[Swift-commit] r8202 - www/ATPESC_2014/swift-k
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Thu Aug 14 12:43:36 CDT 2014
Author: wozniak
Date: 2014-08-14 12:43:36 -0500 (Thu, 14 Aug 2014)
New Revision: 8202
Added:
www/ATPESC_2014/swift-k/README.html
Log:
Adding swift-k/README.html
Added: www/ATPESC_2014/swift-k/README.html
===================================================================
--- www/ATPESC_2014/swift-k/README.html (rev 0)
+++ www/ATPESC_2014/swift-k/README.html 2014-08-14 17:43:36 UTC (rev 8202)
@@ -0,0 +1,1568 @@
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+<body class="article" style="max-width:750px">
+<div id="header">
+<h1>Swift Tutorial for RCC Midway Cluster</h1>
+</div>
+<div id="content">
+<div id="preamble">
+<div class="sectionbody">
+<div class="paragraph"><p>This tutorial is viewable at:
+<a href="http://swiftlang.org/tutorials/midway/tutorial.html">http://swiftlang.org/tutorials/midway/tutorial.html</a></p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_introduction_why_parallel_scripting">Introduction: Why Parallel Scripting?</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>Swift is a simple scripting language for executing many instances of
+ordinary application programs on distributed parallel resources.
+Swift scripts run many copies of ordinary programs concurrently, using
+statements like this:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>foreach protein in proteinList {
+ runBLAST(protein);
+}</code></pre>
+</div></div>
+<div class="paragraph"><p>Swift acts like a structured "shell" language. It runs programs
+concurrently as soon as their inputs are available, reducing the need
+for complex parallel programming. Swift expresses your workflow in a
+portable fashion: The same script runs on multicore computers,
+clusters, clouds, grids, and supercomputers.</p></div>
+<div class="paragraph"><p>In this tutorial, you’ll be able to first try a few Swift examples
+(parts 1-3) on a Midway login host, to get a sense of the
+language. Then in parts 4-6 you’ll run similar workflows on Midway
+compute nodes, and see how more complex workflows can be expressed
+with Swift scripts.</p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_swift_tutorial_setup">Swift tutorial setup</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>If you are using a temporary/guest account to access Midway, follow
+the instructions at <a href="http://docs.rcc.uchicago.edu/tutorials/intro-to-rcc-workshop.html">http://docs.rcc.uchicago.edu/tutorials/intro-to-rcc-workshop.html</a>
+for more information on using a yubikey to log in.</p></div>
+<div class="paragraph"><p>Once you are logged into the Midway login host, run the following commands
+to set up your environment.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cd $HOME
+$ wget http://swiftlang.org/tutorials/midway/swift-midway-tutorial.tar.gz
+$ tar xvfz swift-midway-tutorial.tar.gz
+$ cd swift-midway-tutorial
+$ source setup.sh</code></pre>
+</div></div>
+<div class="sect2">
+<h3 id="_verify_your_environment">Verify your environment</h3>
+<div class="paragraph"><p>To verify that Swift loaded, do:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ swift -version # verify that you have Swift 0.95 RC1</code></pre>
+</div></div>
+<div class="admonitionblock">
+<table><tr>
+<td class="icon">
+<div class="title">Note</div>
+</td>
+<td class="content">If you re-login or open new ssh sessions, you must re-run <code>source setup.sh</code> in each ssh shell/window.</td>
+</tr></table>
+</div>
+</div>
+<div class="sect2">
+<h3 id="_to_check_out_the_tutorial_scripts_from_svn">To check out the tutorial scripts from SVN</h3>
+<div class="paragraph"><p>If you later want to get the most recent version of this tutorial from
+the Swift Subversion repository, do:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftTutorials/swift-midway-tutorial</code></pre>
+</div></div>
