Hi, thanks for the fix. I guess it's one step closer to a worlable solution. I am now getting this error:
10/02/12 16:59:25 INFO mapred.JobClient: Task Id : attempt_201001192218_0234_m_000004_1, Status : FAILED java.lang.ArrayIndexOutOfBoundsException: 104017 at org.apache.mahout.math.DenseMatrix.getQuick(DenseMatrix.java:75) at org.apache.mahout.clustering.lda.LDAState.logProbWordGivenTopic(LDAState.java:40) at org.apache.mahout.clustering.lda.LDAInference.eStepForWord(LDAInference.java:204) at org.apache.mahout.clustering.lda.LDAInference.infer(LDAInference.java:117) at org.apache.mahout.clustering.lda.LDAMapper.map(LDAMapper.java:47) at org.apache.mahout.clustering.lda.LDAMapper.map(LDAMapper.java:37) at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:144) at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:583) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305) at org.apache.hadoop.mapred.Child.main(Child.java:170) Ovi --- Ovidiu Dan - http://www.ovidiudan.com/ Please do not print this e-mail unless it is mandatory My public key can be downloaded from subkeys.pgp.net, or http://www.ovidiudan.com/public.pgp On Fri, Feb 12, 2010 at 4:29 PM, Ovidiu Dan <[email protected]> wrote: > > Will do in a bit, thanks! > > --- > Ovidiu Dan - http://www.ovidiudan.com/ > > Please do not print this e-mail unless it is mandatory > > My public key can be downloaded from subkeys.pgp.net, or > http://www.ovidiudan.com/public.pgp > > > On Fri, Feb 12, 2010 at 4:27 PM, Robin Anil <[email protected]> wrote: > >> Ovidiu we just commited the fix. Just recreate vectors using the -seq >> option >> added to it. >> >> Remember to svnup and recompile >> >> Robin >> On Sat, Feb 13, 2010 at 2:39 AM, Jake Mannix <[email protected]> >> wrote: >> >> > Robin and I are trying out a fix. I already ran into this in hooking >> > the Vectorizer up to my SVD code. >> > >> > -jake >> > >> > On Fri, Feb 12, 2010 at 1:08 PM, Ovidiu Dan <[email protected]> wrote: >> > >> > > Well, I tried it. The previous problem is fixed, but now I have a new >> and >> > > shiny one :( >> > > >> > > Meet line 95 of LDAInference,java: >> > > DenseMatrix phi = new DenseMatrix(state.numTopics, docLength); >> > > >> > > docLength is calculated above on line 88: >> > > int docLength = wordCounts.size(); >> > > >> > > My problem is that docLength is always 2147483647. Since DenseMatrix >> > > allocated an array based (also) on this value, I get multiple >> "Requested >> > > array size exceeds VM limit" messages (an array with 2147483647 >> columns >> > > would be quite large). >> > > >> > > I added a trivial toString function that displays vector.size() >> > > in org/apache/mahout/math/VectorWritable.java, recompiled the project, >> > then >> > > ran: >> > > >> > > ./hadoop fs -text >> > > /user/MY_USERNAME/projects/lda/mahout_vectors/vectors/part-00000 >> > > >> > > All lines were DOCUMENT_ID (tab) 2147483647. So all vectors report >> > > size 2147483647 >> > > >> > > I checked the output for vector.zSum() as well, that one looks fine. >> > > >> > > I can confirm that my input SequenceFile is correct, it has the >> following >> > > format: >> > > - key: Text with unique id of document >> > > - value: Text with the contents of the document >> > > >> > > Ovi >> > > >> > > --- >> > > Ovidiu Dan - http://www.ovidiudan.com/ >> > > >> > > Please do not print this e-mail unless it is