Released November 5, 2015





The Joshua Pipeline

Please note that the Joshua 6.0.3 included some big changes to directory organization of the pipeline’s files.

This page describes the Joshua pipeline script, which manages the complexity of training and evaluating machine translation systems. The pipeline eases the pain of two related tasks in statistical machine translation (SMT) research:

  • Training SMT systems involves a complicated process of interacting steps that are time-consuming and prone to failure.

  • Developing and testing new techniques requires varying parameters at different points in the pipeline. Earlier results (which are often expensive) need not be recomputed.

To facilitate these tasks, the pipeline script:

  • Runs the complete SMT pipeline, from corpus normalization and tokenization, through alignment, model building, tuning, test-set decoding, and evaluation.

  • Caches the results of intermediate steps (using robust SHA-1 checksums on dependencies), so the pipeline can be debugged or shared across similar runs while doing away with time spent recomputing expensive steps.

  • Allows you to jump into and out of the pipeline at a set of predefined places (e.g., the alignment stage), so long as you provide the missing dependencies.

The Joshua pipeline script is designed in the spirit of Moses’ train-model.pl, and shares (and has borrowed) many of its features. It is not as extensive as Moses’ Experiment Management System, which allows the user to define arbitrary execution dependency graphs. However, it is significantly simpler to use, allowing many systems to be built with a single command (that may run for days or weeks).

Dependencies

The pipeline has no required external dependencies. However, it has support for a number of external packages, some of which are included with Joshua.

  • GIZA++ (included)

    GIZA++ is the default aligner. It is included with Joshua, and should compile successfully when you typed ant from the Joshua root directory. It is not required because you can use the (included) Berkeley aligner (--aligner berkeley). We have recently also provided support for the Jacana-XY aligner (--aligner jacana).

  • Hadoop (included)

    The pipeline uses the Thrax grammar extractor, which is built on Hadoop. If you have a Hadoop installation, simply ensure that the $HADOOP environment variable is defined, and the pipeline will use it automatically at the grammar extraction step. If you are going to attempt to extract very large grammars, it is best to have a good-sized Hadoop installation.

    (If you do not have a Hadoop installation, you might consider setting one up. Hadoop can be installed in a “pseudo-distributed” mode that allows it to use just a few machines or a number of processors on a single machine. The main issue is to ensure that there are a lot of independent physical disks, since in our experience Hadoop starts to exhibit lots of hard-to-trace problems if there is too much demand on the disks.)

    If you don’t have a Hadoop installation, there are still no worries. The pipeline will unroll a standalone installation and use it to extract your grammar. This behavior will be triggered if $HADOOP is undefined.

  • Moses (not included). Moses is needed if you wish to use its ‘kbmira’ tuner (–tuner kbmira), or if you wish to build phrase-based models.

  • SRILM (not included; not needed; not recommended)

    By default, the pipeline uses the included KenLM for building (and also querying) language models. Joshua also includes a Java program from the Berkeley LM package that contains code for constructing a Kneser-Ney-smoothed language model in ARPA format from the target side of your training data.
    There is no need to use SRILM, but if you do wish to use it, you need to do the following:

    1. Install SRILM and set the $SRILM environment variable to point to its installed location.
    2. Add the --lm-gen srilm flag to your pipeline invocation.

    More information on this is available in the LM building section of the pipeline. SRILM is not used for representing language models during decoding (and in fact is not supported, having been supplanted by KenLM (the default) and BerkeleyLM).

After installing any dependencies, follow the brief instructions on the installation page, and then you are ready to build models.

A basic pipeline run

The pipeline takes a set of inputs (training, tuning, and test data), and creates a set of intermediate files in the run directory. By default, the run directory is the current directory, but it can be changed with the --rundir parameter.

For this quick start, we will be working with the example that can be found in $JOSHUA/examples/training. This example contains 1,000 sentences of Urdu-English data (the full dataset is available as part of the Indian languages parallel corpora with 100-sentence tuning and test sets with four references each.

Running the pipeline requires two main steps: data preparation and invocation.