+<div class="paragraph"><p>This will create a directory called "swift-midway-tutorial" which contains all of the
+files used in this tutorial.</p></div>
+</div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_simple_science_applications_for_the_workflow_tutorial">Simple "science applications" for the workflow tutorial</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>This tutorial is based on two intentionally trivial example programs,
+<code>simulation</code> and <code>stats</code>, (implemented as bash shell scripts)
+that serve as easy-to-understand proxies for real science
+applications. These "programs" behave as follows.</p></div>
+<div class="sect2">
+<h3 id="_simulate_sh">simulate.sh</h3>
+<div class="paragraph"><p>The simulation script serves as a trivial proxy for any more
+complex scientific simulation application. It generates and prints a
+set of one or more random integers in the range [0-2^62) as controlled
+by its command line arguments, which are:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ simulate -help
+simulate: usage:
+ -b|--bias offset bias: add this integer to all results
+ -B|--biasfile file of integer biases to add to results
+ -l|--log generate a log in stderr if not null
+ -n|--nvalues print this many values per simulation
+ -r|--range range (limit) of generated results
+ -s|--seed use this integer [0..32767] as a seed
+ -S|--seedfile use this file (containing integer seeds [0..32767]) one per line
+ -t|--timesteps number of simulated "timesteps" in seconds (determines runtime)
+ -x|--scale scale the results by this integer
+ -h|-?|?|--help print this help</code></pre>
+</div></div>
+<div class="paragraph"><p>All of these arguments are optional, with default values indicated above as <code>[n]</code>.</p></div>
+<div class="paragraph"><p>With no arguments, simulate prints 1 number in the range of
+1-100. Otherwise it generates n numbers of the form (R*scale)+bias
+where R is a random integer. By default it logs information about its
+execution environment to stderr. Here’s some examples of its usage:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ simulate 2>log
+ 51
+$ head -5 log
+
+Called as: /home/davidkelly999/swift-midway-tutorial/app/simulate:
+Start time: Mon Dec 2 13:47:41 CST 2013
+Running as user: uid=88848(davidkelly999) gid=88848(davidkelly999) groups=88848(davidkelly999),10008(rcc),10030(pi-gavoth),10031(sp-swift),10036(swift),10058(pi-joshuaelliott),10084(pi-wilde),10118(cron-account),10124(cmts),10138(cmtsworkshop)
+
+$ simulate -n 4 -r 1000000 2>log
+ 239454
+ 386702
+ 13849
+ 873526
+
+$ simulate -n 3 -r 1000000 -x 100 2>log
+ 6643700
+62182300
+ 5230600
+
+$ simulate -n 2 -r 1000 -x 1000 2>log
+ 565000
+ 636000
+
+$ time simulate -n 2 -r 1000 -x 1000 -t 3 2>log
+ 336000
+ 320000
+real 0m3.012s
+user 0m0.005s
+sys 0m0.006s</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_stats">stats</h3>
+<div class="paragraph"><p>The stats script serves as a trivial model of an "analysis"
+program. It reads N files each containing M integers and simply prints
+the average of all those numbers to stdout. Similarly to simulate
+it logs environmental information to the stderr.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ ls f*
+f1 f2 f3 f4
+
+$ cat f*
+25
+60
+40
+75
+
+$ stats f* 2>log
+50</code></pre>
+</div></div>
+</div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_basic_of_the_swift_language_with_local_execution">Basic of the Swift language with local execution</h2>
+<div class="sectionbody">
+<div class="sect2">
+<h3 id="_a_summary_of_swift_in_a_nutshell">A Summary of Swift in a nutshell</h3>
+<div class="ulist"><ul>
+<li>
+<p>
+Swift scripts are text files ending in <code>.swift</code> The <code>swift</code> command
+runs on any host, and executes these scripts. <code>swift</code> is a Java
+application, which you can install almost anywhere. On Linux, just
+unpack the distribution <code>tar</code> file and add its <code>bin/</code> directory to
+your <code>PATH</code>.