mandatory >> > > >> > > My public key can be downloaded from subkeys.pgp.net, or >> > > http://www.ovidiudan.com/public.pgp >> > > >> > > >> > > On Fri, Feb 12, 2010 at 3:30 PM, Ovidiu Dan <[email protected]> wrote: >> > > >> > > > >> > > > Thanks, I also patched it myself but now I have some other problems. >> > I'll >> > > > run it and let you know how it goes. >> > > > >> > > > Ovi >> > > > >> > > > --- >> > > > Ovidiu Dan - http://www.ovidiudan.com/ >> > > > >> > > > Please do not print this e-mail unless it is mandatory >> > > > >> > > > My public key can be downloaded from subkeys.pgp.net, or >> > > > http://www.ovidiudan.com/public.pgp >> > > > >> > > > >> > > > On Fri, Feb 12, 2010 at 3:25 PM, Robin Anil <[email protected]> >> > > wrote: >> > > > >> > > >> I fixed the bug here >> https://issues.apache.org/jira/browse/MAHOUT-289 >> > > >> >> > > >> >> > > >> Try running now. >> > > >> >> > > >> Robin >> > > >> >> > > >> On Sat, Feb 13, 2010 at 1:09 AM, Ovidiu Dan <[email protected]> >> wrote: >> > > >> >> > > >> > I checked the code. >> > > >> > >> > > >> > Line 36 of LDAMapper.java references Vector: >> > > >> > >> > > >> > public class LDAMapper extends >> > > >> > Mapper<WritableComparable<?>, *Vector*, IntPairWritable, >> > > >> DoubleWritable> >> > > >> > { >> > > >> > >> > > >> > Aren't all elements in Mapper<...> supposed to be Writable? Do >> you >> > > need >> > > >> to >> > > >> > do a conversion to VectorWritable? >> > > >> > >> > > >> > Ovi >> > > >> > >> > > >> > --- >> > > >> > Ovidiu Dan - http://www.ovidiudan.com/ >> > > >> > >> > > >> > Please do not print this e-mail unless it is mandatory >> > > >> > >> > > >> > My public key can be downloaded from subkeys.pgp.net, or >> > > >> > http://www.ovidiudan.com/public.pgp >> > > >> > >> > > >> > >> > > >> > On Fri, Feb 12, 2010 at 2:32 PM, Ovidiu Dan <[email protected]> >> > wrote: >> > > >> > >> > > >> > > >> > > >> > > Ok I did a clean checkout & install and ran everything again, >> then >> > > >> > pointed >> > > >> > > LDA to mahout_vectors/vectors. >> > > >> > > >> > > >> > > Now I get this error: >> > > >> > > >> > > >> > > 10/02/12 14:28:35 INFO mapred.JobClient: Task Id : >> > > >> > > attempt_201001192218_0216_m_000005_0, Status : FAILED >> > > >> > > java.lang.ClassCastException: >> > *org.apache.mahout.math.VectorWritable >> > > >> > > cannot be cast to org.apache.mahout.math.Vector* >> > > >> > > at >> > > org.apache.mahout.clustering.lda.LDAMapper.map(LDAMapper.java:36) >> > > >> > > at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:144) >> > > >> > > at >> > org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:583) >> > > >> > > at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305) >> > > >> > > at org.apache.hadoop.mapred.Child.main(Child.java:170) >> > > >> > > >> > > >> > > Ovi >> > > >> > > >> > > >> > > --- >> > > >> > > Ovidiu Dan - http://www.ovidiudan.com/ >> > > >> > > >> > > >> > > Please do not print this e-mail unless it is mandatory >> > > >> > > >> > > >> > > My public key can be downloaded from subkeys.pgp.net, or >> > > >> > > http://www.ovidiudan.com/public.pgp >> > > >> > > >> > > >> > > >> > > >> > > On Fri, Feb 12, 2010 at 1:50 PM, Robin Anil < >> [email protected] >> > > >> > > >> > wrote: >> > > >> > > >> > > >> > >> Hi Ovidu, >> > > >> > >> If you choose tf, the vectors are generated in >> > > >> > >> outputfolder/vectors