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 > > >> > >> > > > > > >> > >> > > > > >> > >> > > > >> > >> > > >> > > > > >> > > > > >> > > > >> > > > > > > > > >