+</p>
+</li>
+<li>
+<p>
+Swift scripts run ordinary applications, just like shell scripts
+do. Swift makes it easy to run these applications on parallel and
+remote computers (from laptops to supercomputers). If you can <code>ssh</code> to
+the system, Swift can likely run applications there.
+</p>
+</li>
+<li>
+<p>
+The details of where to run applications and how to get files back
+and forth are described in configuration files separate from your
+program. Swift speaks ssh, PBS, Condor, SLURM, LSF, SGE, Cobalt, and
+Globus to run applications, and scp, http, ftp, and GridFTP to move
+data.
+</p>
+</li>
+<li>
+<p>
+The Swift language has 5 main data types: <code>boolean</code>, <code>int</code>,
+<code>string</code>, <code>float</code>, and <code>file</code>. Collections of these are dynamic,
+sparse arrays of arbitrary dimension and structures of scalars and/or
+arrays defined by the <code>type</code> declaration.
+</p>
+</li>
+<li>
+<p>
+Swift file variables are "mapped" to external files. Swift sends
+files to and from remote systems for you automatically.
+</p>
+</li>
+<li>
+<p>
+Swift variables are "single assignment": once you set them you can’t
+change them (in a given block of code). This makes Swift a natural,
+"parallel data flow" language. This programming model keeps your
+workflow scripts simple and easy to write and understand.
+</p>
+</li>
+<li>
+<p>
+Swift lets you define functions to "wrap" application programs, and
+to cleanly structure more complex scripts. Swift <code>app</code> functions take
+files and parameters as inputs and return files as outputs.
+</p>
+</li>
+<li>
+<p>
+A compact set of built-in functions for string and file
+manipulation, type conversions, high level IO, etc. is provided.
+Swift’s equivalent of <code>printf()</code> is <code>tracef()</code>, with limited and
+slightly different format codes.
+</p>
+</li>
+<li>
+<p>
+Swift’s <code>foreach {}</code> statement is the main parallel workhorse of the
+language, and executes all iterations of the loop concurrently. The
+actual number of parallel tasks executed is based on available
+resources and settable "throttles".
+</p>
+</li>
+<li>
+<p>
+In fact, Swift conceptually executes <strong>all</strong> the statements,
+expressions and function calls in your program in parallel, based on
+data flow. These are similarly throttled based on available resources
+and settings.
+</p>
+</li>
+<li>
+<p>
+Swift also has <code>if</code> and <code>switch</code> statements for conditional
+execution. These are seldom needed in simple workflows but they enable
+very dynamic workflow patterns to be specified.
+</p>
+</li>
+</ul></div>
+<div class="paragraph"><p>We’ll see many of these points in action in the examples below. Lets
+get started!</p></div>
+</div>
+<div class="sect2">
+<h3 id="_part_1_run_a_single_application_under_swift">Part 1: Run a single application under Swift</h3>
+<div class="paragraph"><p>The first swift script, p1.swift, runs simulate to generate a
+single random number. It writes the number to a file.</p></div>
+<div class="imageblock" style="text-align:center;">
+<div class="content">
+<img src="part01.png" alt="p1 workflow" />
+</div>
+</div>
+<div class="listingblock">
+<div class="title">p1.swift</div>
+<div class="content">
+<pre><code>type file;
+
+app (file o) simulation ()
+{
+ simulate stdout=filename(o);
+}
+
+file f <"sim.out">;
+f = simulation();</code></pre>
+</div></div>
+<div class="paragraph"><p>To run this script, run the following command:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cd part01
+$ swift p1.swift
+Swift 0.94.1 RC2 swift-r6895 cog-r3765
+
+RunID: 20130827-1413-oa6fdib2
+Progress: time: Tue, 27 Aug 2013 14:13:33 -0500
+Final status: Tue, 27 Aug 2013 14:13:33 -0500 Finished successfully:1
+$ cat sim.out
+ 84
+$ swift p1.swift
+$ cat sim.out
+ 36</code></pre>