and if you choose tfidf the vectors are >> > > >> generated >> > > >> > in >> > > >> > >> outputfolder/tfidf/vectors. I am in the process of changing >> the >> > > code >> > > >> to >> > > >> > >> move >> > > >> > >> the output of the map/reduce to a fixed destination and that >> > > >> exception >> > > >> > >> would >> > > >> > >> have caused the folders not to move. >> > > >> > >> Thats the reason for the last error. >> > > >> > >> >> > > >> > >> For the first error, I am not sure what is happening. Could >> you >> > do >> > > a >> > > >> > clean >> > > >> > >> compile of mahout >> > > >> > >> >> > > >> > >> mvn clean install -DskipTests=true and make sure you svn up >> the >> > > trunk >> > > >> > >> before >> > > >> > >> doing that >> > > >> > >> >> > > >> > >> Then point your LDA to mahout_vectors/vectors >> > > >> > >> >> > > >> > >> Robin >> > > >> > >> >> > > >> > >> >> > > >> > >> On Sat, Feb 13, 2010 at 12:14 AM, Ovidiu Dan < >> [email protected]> >> > > >> wrote: >> > > >> > >> >> > > >> > >> > Hi again, >> > > >> > >> > >> > > >> > >> > Is there any workaround for my problem(s)? Or is there any >> > other >> > > >> way >> > > >> > >> that >> > > >> > >> > would allow me to transform many many small messages >> (they're >> > > >> Tweets) >> > > >> > >> into >> > > >> > >> > Mahout vectors, and the run LDA on them, without getting >> these >> > > >> errors? >> > > >> > >> > Converting them to txt files would be a bit of a pain >> because I >> > > >> would >> > > >> > >> get >> > > >> > >> > millions of very small files. And a Lucene index would be a >> bit >> > > >> > overkill >> > > >> > >> I >> > > >> > >> > think. >> > > >> > >> > >> > > >> > >> > Thanks, >> > > >> > >> > Ovi >> > > >> > >> > >> > > >> > >> > --- >> > > >> > >> > Ovidiu Dan - http://www.ovidiudan.com/ >> > > >> > >> > >> > > >> > >> > Please do not print this e-mail unless it is mandatory >> > > >> > >> > >> > > >> > >> > My public key can be downloaded from subkeys.pgp.net, or >> > > >> > >> > http://www.ovidiudan.com/public.pgp >> > > >> > >> > >> > > >> > >> > >> > > >> > >> > On Fri, Feb 12, 2010 at 3:51 AM, Robin Anil < >> > > [email protected]> >> > > >> > >> wrote: >> > > >> > >> > >> > > >> > >> > > Was meant for the dev list. I am looking into the first >> error >> > > >> > >> > > >> > > >> > >> > > -bcc mahout-user >> > > >> > >> > > >> > > >> > >> > > >> > > >> > >> > > ---------- Forwarded message ---------- >> > > >> > >> > > From: Robin Anil <[email protected]> >> > > >> > >> > > Date: Fri, Feb 12, 2010 at 2:20 PM >> > > >> > >> > > Subject: Re: Problem converting SequenceFile to vectors, >> then >> > > >> > running >> > > >> > >> LDA >> > > >> > >> > > To: [email protected] >> > > >> > >> > > >> > > >> > >> > > >> > > >> > >> > > Hi, >> > > >> > >> > > >> > > >> > >> > > This confusion arises from the fact that we use >> > > intermediate >> > > >> > >> folders >> > > >> > >> > > as subfolders under output folder. How about we >> standardize >> > on >> > > >> all >> > > >> > the >> > > >> > >> > jobs >> > > >> > >> > > taking input, intermediate and output folder?. If not this >> > then >> > > >> for >> > > >> > >> the >> > > >> > >> > > next >> > > >> > >> > > release? >> > > >> > >> > > >> > > >> > >> > > Robin >> > > >> > >> > > >> > > >> > >> > > >> > > >> > >> > > >> > > >> > >> > > >> > > >> > >> > > On Fri, Feb 12, 