[Swift-commit] r8396 - SwiftApps/subjobs
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Mon Mar 16 15:45:45 CDT 2015
Author: ketan
Date: 2015-03-16 15:45:44 -0500 (Mon, 16 Mar 2015)
New Revision: 8396
Added:
SwiftApps/subjobs/README.html
Log:
add html version of README to svn
Added: SwiftApps/subjobs/README.html
===================================================================
--- SwiftApps/subjobs/README.html (rev 0)
+++ SwiftApps/subjobs/README.html 2015-03-16 20:45:44 UTC (rev 8396)
@@ -0,0 +1,1093 @@
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+<body class="article" style="max-width:750px">
+<div id="header">
+<h1>Running Sub-block jobs via Swift</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 class="sect1">
+<h2 id="_introduction">1. Introduction</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>This document describes an approach to run multiple jobs over a single large
+block of compute nodes on BlueGene/Q systems.</p></div>
+<div class="paragraph"><p>The technique, called sub-block jobs lets users submit multiple, independent,
+repeated jobs within a single larger Cobalt block. Sub-block jobs is a mode of
+running jobs on BlueGene/Q systems wherein one can allocate a larger "outer"
+block of compute nodes and repeatedly submit jobs of smaller sized sub-blocks
+to this block.</p></div>
+<div class="paragraph"><p>The current package provides tools, scripts and example use-cases to run Swift
+applications in sub-block mode over the ALCF BlueGene/Q resources: <code>Vesta</code>,
+<code>Cetus</code> and <code>Mira</code>. The benefit of this approach is that the user does not have
+to invoke the sub-block specific routines involving the details of the
+underlying node interconnect hardware. Additionally, with the same Swift script
+and configuration, user gets a flexibility to run jobs in sub-block or
+non-sub-block mode depending on the scale and size of a run. The approach
+transparently allows user to run jobs directly via Swift. Users can run
+multiple <em>waves</em> of jobs asynchronously and in parallel without restarting the
+outer block.</p></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_swift_sub_block_jobs">2. Swift sub-block jobs</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>To download the package, checkout the directory as follows:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/subjobs</code></pre>
+</div></div>
+<div class="paragraph"><p>followed by:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>cd subjobs</code></pre>
+</div></div>
+<div class="paragraph"><p>To set up the environment:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>source setup</code></pre>
+</div></div>
+<div class="paragraph"><p>To run an example application</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>./runswift.sh</code></pre>
+</div></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_how_to">3. How To</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>To convert an ordinary Swift application run in sub-block mode, the following changes are required:</p></div>
+<div class="paragraph"><p>First, Add bg.sh as the application invoker in place of <code>sh</code> or any other invoker. For example, if the app definition is as follows:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>sh @exe @i @o arg("s","1") stdout=@sout stderr=@serr;</code></pre>
+</div></div>
+<div class="paragraph"><p>Replace the shell invocation with the bg.sh invocations like so:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>bg.sh @exe @i @o arg("s","1") stdout=@sout stderr=@serr;</code></pre>
+</div></div>
+<div class="paragraph"><p>Second, add the <code>SUBBLOCK_SIZE</code> environment variable to the sites file. For example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code><profile key="SUBBLOCK_SIZE" namespace="env">16</profile></code></pre>
+</div></div>
+<div class="admonitionblock">
+<table><tr>
+<td class="icon">
+<div class="title">Note</div>
+</td>
+<td class="content">The value of <code>SUBBLOCK_SIZE</code> variable must be a power of 2 greater than 8 and less than the <code>maxnodes</code> value.</td>
+</tr></table>
+</div>
+<div class="paragraph"><p>A complete example sites file for a sub-block job run on ALCF <code>Vesta</code> is shown below:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code><?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+
+<pool handle="cluster">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<!-- "slots" determine the number of Cobalt jobs -->
+<profile namespace="globus" key="slots">1</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">2.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:40:00</profile>
+<profile namespace="globus" key="walltime">2050</profile>
+<profile namespace="globus" key="maxnodes">256</profile>
+<profile namespace="globus" key="nodegranularity">256</profile>
+
+<!-- required for sub-block jobs, remove for non-sub-block jobs -->
+<profile key="SUBBLOCK_SIZE" namespace="env">16</profile>