  1. Prepare your data. The pipeline script needs to be told where to find the raw training, tuning, and test data. A good convention is to place these files in an input/ subdirectory of your run’s working directory (NOTE: do not use data/, since a directory of that name is created and used by the pipeline itself for storing processed files). The expected format (for each of training, tuning, and test) is a pair of files that share a common path prefix and are distinguished by their extension, e.g.,

    input/
          train.SOURCE
          train.TARGET
          tune.SOURCE
          tune.TARGET
          test.SOURCE
          test.TARGET
    

    These files should be parallel at the sentence level (with one sentence per line), should be in UTF-8, and should be untokenized (tokenization occurs in the pipeline). SOURCE and TARGET denote variables that should be replaced with the actual target and source language abbreviations (e.g., “ur” and “en”).

  2. Run the pipeline. The following is the minimal invocation to run the complete pipeline:

    $JOSHUA/bin/pipeline.pl  \
      --rundir .             \
      --type hiero           \
      --corpus input/train   \
      --tune input/tune      \
      --test input/devtest   \
      --source SOURCE        \
      --target TARGET
    

    The --corpus, --tune, and --test flags define file prefixes that are concatened with the language extensions given by --target and --source (with a “.” in between). Note the correspondences with the files defined in the first step above. The prefixes can be either absolute or relative pathnames. This particular invocation assumes that a subdirectory input/ exists in the current directory, that you are translating from a language identified “ur” extension to a language identified by the “en” extension, that the training data can be found at input/train.en and input/train.ur, and so on.

Don’t run the pipeline directly from $JOSHUA, or, for that matter, in any directory with lots of other files. This can cause problems because the pipeline creates lots of files under --rundir that can clobber existing files. You should run experiments in a clean directory. For example, if you have Joshua installed in $HOME/code/joshua, manage your runs in a different location, such as $HOME/expts/joshua.

Assuming no problems arise, this command will run the complete pipeline in about 20 minutes, producing BLEU scores at the end. As it runs, you will see output that looks like the following:

[train-copy-en] rebuilding...
  dep=/Users/post/code/joshua/test/pipeline/input/train.en 
  dep=data/train/train.en.gz [NOT FOUND]
  cmd=cat /Users/post/code/joshua/test/pipeline/input/train.en | gzip -9n > data/train/train.en.gz
  took 0 seconds (0s)
[train-copy-ur] rebuilding...
  dep=/Users/post/code/joshua/test/pipeline/input/train.ur 
  dep=data/train/train.ur.gz [NOT FOUND]
  cmd=cat /Users/post/code/joshua/test/pipeline/input/train.ur | gzip -9n > data/train/train.ur.gz
  took 0 seconds (0s)
...

And in the current directory, you will see the following files (among other files, including intermediate files generated by the individual sub-steps).

data/
    train/
        corpus.ur
        corpus.en
        thrax-input-file
    tune/
        corpus.ur -> tune.tok.lc.ur
        corpus.en -> tune.tok.lc.en
        grammar.filtered.gz
        grammar.glue
    test/
        corpus.ur -> test.tok.lc.ur
        corpus.en -> test.tok.lc.en
        grammar.filtered.gz
        grammar.glue
alignments/
    0/
        [giza/berkeley aligner output files]
    1/
    ...
    training.align
thrax-hiero.conf
thrax.log
grammar.gz
lm.gz
tune/
     decoder_command
     model/
           [model files]
     params.txt
     joshua.log
     mert.log
     joshua.config.final
     final-bleu
test/
     model/
           [model files]
     output
     final-bleu

These files will be described in more detail in subsequent sections of this tutorial.

Another useful flag is the --rundir DIR flag, which chdir()s to the specified directory before running the pipeline. By default the rundir is the current directory. Changing it can be useful for organizing related pipeline runs. In fact, we highly recommend that you organize your runs using consecutive integers, also taking a minute to pass a short note with the --readme flag, which allows you to quickly generate reports on groups of related experiments. Relative paths specified to other flags (e.g., to --corpus or --lmfile) are relative to the directory the pipeline was called from, not the rundir itself (unless they happen to be the same, of course).

The complete pipeline comprises many tens of small steps, which can be grouped together into a set of traditional pipeline tasks:

  1. Data preparation
  2. Alignment
  3. Parsing (syntax-based grammars only)
  4. Grammar extraction
  5. Language model building
  6. Tuning
  7. Testing
  8. Analysis

These steps are discussed below, after a few intervening sections about high-level details of the pipeline.

