Monday Exercise 2.6: Submit With “queue from”

The goal of this exercise is to submit many jobs from a single submit file by using the queue ... from syntax to read variable values from a file.

More Job Submission Alternatives

In the previous exercise, we use the queue ... matching syntax, which is primarily useful for collections of files with similar names. But that method has its weaknesses, too. It is less useful when a collection of files does not have a consistent and unique pattern for its names, or when the values for different job conditions are not filenames, or both.

Queue Jobs From File Contents

Suppose we want to modify our word-frequency analysis a little bit so that it outputs only the most common N words of a document. Further, we want to experiment with different values of N. And finally, even though we downloaded it, we no longer want to analyze the Sherlock Holmes stories in the TAoSH.txt file. Clearly, queue ... matching will not help us in this case.

First, we need a new version of the word counting program so that in accepts an extra number as a command line argument and outputs only that many of the most common words. Here is the new code:

#!/usr/bin/env python

import os
import sys
import operator

if len(sys.argv) != 3:
    print 'Usage: %s DATA NUM_WORDS' % (os.path.basename(sys.argv[0]))
input_filename = sys.argv[1]
num_words = int(sys.argv[2])

words = {}

my_file = open(input_filename, 'r')
for line in my_file:
    line_words = line.split()
    for word in line_words:
        if word in words:
            words[word] += 1
            words[word] = 1

sorted_words = sorted(words.items(), key=operator.itemgetter(1))
for word in sorted_words[-num_words:]:
    print '%s %8d' % (word[0], word[1])

To submit this program with a collection of two variables values for each run:

  1. In the same directory as the last exercise, save the script as
  2. Copy your submit file from the last exercise to a new name (maybe wordcount-top.sub)
  3. Update the executable and log statements as appropriate
  4. Update other statements to work with two variables, book and n:\

output = $(book)_top_$(n).out error = $(book)_top_$(n).err transfer_input_files = $(book) arguments = "$(book) $(n)" queue book, n from books_n.txt \

Note especially the changes to the queue statement; it now tells HTCondor to read a separate text file of pairs of values, which will be assigned to book and n respectively.

  1. Create the separate text file of job variable values and save it as books_n.txt:

AAiW.txt, 10 AAiW.txt, 25 AAiW.txt, 50 PandP.txt, 10 PandP.txt, 25 PandP.txt, 50 \

Note that we used 3 different values for N for each book, and that we dropped the Sherlock Holmes book, TAoSH.txt.

  1. Submit the file
  2. Do a quick sanity check: How many jobs were submitted? How many log, output, and error files were created?

Extra Challenge 1

Between this exercise and the previous one, you have explored two of the three primary queue statements. How would you use the queue in ... list statement to accomplish the same thing(s) as one or both of the exercises?

Extra Challenge 2

You may have noticed that the output of these jobs has a messy naming convention. Because our macros resolve to the filenames, including their extension (e.g., AAiW.txt), the output filenames contain with multiple extensions (e.g., AAiW.txt.err). Although the extra extension is acceptable, it makes the filenames harder to read and possibly organize. Change your submit file for this exercise so that the output filenames do not include the .txt extension.

Extra Challenge 3

Adjust your queue...matching submit file so that those results also don't include the .txt extension. (Hint: You can use function macros to format variables. Check the HTCondor Manual.)