+<profile namespace="globus" key="jobsPerNode">16</profile>
+
+<workdirectory>/tmp/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+</config></code></pre>
+</div></div>
+<div class="paragraph"><p>Of note are the <code>SUBBLOCK_SIZE</code> and the <code>mode</code> properties which must be present
+in the sites definition. The former defines the size of the subblock needed and
+the latter specifies that the "mode" to run the outer cobalt job would be
+<code>script</code> mode. In this particular example, we have the outer block size to be
+256 nodes whereas the subblock size is 16 nodes. This results in a total of 16
+subblocks resulting in <code>jobsPerNode</code> value to be 16.</p></div>
+<div class="admonitionblock">
+<table><tr>
+<td class="icon">
+<div class="title">Note</div>
+</td>
+<td class="content">Swift installation for sub-block jobs on Vesta and Mira machines can be found at <code>/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift</code></td>
+</tr></table>
+</div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_use_case_applications">4. Use-Case Applications</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>This section discusses some of the real-world use-case applications that are set up
+with this package. These applications are tested with subblock and non-subblock
+runs on ALCF Vesta, a 2-rack (2048 nodes) BlueGene/Q system.</p></div>
+<div class="sect2">
+<h3 id="_namd">4.1. NAMD</h3>
+<div class="paragraph"><p><code>NAMD</code> is a molecular dynamics simulation code developed at
+<a href="http://www.ks.uiuc.edu/Research/namd">uiuc</a>. The Swift source and configuration
+files along with application inputs can be found in the <code>namd</code> directory in the
+subjobs pacjage. To run NAMD example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>cd namd #change to the package's namd directory
+./runvesta.sh #run on vesta
+./runmira.sh #run on mira</code></pre>
+</div></div>
+<div class="paragraph"><p>To run NAMD with a different input dataset, change the input files in the
+<code>input_files</code> directory and reflect the changes in the <code>namd.swift</code> source code,
+especially the data definitions part:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>file psf <"input_files/h0_solvion.psf">;
+file pdb <"input_files/h0_solvion.pdb">;
+file coord_restart <"input_files/h0_eq.0.restart.coor">;
+file velocity_restart <"input_files/h0_eq.0.restart.vel">;
+file system_restart <"input_files/h0_eq.0.restart.xsc">;
+file namd_config <"input_files/h0_eq.conf">;
+file charmm_parameters <"input_files/par_all22_prot.inp">;</code></pre>
+</div></div>
+<div class="paragraph"><p>Similarly, in order to change the scale and size of runs, make changes to the
+parameters in the sites file as described in section 1 above.</p></div>
+<div class="paragraph"><p>ToDo: Visualize NAMD results with VMD.</p></div>
+</div>
+<div class="sect2">
+<h3 id="_rosetta">4.2. Rosetta</h3>
+<div class="paragraph"><p><code>Rosetta</code> is a molecular <a href="http://rosie.rosettacommons.org/docking">docking</a>
+toolkit with many related programs used by many large-scale HPC science
+applications. This implementation shows how to run <code>FlexPeptide Docking</code> on
+ALCF systems. The Swift scripts, configuration and application specific inputs
+are found in the <code>rosetta</code> directory. To run the example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>cd rosetta
+./runvesta.sh #run on vesta
+./runmira.sh #run on mira</code></pre>
+</div></div>
+<div class="paragraph"><p>To change scale, size and/or inputs of the run, change the location of input
+files in the Swift source file (<code>rosetta.swift</code>) like so:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>file pdb_files[] <filesys_mapper; location="hlac_complex", suffix=".pdb">;</code></pre>
+</div></div>
+<div class="paragraph"><p>In the above line all <code>.pdb</code> files in the directory <code>hlac_complex</code> will be
+processed in parallel. Change the <code>location</code> from <code>hlac_complex</code> to where you
+have your input files.</p></div>
+<div class="paragraph"><p>To change the number of generated <code>structs</code> by Flexpep Docking program, change
+the struct argument in the call to the rosetta application like so:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>(scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2);</code></pre>
+</div></div>
+<div class="paragraph"><p>In the above line, the number <code>2</code> indicates the number of <code>structs</code> to be generated by the docking. Change this value to the desired size to change the desired number of <code>structs</code>. To make changes to other parameters, make changes to the commandline as invoked in the <code>app</code> definition in the Swift script like so:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>bgsh "/home/ketan/openmp-gnu-july16-mini/build/src/debug/linux/2.6/64/ppc64/xlc/static-mpi/FlexPepDocking.staticmpi.linuxxlcdebug" "-database" "/home/ketan/minirosetta_database" "-pep_refine" "-s" @pdb_file "-ex1" "-ex2aro" "-use_input_sc" "-nstruct" nstruct "-overwrite" "-scorefile" @_scorefile stdout=@out stderr=@err;</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_dock">4.3. Dock</h3>
