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POWhat is this cProfile result telling me I need to fix?
 

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  1. POWhat is this cProfile result telling me I need to fix?
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    <p>I would like to improve the performance of a Python script and have been using <code>cProfile</code> to generate a performance report:</p> <pre><code>python -m cProfile -o chrX.prof ./bgchr.py ...args... </code></pre> <p>I opened this <code>chrX.prof</code> file with Python's <code>pstats</code> and printed out the statistics:</p> <pre><code>Python 2.7 (r27:82500, Oct 5 2010, 00:24:22) [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2 Type "help", "copyright", "credits" or "license" for more information. &gt;&gt;&gt; import pstats &gt;&gt;&gt; p = pstats.Stats('chrX.prof') &gt;&gt;&gt; p.sort_stats('name') &gt;&gt;&gt; p.print_stats() Sun Oct 10 00:37:30 2010 chrX.prof 8760583 function calls in 13.780 CPU seconds Ordered by: function name ncalls tottime percall cumtime percall filename:lineno(function) 1 0.000 0.000 0.000 0.000 {_locale.setlocale} 1 1.128 1.128 1.128 1.128 {bz2.decompress} 1 0.002 0.002 13.780 13.780 {execfile} 1750678 0.300 0.000 0.300 0.000 {len} 48 0.000 0.000 0.000 0.000 {method 'append' of 'list' objects} 1 0.000 0.000 0.000 0.000 {method 'close' of 'file' objects} 1 0.000 0.000 0.000 0.000 {method 'disable' of '_lsprof.Profiler' objects} 1750676 0.496 0.000 0.496 0.000 {method 'join' of 'str' objects} 1 0.007 0.007 0.007 0.007 {method 'read' of 'file' objects} 1 0.000 0.000 0.000 0.000 {method 'readlines' of 'file' objects} 1 0.034 0.034 0.034 0.034 {method 'rstrip' of 'str' objects} 23 0.000 0.000 0.000 0.000 {method 'seek' of 'file' objects} 1757785 1.230 0.000 1.230 0.000 {method 'split' of 'str' objects} 1 0.000 0.000 0.000 0.000 {method 'startswith' of 'str' objects} 1750676 0.872 0.000 0.872 0.000 {method 'write' of 'file' objects} 1 0.007 0.007 13.778 13.778 ./bgchr:3(&lt;module&gt;) 1 0.000 0.000 13.780 13.780 &lt;string&gt;:1(&lt;module&gt;) 1 0.001 0.001 0.001 0.001 {open} 1 0.000 0.000 0.000 0.000 {sys.exit} 1 0.000 0.000 0.000 0.000 ./bgchr:36(checkCommandLineInputs) 1 0.000 0.000 0.000 0.000 ./bgchr:27(checkInstallation) 1 1.131 1.131 13.701 13.701 ./bgchr:97(extractData) 1 0.003 0.003 0.007 0.007 ./bgchr:55(extractMetadata) 1 0.064 0.064 13.771 13.771 ./bgchr:5(main) 1750677 8.504 0.000 11.196 0.000 ./bgchr:122(parseJarchLine) 1 0.000 0.000 0.000 0.000 ./bgchr:72(parseMetadata) 1 0.000 0.000 0.000 0.000 /home/areynolds/proj/tools/lib/python2.7/locale.py:517(setlocale) </code></pre> <p>Question: What can I do about <code>join</code>, <code>split</code> and <code>write</code> operations to reduce the apparent impact they have on the performance of this script?</p> <p>If it is relevant, here is the full source code to the script in question:</p> <pre><code>#!/usr/bin/env python import sys, os, time, bz2, locale def main(*args): # Constants global metadataRequiredFileSize metadataRequiredFileSize = 8192 requiredVersion = (2,5) # Prep global whichChromosome whichChromosome = "all" checkInstallation(requiredVersion) checkCommandLineInputs() extractMetadata() parseMetadata() if whichChromosome == "--list": listMetadata() sys.exit(0) # Extract extractData() return 0 def checkInstallation(rv): currentVersion = sys.version_info if currentVersion[0] == rv[0] and currentVersion[1] &gt;= rv[1]: pass else: sys.stderr.write( "\n\t[%s] - Error: Your Python interpreter must be %d.%d or greater (within major version %d)\n" % (sys.argv[0], rv[0], rv[1], rv[0]) ) sys.exit(-1) return def checkCommandLineInputs(): cmdName = sys.argv[0] argvLength = len(sys.argv[1:]) if (argvLength == 0) or (argvLength &gt; 2): sys.stderr.write( "\n\t[%s] - Usage: %s [&lt;chromosome&gt; | --list] &lt;bjarch-file&gt;\n\n" % (cmdName, cmdName) ) sys.exit(-1) else: global inFile global whichChromosome if argvLength == 1: inFile = sys.argv[1] elif argvLength == 2: whichChromosome = sys.argv[1] inFile = sys.argv[2] if inFile == "-" or inFile == "--list": sys.stderr.write( "\n\t[%s] - Usage: %s [&lt;chromosome&gt; | --list] &lt;bjarch-file&gt;\n\n" % (cmdName, cmdName) ) sys.exit(-1) return