Managing groups of experiments

The real utility of the pipeline comes when you use it to manage groups of experiments. Typically, there is a held-out test set, and we want to vary a number of training parameters to determine what effect this has on BLEU scores or some other metric. Joshua comes with a script $JOSHUA/scripts/training/summarize.pl that collects information from a group of runs and reports them to you. This script works so long as you organize your runs as follows:

  1. Your runs should be grouped together in a root directory, which I’ll call $EXPDIR.

  2. For comparison purposes, the runs should all be evaluated on the same test set.

  3. Each run in the run group should be in its own numbered directory, shown with the files used by the summarize script:

    $RUNDIR/
        1/
            README.txt
            test/
                final-bleu
                final-times
            [other files]
        2/
            README.txt
            test/
                final-bleu
                final-times
            [other files]
            ...
    

You can get such directories using the --rundir N flag to the pipeline.

Run directories can build off each other. For example, 1/ might contain a complete baseline run. If you wanted to just change the tuner, you don’t need to rerun the aligner and model builder, so you can reuse the results by supplying the second run with the information it needs that was computed in step 1:

$JOSHUA/bin/pipeline.pl \
  --first-step tune \
  --grammar 1/grammar.gz \
  ...

More details are below.

Grammar options

Hierarchical Joshua can extract three types of grammars: Hiero grammars, GHKM, and SAMT grammars. As described on the file formats page, all of them are encoded into the same file format, but they differ in terms of the richness of their nonterminal sets.

Hiero grammars make use of a single nonterminals, and are extracted by computing phrases from word-based alignments and then subtracting out phrase differences. More detail can be found in Chiang (2007) [PDF]. GHKM (new with 5.0) and SAMT grammars make use of a source- or target-side parse tree on the training data, differing in the way they extract rules using these trees: GHKM extracts synchronous tree substitution grammar rules rooted in a subset of the tree constituents, whereas SAMT projects constituent labels down onto phrases. SAMT grammars are usually many times larger and are much slower to decode with, but sometimes increase BLEU score. Both grammar formats are extracted with the Thrax software.

By default, the Joshua pipeline extract a Hiero grammar, but this can be altered with the --type (ghkm|samt) flag. For GHKM grammars, the default is to use Michel Galley’s extractor, but you can also use Moses’ extractor with --ghkm-extractor moses. Galley’s extractor only outputs two features, so the scores tend to be significantly lower than that of Moses’.

Joshua (new in version 6) also includes an unlexicalized phrase-based decoder. Building a phrase-based model requires you to have Moses installed, since its train-model.perl script is used to extract the phrase table. You can enable this by defining the $MOSES environment variable and then specifying --type phrase.

Other high-level options

The following command-line arguments control run-time behavior of multiple steps:

  • --threads N (1)

    This enables multithreaded operation for a number of steps: alignment (with GIZA, max two threads), parsing, and decoding (any number of threads)

  • --jobs N (1)

    This enables parallel operation over a cluster using the qsub command. This feature is not well-documented at this point, but you will likely want to edit the file $JOSHUA/scripts/training/parallelize/LocalConfig.pm to setup your qsub environment, and may also want to pass specific qsub commands via the --qsub-args "ARGS" command. We suggest you stick to the standard Joshua model that tries to use as many cores as are available with the --threads N option.

Restarting failed runs

If the pipeline dies, you can restart it with the same command you used the first time. If you rerun the pipeline with the exact same invocation as the previous run (or an overlapping configuration – one that causes the same set of behaviors), you will see slightly different output compared to what we saw above:

[train-copy-en] cached, skipping...
[train-copy-ur] cached, skipping...
...

This indicates that the caching module has discovered that the step was already computed and thus did not need to be rerun. This feature is quite useful for restarting pipeline runs that have crashed due to bugs, memory limitations, hardware failures, and the myriad other problems that plague MT researchers across the world.

Often, a command will die because it was parameterized incorrectly. For example, perhaps the decoder ran out of memory. This allows you to adjust the parameter (e.g., --joshua-mem) and rerun the script. Of course, if you change one of the parameters a step depends on, it will trigger a rerun, which in turn might trigger further downstream reruns.

Skipping steps, quitting early

You will also find it useful to start the pipeline somewhere other than data preparation (for example, if you have already-processed data and an alignment, and want to begin with building a grammar) or to end it prematurely (if, say, you don’t have a test set and just want to tune a model). This can be accomplished with the --first-step and --last-step flags, which take as argument a case-insensitive version of the following steps:

  • FIRST: Data preparation. Everything begins with data preparation. This is the default first step, so there is no need to be explicit about it.