+<div class="paragraph"><p>Dock is another molecular docking
+<a href="http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm">program</a> used by many
+applications. The Swift source, configuration and application related inputs
+can be found in the <code>dock</code> directory. To run the Dock example:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>cd dock
+./runvesta.sh #run on vesta
+./runmira.sh #run on mira</code></pre>
+</div></div>
+</div>
+<div class="sect2">
+<h3 id="_gridpack">4.4. GridPack</h3>
+<div class="paragraph"><p>GridPack is a simulation package designed for powergrid design application.</p></div>
+</div>
+<div class="sect2">
+<h3 id="_halo">4.5. HALO</h3>
+<div class="paragraph"><p>HALO is a astrophysics application.</p></div>
+</div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_internals">5. Internals</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>The key driver of the Swift sub-block jobs is a script called <code>bg.sh</code> that does the sub-block jobs calculations and othe chores for the users. The script looks as follows:</p></div>
+<div class="listingblock">
+<div class="content">
+<pre><code>#!/bin/bash
+
+set -x
+
+mname=$(hostname)
+
+# vesta and mira has different path than cetus
+if [[ $mname == *vesta* || $mname == *mira* ]]
+then
+ export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH
+else
+ export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH
+fi
+
+#export SUBBLOCK_SIZE=16
+
+# Prepare shape based on subblock size
+# provided by user in sites environment
+case "$SUBBLOCK_SIZE" in
+1) SHAPE="1x1x1x1x1"
+;;
+8) SHAPE="1x2x2x2x1"
+;;
+16) SHAPE="2x2x2x2x1"
+;;
+32) SHAPE="2x2x2x2x2"
+;;
+64) SHAPE="2x2x4x2x2"
+;;
+128) SHAPE="2x4x4x2x2"
+;;
+256) SHAPE="2x4x4x4x2"
+;;
+512) SHAPE="4x4x4x4x2"
+;;
+*) echo "SUBBLOCK_SIZE not set or incorrectly set: will not use subblock jobs"
+;;
+esac
+
+# If subblock size is provided, do subblock business
+if [ "$SUBBLOCK_SIZE"_ != "_" ]
+then
+ export SWIFT_SUBBLOCKS=$(get-corners.py "$COBALT_PARTNAME" $SHAPE)
+ export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+
+ #echo "$0": SWIFT_SUBBLOCKS="$SWIFT_SUBBLOCKS"
+
+ if [ "_$SWIFT_SUBBLOCKS" = _ ]; then
+ echo ERROR: "$0": SWIFT_SUBBLOCKS is null.
+ exit 1
+ fi
+
+ nsb=${#SWIFT_SUBBLOCK_ARRAY[@]}
+
+ CORNER=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
+
+ #Some logging
+ echo "$0": running BLOCK="$COBALT_PARTNAME" SLOT="$SWIFT_JOB_SLOT"
+ echo "$0": running cmd: "$0" args: "$@"
+ echo "$0": running runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+
+ #without timeout
+ #runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+ runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+
+ echo "Runjob finished."
+else
+ # run w/o subblocks if no subblock size provided
+ echo "Running in nonsubblock mode."
+ echo "$0": running runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
+ #strace -o "$HOME/strace.runjob.out" runjob --strace none -p 16 --block $COBALT_PARTNAME : "$@"
+ runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
+ echo "Finished Running in nonsubblock mode."
+fi
+exit 0</code></pre>
+</div></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_sub_block_limitations">6. Sub-block limitations</h2>
+<div class="sectionbody">
+<div class="paragraph"><p>There are currently the following two limitations with sub-block jobs:</p></div>
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+The maximum size of the outer Cobalt job must not exceed 512 nodes, ie. half
+of a hardware rack.
+</p>
+</li>
+<li>
+<p>
+The successive subjobs must be submitted with a gap of at least 3 seconds in
+between. This means for a large number of shorter than 5 seconds jobs, the
+system will be underutilized. Consequently, subblocks are suitable for
+tasks which are more than a couple of minutes in duration.
+</p>
+</li>
+</ol></div>
+</div>
+</div>
+<div class="sect1">
+<h2 id="_further_information">7. Further Information</h2>
+<div class="sectionbody">
+<div class="olist arabic"><ol class="arabic">
+<li>
+<p>
+More information about Swift can be found <a href="http://swift-lang.org/main">here</a>.
+</p>
+</li>
+<li>
+<p>
+More about ALCF can be found <a href="http://www.alcf.anl.gov">here</a>.
+</p>
+</li>
+<li>
+<p>
+More about IBM BlueGene sub-block jobs can be found <a href="http://www.alcf.anl.gov/files/ensemble_jobs_0.pdf">here</a> (warning: pdf).
+</p>
+</li>
+</ol></div>
+</div>
+</div>
+</div>
+<div id="footnotes"><hr /></div>
+<div id="footer">
+<div id="footer-text">
+Last updated 2014-11-07 10:58:42 CST
+</div>
+</div>
+</body>
+</html>
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