Add v0 of scipy on htcondor tools

AUTHORS

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+Steve Goldstein  [email protected]

README.md

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-scipy-on-htcondor
-=================
+Running python+numpy+scipy on HTCondor
+======================================
+
+Author:  Steve Goldstein  [email protected]  July, 2014 
+
+To run python with numpy or scipy on condor, you have to ensure that
+the execute node has a version of python that includes those
+libraries.   CHTC has solved that problem by building such a version of
+python and providing a means to install that version on the execute
+node.
+
+The purpose of the scipy-on-htcondor project is to give you an easy way to
+implement CHTC's solution that can be widely applied.  On the CHTC web
+pages, you can read about some of the details and a more general
+implementation. 
+
+Step by step instructions:
+
+1. Log on to the CHTC submit node:
+
+   ```
+   ssh <netID>@submit-3.chtc.wisc.edu
+   ```
+
+1. Make a directory for your python work.
+
+   ```
+   mkdir myProject
+   cd myProject
+   ```
+
+1. Copy the scipy-on-htcondor.tar.gz tar file to your workspace and extract the
+archive.
+
+   ```
+   wget <URL here...>
+   tar zxvf scipy-on-htcondor.tgz
+   ```
+
+1. Open a another terminal on your own local machine and transfer the program
+   to the indir/ subdirectory.
+
+    ```
+    scp /path/to/my/myPythonProgram.py <netID>@submit-3.chtc.wisc.edu:myProject/indir
+    ```
+
+1. Transfer any other input files to the indir/ subdirectory.
+
+   ```
+   scp /path/to/other/necessary_input_files <netID>@submit-3.chtc.wisc.edu:myProject/indir
+   ```
+
+1. Now back on the terminal in which you are logged into the CHTC submit node,
+   make sure the first line of the python program looks like this:
+
+   ```
+   #!/usr/bin/env python
+   ```
+
+   It should match the first line of the pythontest.py program:
+
+   ```
+   head -1 indir/*py
+   ```
+
+1. Edit the condor submit file, following the (albeit, sparse) directions in
+   that file:
+
+   ```
+   nano queue/process.cmd
+   ```
+
+1. Submit the jobs to condor:
+
+   ```
+   condor_submit queue/process.cmd
+   ```
+
+1. When the jobs have finished, run the cleanup script:
+
+   ```
+   queue/cleanupCHTCPython.pl
+   ```
+
+Your output will be in the outdir directory.  Check the files in `chtcOutput/`
+for errors.
+
 
-Tools to effectively launch SciPy based jobs on HTCondor environments

indir/pythontest.py

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+#!/usr/bin/env python
+
+import os
+import platform
+import sys
+import time
+import numpy
+from scipy import sqrt, pi
+
+print >> sys.stderr, __doc__
+print "Version :", platform.python_version()
+print "Program :", sys.executable
+print 'Script  :', os.path.abspath(__file__)
+print 'Args    :', sys.argv[1:]
+print
+
+a = numpy.arange(10000000)
+b = numpy.arange(10000000)
+c = a + b
+
+
+h1 = sqrt(pi/2)
+
+print a,b
+print c
+print h1
+print 
+
+f = open('DONE','w')
+print >>f,'all','done'
+sys.exit(0)
+

outdir/.gitignore

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+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

queue/cleanupCHTCPython.pl

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+#!/usr/bin/perl -w
+
+
+use strict;
+use Carp;
+use English;
+use Getopt::Long;
+use Cwd;
+
+GetOptions (
+
+            );
+
+my $chtcNoise = "./chtcOutput";
+croak "$chtcNoise directory already exists." 
+    if ( -e $chtcNoise);
+
+croak "Can't create $chtcNoise directory" 
+    unless (mkdir $chtcNoise);
+
+my @filelist = 
+    qw 
+    (
+     ChtcWrapper*out
+     AuditLog*
+     CURLTIME*
+     outdir/*
+     queue/error/*
+     DONE
+     harvest.log
+     CODEBLOWUP
+    );
+
+foreach my $fileSpec (@filelist) {
+    `mv $fileSpec $chtcNoise 2> /dev/null`;
+}
+
+opendir D, "." or croak "Can't read directory";
+my @outputFiles = grep {/^\d+\.\d+\.out$/} readdir D;
+closedir D;
+
+`mv @outputFiles outdir`;
+
+
+__END__

queue/process.cmd

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+###############
+universe = vanilla
+
+
+###################################################
+# 1.  Edit these 2 lines to run your python program. 
+###################################################
+
+PythonProgram          = pythontest.py
+PythonProgramArguments = $(PROCESS)
+###################################################
+
+###################################################
+# 2.  Edit the last line in this file 
+#
+#              queue N
+#
+#     to run N instances of this program.
+###################################################
+
+###################################################
+# 3 . Edit these lines if appropriate
+###################################################
+transfer_input_files = indir/
+
+# Tell Condor how many CPUs (cores), how much memory (MB) and how much 
+# disk space (KB) each job will need:
+request_cpus = 1
+request_memory = 1000
+request_disk = 1000000
+###################################################
+
+
+###################################################
+# 4. Most of the rest of this file does not need editing
+###################################################
+
+executable = /squid/example/ChtcRun/chtcjobwrapper 
+arguments =  --type=Other --version=Python-2.7.3 --cmdtorun $(PythonProgram) --unique=$(CLUSTER).$(PROCESS) -- $(PythonProgramArguments) 
+
+
+output = outdir/process.$(CLUSTER).$(PROCESS).out
+error  = queue/error/process.$(CLUSTER).$(PROCESS).err
+log  = queue/process.$(CLUSTER).log
+
+#################################################################
+
+requirements = (OpSysAndVer =?= "SL6")
+
+should_transfer_files = YES
+when_to_transfer_output = ON_EXIT
+
+#################################################################
+# By default, your job will be submitted to the CHTC's HTCondor 
+# Pool only, which is good for jobs that are each less than 24 hours.
+#
+# If your jobs are less than 4 hours long, "flock" them additionally to 
+# other HTCondor pools on campus by uncommenting the below line:
+#+WantFlocking = true
+
+#
+# If your jobs are less than ~2 hours long, "glide" them to the national
+# Open Science Grid (OSG) for access to even more computers and the
+# fastest overall throughput. Uncomment the below line:
+#+WantGlidein = true
+###################################################
+
+# Release a job from being on hold hold after 5 minutes (300 seconds), up to 4 times,
+# as long as the executable could be started, the input files and initial directory
+# were accessible and the user log could be created. This will help your jobs to retry
+# if they happen to fail due to a computer issue (not an issue with your job)
+periodic_release = (JobStatus == 5) && ((CurrentTime - EnteredCurrentStatus) > 300) && (JobRunCount < 5) && (HoldReasonCode != 6) && (HoldReasonCode != 14) && (HoldReasonCode != 22)
+
+# If you want your jobs to go on hold because they are
+# running longer then expected,  uncomment this line and
+# change from 24 hours to desired limit:
+#periodic_hold = (JobStatus == 2) && ((CurrentTime - EnteredCurrentStatus) > (60 * 60 * 24))
+
+# We don't want email about our jobs.
+notification = never
+
+###################################################
+## This must be the last line
+queue 2