def extractMetadata(): global metadataList global dataHandle metadataList = [] dataHandle = open(inFile, 'rb') try: for data in dataHandle.readlines(metadataRequiredFileSize): metadataLine = data metadataLines = metadataLine.split('\n') for line in metadataLines: if line: metadataList.append(line) except IOError: sys.stderr.write( "\n\t[%s] - Error: Could not extract metadata from %s\n\n" % (sys.argv[0], inFile) ) sys.exit(-1) return def parseMetadata(): global metadataList global metadata metadata = [] if not metadataList: # equivalent to "if len(metadataList) &gt; 0" sys.stderr.write( "\n\t[%s] - Error: No metadata in %s\n\n" % (sys.argv[0], inFile) ) sys.exit(-1) for entryText in metadataList: if entryText: # equivalent to "if len(entryText) &gt; 0" entry = entryText.split('\t') filename = entry[0] chromosome = entry[0].split('.')[0] size = entry[1] entryDict = { 'chromosome':chromosome, 'filename':filename, 'size':size } metadata.append(entryDict) return def listMetadata(): for index in metadata: chromosome = index['chromosome'] filename = index['filename'] size = long(index['size']) sys.stdout.write( "%s\t%s\t%ld" % (chromosome, filename, size) ) return def extractData(): global dataHandle global pLength global lastEnd locale.setlocale(locale.LC_ALL, 'POSIX') dataHandle.seek(metadataRequiredFileSize, 0) # move cursor past metadata for index in metadata: chromosome = index['chromosome'] size = long(index['size']) pLength = 0L lastEnd = "" if whichChromosome == "all" or whichChromosome == index['chromosome']: dataStream = dataHandle.read(size) uncompressedData = bz2.decompress(dataStream) lines = uncompressedData.rstrip().split('\n') for line in lines: parseJarchLine(chromosome, line) if whichChromosome == chromosome: break else: dataHandle.seek(size, 1) # move cursor past chromosome chunk dataHandle.close() return def parseJarchLine(chromosome, line): global pLength global lastEnd elements = line.split('\t') if len(elements) &gt; 1: if lastEnd: start = long(lastEnd) + long(elements[0]) lastEnd = long(start + pLength) sys.stdout.write("%s\t%ld\t%ld\t%s\n" % (chromosome, start, lastEnd, '\t'.join(elements[1:]))) else: lastEnd = long(elements[0]) + long(pLength) sys.stdout.write("%s\t%ld\t%ld\t%s\n" % (chromosome, long(elements[0]), lastEnd, '\t'.join(elements[1:]))) else: if elements[0].startswith('p'): pLength = long(elements[0][1:]) else: start = long(long(lastEnd) + long(elements[0])) lastEnd = long(start + pLength) sys.stdout.write("%s\t%ld\t%ld\n" % (chromosome, start, lastEnd)) return if __name__ == '__main__': sys.exit(main(*sys.argv)) </code></pre> <p><strong>EDIT</strong></p> <p>If I comment out the <code>sys.stdout.write</code> statement in the first conditional of <code>parseJarchLine()</code>, then my runtime goes from 10.2 sec to 4.8 sec:</p> <pre><code># with first conditional's "sys.stdout.write" enabled $ time ./bgchr chrX test.bjarch &gt; /dev/null real 0m10.186s user 0m9.917s sys 0m0.160s # after first conditional's "sys.stdout.write" is commented out $ time ./bgchr chrX test.bjarch &gt; /dev/null real 0m4.808s user 0m4.561s sys 0m0.156s </code></pre> <p>Is writing to <code>stdout</code> really that expensive in Python?</p>
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    1. COBreak the code to small functions. Python's cProfile is pretty much useless for code that is written as one big chunk, because it's a function-level profiler, not line-by-line profiler. In the meantime, you can gain some speed increase if you put everything in a main() function, since in Python accessing global variables is slower than accessing a local variable.
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      1. USLie Ryan
    2. CO@Lie Ryan: Look at the numbers! These are detailed enough to show where optimization is needed. Access to global variables is not relevant here, and the times for bgchr:4(<module>) and <string>:1(<module>) correspond to the total execution time.
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      1. USBernd Petersohn
    3. CO@Bernd Petersohn: Please consider the possibility that you are mistaken. See my answer.
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