
+The <code>md.swift</code> library shows the calling sequence for MD.
+</p>
+</li>
+<li>
+<p>
+The <code>run-md.swift</code> script shows how to call MD once. The output
+files are indicated in the script, in addition to the usual
+<code>output.txt</code>. Run this with <code>./run-*-md.sh</code>.
+</p>
+</li>
+<li>
+<p>
+A concurrent ensemble of simulations is launched by
+<code>run-mds.swift</code>. This script accepts many arguments on the command
+line: see <code>run-*-mds.sh</code>.
+</p>
+</li>
+</ol></div>
+</div>
+</div>
+</div>
+</div>
+<div id="footnotes"><hr /></div>
+<div id="footer">
+<div id="footer-text">
+Last updated 2014-08-14 11:32:40 CDT
+</div>
+</div>
+</body>
+</html>
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