+</div></div>
+<div class="paragraph"><p>To cleanup the directory and remove all outputs (including the log
+files and directories that Swift generates), run the cleanup script
+which is located in the tutorial PATH:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cleanup</code></pre>
+</div></div>
+<div class="admonitionblock">
+<table><tr>
+<td class="icon">
+<div class="title">Note</div>
+</td>
+<td class="content">You’ll also find a Swift configuration file in each <code>partNN</code>
+directory of this tutorial. This file specifies the environment-specific
+details of how to run. These files will be explained in more
+detail in parts 4-6, and can be ignored for now.</td>
+</tr></table>
+</div>
+</div>
+<div class="sect2">
+<h3 id="_part_2_running_an_ensemble_of_many_apps_in_parallel_with_a_foreach_loop">Part 2: Running an ensemble of many apps in parallel with a "foreach" loop</h3>
+<div class="paragraph"><p>The <code>p2.swift</code> script introduces the <code>foreach</code> parallel iteration
+construct to run many concurrent simulations.</p></div>
+<div class="imageblock" style="text-align:center;">
+<div class="content">
+<img src="part02.png" alt="part02.png" />
+</div>
+</div>
+<div class="listingblock">
+<div class="title">p2.swift</div>
+<div class="content">
+<pre><code>type file;
+
+app (file o) simulation ()
+{
+ simulate stdout=filename(o);
+}
+
+foreach i in [0:9] {
+ file f <single_file_mapper; file=strcat("output/sim_",i,".out")>;
+ f = simulation();
+}</code></pre>
+</div></div>
+<div class="paragraph"><p>The script also shows an
+example of naming the output files of an ensemble run. In this case, the output files will be named
+<code>output/sim_N.out</code>.</p></div>
+<div class="paragraph"><p>To run the script and view the output:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cd ../part02
+$ swift p2.swift
+$ ls output
+sim_0.out sim_1.out sim_2.out sim_3.out sim_4.out sim_5.out sim_6.out sim_7.out sim_8.out sim_9.out
+$ more output/*
+::::::::::::::
+output/sim_0.out
+::::::::::::::
+ 44
+::::::::::::::
+output/sim_1.out
+::::::::::::::
+ 55
+...
+::::::::::::::
+output/sim_9.out
+::::::::::::::
+ 82</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_part_3_analyzing_results_of_a_parallel_ensemble">Part 3: Analyzing results of a parallel ensemble</h3>
+<div class="paragraph"><p>After all the parallel simulations in an ensemble run have completed,
+its typically necessary to gather and analyze their results with some
+kind of post-processing analysis program or script. p3.swift
+introduces such a postprocessing step. In this case, the files created
+by all of the parallel runs of <code>simulation</code> will be averaged by by
+the trivial "analysis application" <code>stats</code>:</p></div>
+<div class="imageblock" style="text-align:center;">
+<div class="content">
+<img src="part03.png" alt="part03.png" />
+</div>
+</div>
+<div class="listingblock">
+<div class="title">p3.swift</div>
+<div class="content">
+<pre><code>type file;
+
+app (file o) simulation (int sim_steps, int sim_range, int sim_values)
+{
+ simulate "--timesteps" sim_steps "--range" sim_range "--nvalues" sim_values stdout=filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+ stats filenames(s) stdout=filename(o);
+}
+
+int nsim = toInt(arg("nsim","10"));
+int steps = toInt(arg("steps","1"));
+int range = toInt(arg("range","100"));
+int values = toInt(arg("values","5"));
+
+file sims[];
+
+foreach i in [0:nsim-1] {
+ file simout <single_file_mapper; file=strcat("output/sim_",i,".out")>;
+ simout = simulation(steps,range,values);
+ sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);</code></pre>
+</div></div>
+<div class="paragraph"><p>To run:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cd part03
+$ swift p3.swift</code></pre>
+</div></div>
