[Swift-commit] r8213 - www/ATPESC_2014/swift-t
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Thu Aug 14 14:44:54 CDT 2014
Author: wozniak
Date: 2014-08-14 14:44:54 -0500 (Thu, 14 Aug 2014)
New Revision: 8213
Modified:
www/ATPESC_2014/swift-t/tutorial.html
Log:
Minor fix
Modified: www/ATPESC_2014/swift-t/tutorial.html
===================================================================
--- www/ATPESC_2014/swift-t/tutorial.html 2014-08-14 19:41:57 UTC (rev 8212)
+++ www/ATPESC_2014/swift-t/tutorial.html 2014-08-14 19:44:54 UTC (rev 8213)
@@ -3,26 +3,29 @@
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@@ -548,6 +407,7 @@
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@@ -777,24 +575,26 @@
<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
+<div class="paragraph"><p>The examples are in the <tt>examples/</tt> directory.</p></div>
+<div class="paragraph"><p>Each example directory is numbered from <tt>01</tt> to <tt>05</tt>.</p></div>
+<div class="paragraph"><p>Configuration files are in <tt>cfg/</tt>. 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 class="paragraph"><p>Each example contains a <tt>*.swift</tt> Swift script that is the Swift
+program. The Swift/T compiler <tt>stc</tt> translates the Swift script into
+an MPI program encoded in a <tt>*.tcl</tt> file. This is launched by using
+the <tt>turbine</tt> program or a scheduler-specific script, such as the
+provided <tt>turbine-cobalt-run.zsh</tt> script.</p></div>
+<div class="paragraph"><p>There is also a <tt>run-local</tt> script to run the Swift script
+on the login node and a <tt>run-compute</tt> script to submit the Swift
+program to Cobalt. These scripts add <tt>stc</tt> and <tt>turbine</tt> entries to
+your <tt>PATH</tt> automatically.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_swift_t_installations">Swift/T installations</h2>
<div class="sectionbody">
+<div class="paragraph"><p>These instructions assume you will be running a preinstalled version
+of Swift/T on Cetus or Mira.</p></div>
<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
@@ -810,7 +610,7 @@
<div class="olist arabic"><ol class="arabic">
<li>
<p>
-<code>cd</code> into the directory <code>01-hello</code>
+<tt>cd</tt> into the directory <tt>01-hello</tt>
</p>
</li>
<li>
@@ -819,7 +619,7 @@
</p>
<div class="listingblock">
<div class="content">
-<pre><code>./run-local.sh</code></pre>
+<pre><tt>./run-local.sh</tt></pre>
</div></div>
</li>
<li>
@@ -828,7 +628,7 @@
</p>
<div class="listingblock">
<div class="content">
-<pre><code>/**
+<pre><tt>/**
Example 1 - HELLO.SWIFT
*/
@@ -837,7 +637,7 @@
main
{
printf("Hello world!");
-}</code></pre>
+}</tt></pre>
</div></div>
</li>
<li>
@@ -846,26 +646,26 @@
</p>
<div class="listingblock">
<div class="content">
-<pre><code>./run-compute.sh</code></pre>
+<pre><tt>./run-compute.sh</tt></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
+<pre><tt>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>
+JOB_ID=312170</tt></pre>
</div></div>
-<div class="paragraph"><p>Turbine will copy <code>hello.tcl</code> to <code>TURBINE_OUTPUT</code> and run from that
+<div class="paragraph"><p>Turbine will copy <tt>hello.tcl</tt> to <tt>TURBINE_OUTPUT</tt> 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
+directed to <tt>TURBINE_OUTPUT/output.txt</tt>.</p></div>
+<div class="paragraph"><p>The contents of <tt>output.txt</tt> 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>
+<pre><tt>stdout[0]: Hello world!</tt></pre>
</div></div>
</li>
</ol></div>
@@ -875,7 +675,7 @@
<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>/**
+<pre><tt>/**
Example 2 - LOOP.SWIFT
*/
@@ -899,15 +699,15 @@
j = compute(i);
printf("compute(%i) = %i", i, j);
}
-}</code></pre>
+}</tt></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
+<div class="paragraph"><p>The program executes <tt>compute()</tt> 10 times concurrently, because the
+Swift <tt>foreach</tt> loop is concurrent. The <tt>compute()</tt> 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)
+Delay progress with <tt>after</tt> (sleeps for <tt>i*1000</tt> milliseconds)
</p>
</li>
<li>
@@ -921,32 +721,32 @@
</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
+<div class="paragraph"><p>The result value is printed by Swift’s <tt>printf()</tt>.</p></div>
+<div class="paragraph"><p>Note the use of the <tt><<<tt>x</tt>>></tt> syntax, which maps Swift variable <tt>x</tt> 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>
+<tt>-l</tt>
</dt>
<dd>
<p>
-Prepend outputs with the MPI rank number (like <code>mpiexec -l</code>)
+Prepend outputs with the MPI rank number (like <tt>mpiexec -l</tt>)
</p>
</dd>
<dt class="hdlist1">
-<code>-n N</code>
+<tt>-n N</tt>
</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>.