  • ALIGN: Alignment. You might want to start here if you want to skip data preprocessing.

  • PARSE: Parsing. This is only relevant for building SAMT grammars (--type samt), in which case the target side (--target) of the training data (--corpus) is parsed before building a grammar.

  • THRAX: Grammar extraction with Thrax. If you jump to this step, you’ll need to provide an aligned corpus (--alignment) along with your parallel data.

  • TUNE: Tuning. The exact tuning method is determined with --tuner {mert,mira,pro}. With this option, you need to specify a grammar (--grammar) or separate tune (--tune-grammar) and test (--test-grammar) grammars. A full grammar (--grammar) will be filtered against the relevant tuning or test set unless you specify --no-filter-tm. If you want a language model built from the target side of your training data, you’ll also need to pass in the training corpus (--corpus). You can also specify an arbitrary number of additional language models with one or more --lmfile flags.

  • TEST: Testing. If you have a tuned model file, you can test new corpora by passing in a test corpus with references (--test). You’ll need to provide a run name (--name) to store the results of this run, which will be placed under test/NAME. You’ll also need to provide a Joshua configuration file (--joshua-config), one or more language models (--lmfile), and a grammar (--grammar); this will be filtered to the test data unless you specify --no-filter-tm) or unless you directly provide a filtered test grammar (--test-grammar).

  • LAST: The last step. This is the default target of --last-step.

We now discuss these steps in more detail.

1. DATA PREPARATION

Data prepare involves doing the following to each of the training data (--corpus), tuning data (--tune), and testing data (--test). Each of these values is an absolute or relative path prefix. To each of these prefixes, a “.” is appended, followed by each of SOURCE (--source) and TARGET (--target), which are file extensions identifying the languages. The SOURCE and TARGET files must have the same number of lines.

For tuning and test data, multiple references are handled automatically. A single reference will have the format TUNE.TARGET, while multiple references will have the format TUNE.TARGET.NUM, where NUM starts at 0 and increments for as many references as there are.

The following processing steps are applied to each file.

  1. Copying the files into $RUNDIR/data/TYPE, where TYPE is one of “train”, “tune”, or “test”. Multiple --corpora files are concatenated in the order they are specified. Multiple --tune and --test flags are not currently allowed.

  2. Normalizing punctuation and text (e.g., removing extra spaces, converting special quotations). There are a few language-specific options that depend on the file extension matching the two-letter ISO 639-1 designation.

  3. Tokenizing the data (e.g., separating out punctuation, converting brackets). Again, there are language-specific tokenizations for a few languages (English, German, and Greek).

  4. (Training only) Removing all parallel sentences with more than --maxlen tokens on either side. By default, MAXLEN is 50. To turn this off, specify --maxlen 0.

  5. Lowercasing.

This creates a series of intermediate files which are saved for posterity but compressed. For example, you might see

data/
    train/
        train.en.gz
        train.tok.en.gz
        train.tok.50.en.gz
        train.tok.50.lc.en
        corpus.en -> train.tok.50.lc.en

The file “corpus.LANG” is a symbolic link to the last file in the chain.

2. ALIGNMENT

Alignments are between the parallel corpora at $RUNDIR/data/train/corpus.{SOURCE,TARGET}. To prevent the alignment tables from getting too big, the parallel corpora are grouped into files of no more than ALIGNER_CHUNK_SIZE blocks (controlled with a parameter below). The last block is folded into the penultimate block if it is too small. These chunked files are all created in a subdirectory of $RUNDIR/data/train/splits, named corpus.LANG.0, corpus.LANG.1, and so on.

The pipeline parameters affecting alignment are:

  • --aligner ALIGNER {giza (default), berkeley, jacana}

    Which aligner to use. The default is GIZA++, but the Berkeley aligner can be used instead. When using the Berkeley aligner, you’ll want to pay attention to how much memory you allocate to it with --aligner-mem (the default is 10g).

  • --aligner-chunk-size SIZE (1,000,000)

    The number of sentence pairs to compute alignments over. The training data is split into blocks of this size, aligned separately, and then concatenated.