+<div class="paragraph"><p>Note that in <code>p3.swift</code> we expose more of the capabilities of the
+<code>simulate</code> application to the <code>simulation()</code> app function:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>app (file o) simulation (int sim_steps, int sim_range, int sim_values)
+{
+ simulate "--timesteps" sim_steps "--range" sim_range "--nvalues" sim_values stdout=@filename(o);
+}</code></pre>
+</div></div>
+<div class="paragraph"><p><code>p3.swift</code> also shows how to fetch application-specific values from
+the <code>swift</code> command line in a Swift script using <code>arg()</code> which
+accepts a keyword-style argument and its default value:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>int nsim = toInt(arg("nsim","10"));
+int steps = toInt(arg("steps","1"));
+int range = toInt(arg("range","100"));
+int values = toInt(arg("values","5"));</code></pre>
+</div></div>
+<div class="paragraph"><p>Now we can specify that more runs should be performed and that each should run
+for more timesteps, and produce more that one value each, within a specified range,
+using command line arguments placed after the Swift script name in the form <code>-parameterName=value</code>:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ swift p3.swift -nsim=3 -steps=10 -values=4 -range=1000000
+
+Swift 0.94.1 RC2 swift-r6895 cog-r3765
+
+RunID: 20130827-1439-s3vvo809
+Progress: time: Tue, 27 Aug 2013 14:39:42 -0500
+Progress: time: Tue, 27 Aug 2013 14:39:53 -0500 Active:2 Stage out:1
+Final status: Tue, 27 Aug 2013 14:39:53 -0500 Finished successfully:4
+
+$ ls output/
+average.out sim_0.out sim_1.out sim_2.out
+$ more output/*
+::::::::::::::
+output/average.out
+::::::::::::::
+651368
+::::::::::::::
+output/sim_0.out
+::::::::::::::
+ 735700
+ 886206
+ 997391
+ 982970
+::::::::::::::
+output/sim_1.out
+::::::::::::::
+ 260071
+ 264195
+ 869198
+ 933537
+::::::::::::::
+output/sim_2.out
+::::::::::::::
+ 201806
+ 213540
+ 527576
+ 944233</code></pre>
+</div></div>
+<div class="paragraph"><p>Now try running (<code>-nsim=</code>) 100 simulations of (<code>-steps=</code>) 1 second each:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ swift p3.swift -nsim=100 -steps=1
+Swift 0.94.1 RC2 swift-r6895 cog-r3765
+
+RunID: 20130827-1444-rq809ts6
+Progress: time: Tue, 27 Aug 2013 14:44:55 -0500
+Progress: time: Tue, 27 Aug 2013 14:44:56 -0500 Selecting site:79 Active:20 Stage out:1
+Progress: time: Tue, 27 Aug 2013 14:44:58 -0500 Selecting site:58 Active:20 Stage out:1 Finished successfully:21
+Progress: time: Tue, 27 Aug 2013 14:44:59 -0500 Selecting site:37 Active:20 Stage out:1 Finished successfully:42
+Progress: time: Tue, 27 Aug 2013 14:45:00 -0500 Selecting site:16 Active:20 Stage out:1 Finished successfully:63
+Progress: time: Tue, 27 Aug 2013 14:45:02 -0500 Active:15 Stage out:1 Finished successfully:84
+Progress: time: Tue, 27 Aug 2013 14:45:03 -0500 Finished successfully:101
+Final status: Tue, 27 Aug 2013 14:45:03 -0500 Finished successfully:101</code></pre>
+</div></div>
+<div class="paragraph"><p>We can see from Swift’s "progress" status that the tutorial’s default
+parameters for local execution allow Swift to run up to 20
+application invocations concurrently on the login node. We’ll look at
+this in more detail in the next sections where we execute applications
+on the site’s compute nodes.</p></div>
+</div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_running_applications_on_midway_compute_nodes_with_swift">Running applications on Midway compute nodes with Swift</h2>
+<div class="sectionbody">
+<div class="sect2">
+<h3 id="_part_4_running_a_parallel_ensemble_on_midway_compute_nodes">Part 4: Running a parallel ensemble on Midway compute nodes</h3>
+<div class="paragraph"><p><code>p4.swift</code> will run our mock "simulation" applications on Midway