2010 at 10:46 AM, Ovidiu Dan < >> > [email protected] >> > > > >> > > >> > >> wrote: >> > > >> > >> > > >> > > >> > >> > > > Hello Mahout developers / users, >> > > >> > >> > > > >> > > >> > >> > > > I am trying to convert a properly formatted SequenceFile >> to >> > > >> Mahout >> > > >> > >> > > vectors >> > > >> > >> > > > to run LDA on them. As reference I am using these two >> > > >> documents: >> > > >> > >> > > > >> > > http://cwiki.apache.org/MAHOUT/creating-vectors-from-text.html >> > > >> > >> > > > >> > > >> http://cwiki.apache.org/MAHOUT/latent-dirichlet-allocation.html >> > > >> > >> > > > >> > > >> > >> > > > I got the Mahout code from SVN on February 11th 2010. >> Below >> > I >> > > >> am >> > > >> > >> > listing >> > > >> > >> > > > the >> > > >> > >> > > > steps I have took and the problems I have encountered: >> > > >> > >> > > > >> > > >> > >> > > > export HADOOP_HOME=/home/hadoop/hadoop/hadoop_install/ >> > > >> > >> > > > export >> > > >> > >> > >> > MAHOUT_HOME=/home/hadoop/hadoop/hadoop_install/bin/ovi/lda/trunk/ >> > > >> > >> > > > >> > > >> > >> > > > $HADOOP_HOME/bin/hadoop jar >> > > >> > >> > > > >> > $MAHOUT_HOME/examples/target/mahout-examples-0.3-SNAPSHOT.job >> > > >> > >> > > > org.apache.mahout.text.SparseVectorsFromSequenceFiles -i >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/twitter_sequence_files/ >> -o >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/mahout_vectors/ -wt tf >> > -chunk >> > > >> 300 >> > > >> > -a >> > > >> > >> > > > org.apache.lucene.analysis.standard.StandardAnalyzer >> > > >> --minSupport >> > > >> > 2 >> > > >> > >> > > --minDF >> > > >> > >> > > > 1 --maxDFPercent 50 --norm 2 >> > > >> > >> > > > >> > > >> > >> > > > *Problem #1: *Got this error at the end, but I think >> > > everything >> > > >> > >> > finished >> > > >> > >> > > > more or less correctly: >> > > >> > >> > > > Exception in thread "main" java.lang.NoSuchMethodError: >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> org.apache.mahout.common.HadoopUtil.deletePath(Ljava/lang/String;Lorg/apache/hadoop/fs/FileSystem;)V >> > > >> > >> > > > at >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> org.apache.mahout.utils.vectors.text.DictionaryVectorizer.createTermFrequencyVectors(DictionaryVectorizer.java:173) >> > > >> > >> > > > at >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> org.apache.mahout.text.SparseVectorsFromSequenceFiles.main(SparseVectorsFromSequenceFiles.java:254) >> > > >> > >> > > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native >> > > Method) >> > > >> > >> > > > at >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> > > >> > >> > > > at >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> > > >> > >> > > > at java.lang.reflect.Method.invoke(Method.java:597) >> > > >> > >> > > > at org.apache.hadoop.util.RunJar.main(RunJar.java:156) >> > > >> > >> > > > >> > > >> > >> > > > $HADOOP_HOME/bin/hadoop jar >> > > >> > >> > > > >> > $MAHOUT_HOME/examples/target/mahout-examples-0.3-SNAPSHOT.job >> > > >> > >> > > > org.apache.mahout.clustering.lda.LDADriver -i >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/mahout_vectors/ -o >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/lda_out/ -k 20 --numWords >> > > 100000 >> > > >> > >> > > > --numReducers 33 >> > > >> > >> > > > >> > > >> > >> > > > *Problem #2: *Exception in thread "main" >> > > >> > >> java.io.FileNotFoundException: >> > > >> > >> > > > File >> > > >> > >> > > > does not exist: >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> hdfs://SOME_SERVER:8003/user/MY_USERNAME/projects/lda/mahout_vectors/partial-vectors-0/data >> > > >> > >> > > > >> > > >> > >> > > > *Tried to fix:* >> > > >> > >> > > > >> > > >> > >> > > > ../../hadoop fs -mv >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> /user/MY_USERNAME/projects/lda/mahout_vectors/partial-vectors-0/part-00000 >> > > >> > >> > > > >> > > >> > >> /user/MY_USERNAME/projects/lda/mahout_vectors/partial-vectors-0/data >> > > >> > >> > > > >> > > >> > >> > > > *Ran again:* >> > > >> > >> > > > >> > > >> > >> > > > $HADOOP_HOME/bin/hadoop jar >> > > >> > >> > > > >> > $MAHOUT_HOME/examples/target/mahout-examples-0.3-SNAPSHOT.job >> > > >> > >> > > > org.apache.mahout.clustering.lda.LDADriver -i >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/mahout_vectors/ -o >> > > >> > >> > > > /user/MY_USERNAME/projects/lda/lda_out/ -k 20 --numWords >> > > 100000 >> > > >> > >> > > > --numReducers 33 >> > > >> > >> > > > >> > > >> > >> > > > *Problem #3:* >> > > >> > >> > > > >> > > >> > >> > > > Exception in thread "main" >> java.io.FileNotFoundException: >> > > File >> > > >> > does >> > > >> > >> not >> > > >> > >> > > > exist: >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> hdfs://SOME_SERVER:8003/user/MY_USERNAME/projects/lda/mahout_vectors/tokenized-documents/data >> > > >> > >> > > > >> > > >> > >> > > > [had...@some_server retweets]$ ../../hadoop fs -ls >> > > >> > >> > > > >> > > >> /user/MY_USERNAME/projects/lda/mahout_vectors/tokenized-documents/ >> > > >> > >> > > > Found 3 items >> > > >> > >> > > > -rw-r--r-- 3 hadoop supergroup 129721338 2010-02-11 >> > 23:54 >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> /user/MY_USERNAME/projects/lda/mahout_vectors/tokenized-documents/part-00000 >> > > >> > >> > > > -rw-r--r-- 3 hadoop supergroup 128256085 2010-02-11 >> > 23:54 >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> /user/MY_USERNAME/projects/lda/mahout_vectors/tokenized-documents/part-00001 >> > > >> > >> > > > -rw-r--r-- 3 hadoop supergroup 24160265 2010-02-11 >> > 23:54 >> > > >> > >> > > > >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > >> > > >> >> > > >> > >> /user/MY_USERNAME/projects/lda/mahout_vectors/tokenized-documents/part-00002 >> > > >> > >> > > > >> > > >> > >> > > > Also, as a *bonus problem*, If the input >> > > >> > >> > > > folder >> > /user/MY_USERNAME/projects/lda/twitter_sequence_files >> > > >> > >> contains >> > > >> > >> > > more >> > > >> > >> > > > than one file (for example if I run only the maps >> without a >> > > >> final >> > > >> > >> > > reducer), >> > > >> > >> > > > this whole chain doesn't work. >> > > >> > >> > > > >> > > >> > >> > > > Thanks, >> > > >> > >> > > > Ovi >> > > >> > >> > > > >> > > >> > >> > > > --- >> > > >> > >> > > > Ovidiu Dan - http://www.ovidiudan.com/ >> > > >> > >> > > > >> > > >> > >> > > > Please do not print this e-mail unless it is mandatory >> > > >> > >> > > > >> > > >> > >> > > > My public key can be downloaded from subkeys.pgp.net, >> or >> > > >> > >> > > > http://www.ovidiudan.com/public.pgp >> > > >> > >> > > > >> > > >> > >> > > >> > > >> > >> > >> > > >> > >> >> > > >> > > >> > > >> > > >> > > >> > >> > > >> >> > > > >> > > > >> > > >> > >> > >
