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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Based on your suggestion, I came up with the following code. However, I’m having an issue with it. If I use an external mapper I can choose whether to return
a file or not based on whether it already exists. However, once I made a decision not to return a file from the external mapper because it has already been generated, I don’t see how to enable subsequent workflow steps to take it as input. In the code below,
if dataFile exists but copyFile does not, I get the following error:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Execution failed:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> org.griphyn.vdl.mapping.InvalidPathException: Array index '0' not found for f1 of size 0<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> copyFile, testResume.swift, line 20<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> copyFile, testResume.swift, line 20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D">Greg Bronevetsky</span><span style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D">Lawrence Livermore National Lab</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D">(925) 424-5756</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="mailto:bronevetsky@llnl.gov">bronevetsky@llnl.gov</a></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://greg.bronevetsky.com">http://greg.bronevetsky.com</a></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Swift:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">type file;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">string ROOT_PATH="/g/g15/bronevet/apps/swift-0.94.1/examples/test";<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">app (file outF) writeFile(string message) {<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> echo message stdout=@filename(outF);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">app (file outF) copyFile(file inF) {<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> cp @filename(inF) @filename(outF);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">file f1[] <ext;exec=@strcat(ROOT_PATH,"/immutable.py"), fName="dataFile">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">if(@length(f1) == 1) {<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> f1[0] = writeFile("hello");<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">file f2[] <ext;exec=@strcat(ROOT_PATH,"/immutable.py"), fName="copyFile">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">if(@length(f2) == 1) {<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> f2[0] = copyFile(f1[0]);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">External mapper in Python:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">#!/usr/apps/python2.7.3/bin/python<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">import argparse<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">import sys<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">import os<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">def main(argv):<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> parser = argparse.ArgumentParser(description='Merge stats and distances files from experiments.')<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> parser.add_argument('-fName', dest='fName', action='store', nargs="+", help='List of files to check for existence')<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> args = parser.parse_args()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> for i in range(0, len(args.fName)):<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> if(not (os.path.exists(args.fName[i]))):<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> print "["+str(i)+"] "+args.fName[i]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">if __name__ == "__main__":<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> main(sys.argv[1:])<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> swift-user-bounces@ci.uchicago.edu [mailto:swift-user-bounces@ci.uchicago.edu]
<b>On Behalf Of </b>Michael Wilde<br>
<b>Sent:</b> Friday, May 16, 2014 10:53 AM<br>
<b>To:</b> swift-user@ci.uchicago.edu<br>
<b>Subject:</b> Re: [Swift-user] Resuming jobs when script has changed<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Greg,<br>
<br>
The Swift resume mechanism can't do this, as its driven by internal variables name within a Swift run, not by external file existence.<br>
<br>
The best way to do what you describe below is to write an external input file mapper (e.g. a simple shell or py script) that returns only the files that still need to be produced or processed. (This is the "ext" mapper:
<a href="http://swift-lang.org/guides/release-0.94/userguide/userguide.html#_external_mapper">
http://swift-lang.org/guides/release-0.94/userguide/userguide.html#_external_mapper</a> )<br>
<br>
You can also call a local app to determine what files need to be produced, then use readData() to read those file names into an array, and array_mapper to map an array of remaining work to do.<br>
<br>
Would one of these approaches meet your needs?<br>
<br>
- Mike<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 5/16/14, 12:35 PM, Bronevetsky, Greg wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>I have Swift scripts that scan some portion of a design space and after I have scanned a sub-space of all the possibilities I modify the script to target a different, overlapping portion of the design space. However, it seems that when I do this Swift ignores the fact that I've already computed many of the tasks in the new run when I performed the prior run, and re-executes them redundantly. Is there a way for me to avoid such redundant executions? Can the -resume flag be used in this case?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Greg Bronevetsky<o:p></o:p></pre>
<pre>Lawrence Livermore National Lab<o:p></o:p></pre>
<pre>(925) 424-5756<o:p></o:p></pre>
<pre><a href="mailto:bronevetsky@llnl.gov">bronevetsky@llnl.gov</a><a href="mailto:bronevetsky@llnl.gov"><mailto:bronevetsky@llnl.gov></a><o:p></o:p></pre>
<pre><a href="http://greg.bronevetsky.com">http://greg.bronevetsky.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Swift-user mailing list<o:p></o:p></pre>
<pre><a href="mailto:Swift-user@ci.uchicago.edu">Swift-user@ci.uchicago.edu</a><o:p></o:p></pre>
<pre><a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Michael Wilde<o:p></o:p></pre>
<pre>Mathematics and Computer Science Computation Institute<o:p></o:p></pre>
<pre>Argonne National Laboratory The University of Chicago<o:p></o:p></pre>
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