+compute nodes. The script is similar to as <code>p3.swift</code>, but specifies
+that each simulation app invocation should additionally return the
+log file which the application writes to <code>stderr</code>.</p></div>
+<div class="paragraph"><p>Now when you run <code>swift p4.swift</code> you’ll see that two types output
+files will placed in the <code>output/</code> directory: <code>sim_N.out</code> and
+<code>sim_N.log</code>. The log files provide data on the runtime environment of
+each app invocation. For example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cat output/sim_0.log
+Called as: /home/davidkelly999/swift-midway-tutorial/app/simulate: --timesteps 1 --range 100 --nvalues 5
+
+Start time: Mon Dec 2 12:17:06 CST 2013
+Running as user: uid=88848(davidkelly999) gid=88848(davidkelly999) groups=88848(davidkelly999),10008(rcc),10030(pi-gavoth),10031(sp-swift),10036(swift),10058(pi-joshuaelliott),10084(pi-wilde),10118(cron-account),10124(cmts),10138(cmtsworkshop)
+Running on node: midway002
+Node IP address: 10.50.181.2 172.25.181.2
+
+Simulation parameters:
+
+bias=0
+biasfile=none
+initseed=none
+log=yes
+paramfile=none
+range=100
+scale=1
+seedfile=none
+timesteps=1
+output width=8
+
+Environment:
+
+ANTLR_ROOT=/software/antlr-2.7-el6-x86_64
+ANT_HOME=/software/ant-1.8.4-all
+ANT_HOME_modshare=/software/ant-1.8.4-all:3
+...</code></pre>
+</div></div>
+<div class="paragraph"><p>Swift’s <code>swift.properties</code> configuration file allows many parameters to
+specify how jobs should be run on a given cluster.</p></div>
+<div class="paragraph"><p>Consider for example that Midway has several Slurm partitions. The sandyb
+partition has 16 cores, and the westmere partition has 12 cores. Depending
+on the application and which partitions are busy, you may want to modify
+where you run.</p></div>
+<div class="paragraph"><p>Here is an example of the swift.properties in the part04 directory:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>site=westmere
+site.westmere.slurm.reservation=workshop
+site.westmere.slurm.exclusive=false</code></pre>
+</div></div>
+<div class="paragraph"><p>The first line, site=westmere, allows you to define which partition to run on. Swift includes
+templates for each partition that provides some reasonable default values. Other valid partitions
+are amd, bigmem, gpu, local, and sandyb.</p></div>
+<div class="paragraph"><p>The second and third line override some of the default values, by specifying a reservation that will
+be used for this session, and enabling node sharing.</p></div>
+<div class="paragraph"><p>Try changing the queue to run on the sandyb queue. The new swift.properties should look like this:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>site=sandyb
+site.sandyb.slurm.reservation=workshop
+site.sandyb.slurm.exclusive=false</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_performing_larger_swift_runs">Performing larger Swift runs</h3>
+<div class="paragraph"><p>To test with larger runs, there are two changes that are required. The first is a
+change to the command line arguments. The example below will run 1000 simulations
+with each simulation taking 5 seconds.</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ swift p6.swift -steps=5 -nsim=1000</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_plotting_run_activity">Plotting run activity</h3>
+<div class="paragraph"><p>The tutorial <code>bin</code> directory in your <code>PATH</code> provides a script
+<code>plot.sh</code> to plot the progress of a Swift script. It generates two
+image files: <code>activeplot.png</code>, which shows the number of active jobs
+over time, and <code>cumulativeplot.png</code>, which shows the total number of
+app calls completed as the Swift script progresses.</p></div>
+<div class="paragraph"><p>After each Swift run, a new run directory is created called runNNN.