+Run <tt>N</tt> MPI processes (like <tt>mpiexec -n N</tt>). Note that one
+process is dedicated for Swift logic, so choose <tt>N>1</tt>.
</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>,
+completion. Check <tt>output.txt</tt> for the <tt>ADLB Total Elapsed Time:</tt>,
which is a good measure of total execution time (discounts queue and
allocation startup/shutdown time).</p></div>
<div class="admonitionblock">
@@ -964,7 +764,7 @@
<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>/**
+<pre><tt>/**
Example 3 - DOT.SWIFT
*/
@@ -997,10 +797,10 @@
float z = blas_ddot(N, A, B);
printf("\nA*B=%0.1f", z);
-}</code></pre>
+}</tt></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
+<tt>blas.swift</tt>. This calls the CBLAS <tt>cblas_ddot()</tt> function through a
Tcl interface.</p></div>
<div class="olist arabic"><ol class="arabic">
<li>
@@ -1009,22 +809,22 @@
</p>
<div class="listingblock">
<div class="content">
-<pre><code>./build.sh</code></pre>
+<pre><tt>./build.sh</tt></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>.
+Run <tt>./run-*.sh</tt>.
</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>In <tt>dot.swift</tt>, the Swift statement <tt>import blas;</tt> brings <tt>blas.swift</tt>
+into the program. The Swift call to <tt>blas_ddot()</tt> operates on the
+Swift arrays <tt>A</tt> and <tt>B</tt>. In <tt>blas.swift</tt>, the Swift arrays are
+converted to C-compatible arrays of <tt>double</tt>, which are represented in
+Swift/T with the <tt>blob</tt> 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>
@@ -1038,7 +838,7 @@
internally for numerical operations.</p></div>
<div class="listingblock">
<div class="content">
-<pre><code>/**
+<pre><tt>/**
Example 4 - ADD.SWIFT
*/
@@ -1066,17 +866,17 @@
matrix A2 = eye(3);
matrix sum = add(A1, A2);
printf("2*eye(3)=%s", sum);
-}</code></pre>
+}</tt></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
+<tt>numpy.swift</tt>. This is imported into the main Swift script
+<tt>add.swift</tt>.</p></div>
+<div class="paragraph"><p>First, this program calls <tt>f()</tt>, 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
+value in its last line as a string- in this case, we return <tt>"0"</tt>.</p></div>
+<div class="paragraph"><p>Second, we use the <tt>numpy.swift</tt> 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>.
+<div class="paragraph"><p>Swift/T can call into arbitrary Python modules, just set <tt>PYTHONPATH</tt>.
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>
@@ -1092,24 +892,27 @@
<div class="olist arabic"><ol class="arabic">
<li>
<p>
-<code>cd</code> to <code>examples/md-src/</code> and run:
+<tt>cd</tt> to <tt>examples/md-src/</tt> and run:
</p>
<div class="listingblock">
<div class="content">
-<pre><code>make</code></pre>
+<pre><tt>make</tt></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="paragraph"><p>This builds the stand-alone <tt>md</tt> program. You can test it with <tt>test-md-*.sh</tt>.</p></div>
+</li>
+<li>
+<p>
+Run:
+</p>
<div class="listingblock">
<div class="content">
-<pre><code>make swift-pkg</code></pre>
+<pre><tt>make swift-pkg</tt></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;
+Running SWIG to expose the core <tt>simulate()</tt> function to Tcl;
</p>
</li>
<li>
@@ -1117,33 +920,31 @@
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>
+<div class="paragraph"><p>You can test the Tcl function with <tt>./test-md.tcl</tt>, which simply loads
+the package and calls <tt>simulate</tt> once.</p></div>
</li>
</ol></div>
</li>
<li>
<p>
-<code>cd</code> back to <code>examples/05-md/</code>.
+<tt>cd</tt> back to <tt>examples/05-md/</tt>.
</p>
</li>
<li>
<p>
-The <code>md.swift</code> library shows the calling sequence for MD.
+The <tt>md.swift</tt> 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>.
+The <tt>run-md.swift</tt> script shows how to call MD once. The output files are indicated in the script, in addition to the usual <tt>output.txt</tt>. Run this with <tt>./run-*-md.sh</tt>.
</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>.
+<tt>run-mds.swift</tt>. This script accepts many arguments on the command
+line: see <tt>run-*-mds.sh</tt>.
</p>
</li>
</ol></div>
@@ -1154,7 +955,7 @@
<div id="footnotes"><hr /></div>
<div id="footer">
<div id="footer-text">
-Last updated 2014-08-14 11:32:40 CDT
+Last updated 2014-08-14 21:40:27 RDT
</div>
</div>
</body>
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