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From "Dan Brickley (Created) (JIRA)" <>
Subject [jira] [Created] (MAHOUT-978) spectralkmeans utility fails when input filename begins with leading underscore
Date Sun, 19 Feb 2012 13:58:34 GMT
spectralkmeans utility fails when input filename begins with leading underscore

                 Key: MAHOUT-978
             Project: Mahout
          Issue Type: Bug
          Components: Clustering
    Affects Versions: 0.6
         Environment: Tested on a real Linux-based cluster running Hadoop 0.20.2-cdh3u2 and
the 0.6 release; also OSX pseudo cluster running Hadoop running 16 Feb trunk build.

            Reporter: Dan Brickley
            Priority: Minor

The commandline 'bin/mahout spectralkmeans' utility fails with NoSuchElementException after
"Loading vector from: spectral/output/results2/calculations/diagonal/part-r-00000"  when input
data in hdfs has filename beginning with a leading underscore.

This was partially reported in comments for MAHOUT-524 but I believe identified now as a distinct
issue (thanks to Shannon for help diagnosing). I have not investigated if there is an equivalent
problem for API-based use of this piece of Mahout.

Steps to reproduce: 

1. put affinity file into hdfs, following
- note that node IDs count from zero etc. Name your file with a leading underscore. For example,
try and store it in spectral/input/_topic_skm.csv

(I'll leave that example input file in place unchanged for others to try. It is built from
dbpedia data, encoding associations from Wikipedia pages to categories. Whether it is a good
use of spectral clustering I'm not sure, but I'd at least hope the job would run to completion.)

2. Run 'mahout spectralkmeans -k 20 -d 4192499 -x 7 -i spectral/input/ -o spectral/output/results1'

3. Wait for it to fail just after printing "Loading vector from: spectral/output/results1/calculations/diagonal/part-r-00000",
with java.util.NoSuchElementException at

4. Rename the file in hdfs to eliminate the leading underscore. Re-run the command (give a
different results dir or cleanup from the first run, to avoid mixing the tests). This attempt
should succeed and you'll see it proceed deeper into the job, i.e. something like 

12/02/19 14:38:32 INFO common.VectorCache: Loading vector from: spectral/output/results2/calculations/diagonal/part-r-00000
12/02/19 14:38:41 WARN mapred.JobClient: Use GenericOptionsParser for parsing the arguments.
Applications should implement Tool for the same.
12/02/19 14:38:43 INFO input.FileInputFormat: Total input paths to process : 1
12/02/19 14:38:44 INFO mapred.JobClient: Running job: job_201202191410_0005
12/02/19 14:38:45 INFO mapred.JobClient:  map 0% reduce 0%
12/02/19 14:39:31 INFO mapred.JobClient:  map 1% reduce 0%

(5. You might get a memory-based failure some time later; that is a separate problem.)

I'll attach a more detailed transcript. I've made no attempt to diagnose internals yet, but
did make some other tests and can confirm that it does not seem to matter whether the commandline
invocation names the file explicitly, or by directory name only. Also trailing slash does
not seem to be an issue. Finally, a related 'gotcha': make sure the results directory is not
inside the input directory when testing.

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