+Each run directory will have a log file with a similar name called
+runNNN.log. Once you have identified the log file name, run the
+command <code>plot.sh</code> <logfile>` to generate the plots for that
+specific run. For example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ ls
+output p3.swift run000 swift.properties
+
+$ cd run000/
+
+$ ls
+apps cf p3-20131202-2004-0kh4ha6e.d run000.log sites.xml
+
+$ plot.sh run000.log</code></pre>
+</div></div>
+<div class="paragraph"><p>This yields plots like:</p></div>
+<div class="imageblock">
+<div class="content">
+<img src="activeplot.png" alt="width=700" />
+</div>
+</div>
+<div class="imageblock">
+<div class="content">
+<img src="cumulativeplot.png" alt="width=700" />
+</div>
+</div>
+</div>
+<div class="sect2">
+<h3 id="_part_5_controlling_the_compute_node_pools_where_applications_run">Part 5: Controlling the compute-node pools where applications run</h3>
+<div class="paragraph"><p>This section is under development.</p></div>
+</div>
+<div class="sect2">
+<h3 id="_part_6_specifying_more_complex_workflow_patterns">Part 6: Specifying more complex workflow patterns</h3>
+<div class="paragraph"><p>p6.swift expands the workflow pattern of p4.swift to add additional
+stages to the workflow. Here, we generate a dynamic seed value that
+will be used by all of the simulations, and for each simulation, we
+run an pre-processing application to generate a unique "bias
+file". This pattern is shown below, followed by the Swift script.</p></div>
+<div class="imageblock" style="text-align:center;">
+<div class="content">
+<img src="part06.png" alt="part06.png" />
+</div>
+</div>
+<div class="listingblock">
+<div class="title">p6.swift</div>
+<div class="content">
+<pre><code>type file;
+
+# app() functions for application programs to be called:
+
+app (file out) genseed (int nseeds)
+{
+ simulate "-r" 2000000 "-n" nseeds stdout=@out;
+}
+
+app (file out) genbias (int bias_range, int nvalues)
+{
+ simulate "-r" bias_range "-n" nvalues stdout=@out;
+}
+
+app (file out, file log) simulation (int timesteps, int sim_range, file bias_file,
+ int scale, int sim_count, file seed_file)
+{
+ simulate "-t" timesteps "-r" sim_range "-B" @bias_file "-x" scale
+ "-n" sim_count "-S" @seed_file stdout=@out stderr=@log;
+}
+
+app (file out, file log) analyze (file s[])
+{
+ stats filenames(s) stdout=@out stderr=@log;
+}
+
+# Command line arguments
+
+int nsim = toInt(arg("nsim", "10")); # number of simulation programs to run
+int steps = toInt(arg("steps", "1")); # number of timesteps (seconds) per simulation
+int range = toInt(arg("range", "100")); # range of the generated random numbers
+int values = toInt(arg("values", "10")); # number of values generated per simulation
+
+# Main script and data
+file seedfile <"output/seed.dat">; # Dynamically generated bias for simulation ensemble
+
+tracef("\n*** Script parameters: nsim=%i range=%i num values=%i\n\n", nsim, range, values);
+seedfile = genseed(1);
+
+file sims[]; # Array of files to hold each simulation output
+
+foreach i in [0:nsim-1] {
+ file biasfile <single_file_mapper; file=strcat("output/bias_",i,".dat")>;
+ file simout <single_file_mapper; file=strcat("output/sim_",i,".out")>;
+ file simlog <single_file_mapper; file=strcat("output/sim_",i,".log")>;
+ biasfile = genbias(1000, 20);
+ (simout,simlog) = simulation(steps, range, biasfile, 1000000, values, seedfile);
+ sims[i] = simout;
+}
+
+file stats_out<"output/average.out">;
+file stats_log<"output/average.log">;
+(stats_out,stats_log) = analyze(sims);</code></pre>
+</div></div>
+<div class="paragraph"><p>Note that the workflow is based on data flow dependencies: each simulation depends on the seed value, calculated in this statement:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>seedfile = genseed(1);</code></pre>
+</div></div>
+<div class="paragraph"><p>and on the bias file, computed and then consumed in these two dependent statements:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code> biasfile = genbias(1000, 20);
+ (simout,simlog) = simulation(steps, range, biasfile, 1000000, values, seedfile);</code></pre>
+</div></div>
+<div class="paragraph"><p>To run:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cd ../part06
+$ swift p6.swift</code></pre>
+</div></div>
+<div class="paragraph"><p>The default parameters result in the following execution log:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ swift p6.swift
+Swift 0.94.1 RC2 swift-r6895 cog-r3765
+
+RunID: 20130827-1917-jvs4gqm5
+Progress: time: Tue, 27 Aug 2013 19:17:56 -0500
+
+*** Script parameters: nsim=10 range=100 num values=10
+
+Progress: time: Tue, 27 Aug 2013 19:17:57 -0500 Stage in:1 Submitted:10
+Generated seed=382537
+Progress: time: Tue, 27 Aug 2013 19:17:59 -0500 Active:9 Stage out:1 Finished successfully:11
+Final status: Tue, 27 Aug 2013 19:18:00 -0500 Finished successfully:22</code></pre>
+</div></div>
+<div class="paragraph"><p>which produces the following output:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ ls -lrt output
+total 264
+-rw-r--r-- 1 p01532 61532 9 Aug 27 19:17 seed.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_9.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_8.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_7.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_6.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_5.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_4.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_3.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_2.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_1.dat
+-rw-r--r-- 1 p01532 61532 180 Aug 27 19:17 bias_0.dat
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:17 sim_9.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_9.log
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_8.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:17 sim_7.out
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:17 sim_6.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_6.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:17 sim_5.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_5.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:17 sim_4.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_4.log
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_1.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:18 sim_8.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_7.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:18 sim_3.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_3.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:18 sim_2.out
+-rw-r--r-- 1 p01532 61532 14898 Aug 27 19:18 sim_2.log
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:18 sim_1.out
+-rw-r--r-- 1 p01532 61532 90 Aug 27 19:18 sim_0.out
+-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_0.log
+-rw-r--r-- 1 p01532 61532 9 Aug 27 19:18 average.out
+-rw-r--r-- 1 p01532 61532 14675 Aug 27 19:18 average.log</code></pre>
+</div></div>
+<div class="paragraph"><p>Each sim_N.out file is the sum of its bias file plus newly "simulated" random output scaled by 1,000,000:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>$ cat output/bias_0.dat
+ 302
+ 489
+ 81
+ 582
+ 664
+ 290
+ 839
+ 258
+ 506
+ 310
+ 293
+ 508
+ 88
+ 261
+ 453
+ 187
+ 26
+ 198
+ 402
+ 555
+
+$ cat output/sim_0.out
+64000302
+38000489
+32000081
+12000582
+46000664
+36000290
+35000839
+22000258
+49000506
+75000310</code></pre>
+</div></div>
+<div class="paragraph"><p>We produce 20 values in each bias file. Simulations of less than that
+number of values ignore the unneeded number, while simualtions of more
+than 20 will use the last bias number for all remoaining values past
+20. As an exercise, adjust the code to produce the same number of
+bias values as is needed for each simulation. As a further exercise,
+modify the script to generate a unique seed value for each simulation,
+which is a common practice in ensemble computations.</p></div>
+</div>
+</div>
+</div>
+</div>
+<div id="footnotes"><hr /></div>
+<div id="footer">
+<div id="footer-text">
+Last updated 2014-08-14 12:41:54 CDT
+</div>
+</div>
+</body>
+</html>
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