  • --alignment FILE

    If you have an already-computed alignment, you can pass that to the script using this flag. Note that, in this case, you will want to skip data preparation and alignment using --first-step thrax (the first step after alignment) and also to specify --no-prepare so as not to retokenize the data and mess with your alignments.

    The alignment file format is the standard format where 0-indexed many-many alignment pairs for a sentence are provided on a line, source language first, e.g.,

    0-0 0-1 1-2 1-7 …

    This value is required if you start at the grammar extraction step.

When alignment is complete, the alignment file can be found at $RUNDIR/alignments/training.align. It is parallel to the training corpora. There are many files in the alignments/ subdirectory that contain the output of intermediate steps.

3. PARSING

To build SAMT and GHKM grammars (--type samt and --type ghkm), the target side of the training data must be parsed. The pipeline assumes your target side will be English, and will parse it for you using the Berkeley parser, which is included. If it is not the case that English is your target-side language, the target side of your training data (found at CORPUS.TARGET) must already be parsed in PTB format. The pipeline will notice that it is parsed and will not reparse it.

Parsing is affected by both the --threads N and --jobs N options. The former runs the parser in multithreaded mode, while the latter distributes the runs across as cluster (and requires some configuration, not yet documented). The options are mutually exclusive.

Once the parsing is complete, there will be two parsed files:

  • $RUNDIR/data/train/corpus.en.parsed: this is the mixed-case file that was parsed.
  • $RUNDIR/data/train/corpus.parsed.en: this is a leaf-lowercased version of the above file used for grammar extraction.

4. THRAX (grammar extraction)

The grammar extraction step takes three pieces of data: (1) the source-language training corpus, (2) the target-language training corpus (parsed, if an SAMT grammar is being extracted), and (3) the alignment file. From these, it computes a synchronous context-free grammar. If you already have a grammar and wish to skip this step, you can do so passing the grammar with the --grammar /path/to/grammar flag.

The main variable in grammar extraction is Hadoop. If you have a Hadoop installation, simply ensure that the environment variable $HADOOP is defined, and Thrax will seamlessly use it. If you do not have a Hadoop installation, the pipeline will roll out out for you, running Hadoop in standalone mode (this mode is triggered when $HADOOP is undefined). Theoretically, any grammar extractable on a full Hadoop cluster should be extractable in standalone mode, if you are patient enough; in practice, you probably are not patient enough, and will be limited to smaller datasets. You may also run into problems with disk space; Hadoop uses a lot (use --tmp /path/to/tmp to specify an alternate place for temporary data; we suggest you use a local disk partition with tens or hundreds of gigabytes free, and not an NFS partition). Setting up your own Hadoop cluster is not too difficult a chore; in particular, you may find it helpful to install a pseudo-distributed version of Hadoop. In our experience, this works fine, but you should note the following caveats:

  • It is of crucial importance that you have enough physical disks. We have found that having too few, or too slow of disks, results in a whole host of seemingly unrelated issues that are hard to resolve, such as timeouts.
  • NFS filesystems can cause lots of problems. You should really try to install physical disks that are dedicated to Hadoop scratch space.

Here are some flags relevant to Hadoop and grammar extraction with Thrax:

  • --hadoop /path/to/hadoop

    This sets the location of Hadoop (overriding the environment variable $HADOOP)

  • --hadoop-mem MEM (2g)

    This alters the amount of memory available to Hadoop mappers (passed via the mapred.child.java.opts options).

  • --thrax-conf FILE

    Use the provided Thrax configuration file instead of the (grammar-specific) default. The Thrax templates are located at $JOSHUA/scripts/training/templates/thrax-TYPE.conf, where TYPE is one of “hiero” or “samt”.

When the grammar is extracted, it is compressed and placed at $RUNDIR/grammar.gz.

5. Language model

Before tuning can take place, a language model is needed. A language model is always built from the target side of the training corpus unless --no-corpus-lm is specified. In addition, you can provide other language models (any number of them) with the --lmfile FILE argument. Other arguments are as follows.

  • --lm {kenlm (default), berkeleylm}

    This determines the language model code that will be used when decoding. These implementations are described in their respective papers (PDFs: KenLM, BerkeleyLM). KenLM is written in C++ and requires a pass through the JNI, but is recommended because it supports left-state minimization.

  • --lmfile FILE

    Specifies a pre-built language model to use when decoding. This language model can be in ARPA format, or in KenLM format when using KenLM or BerkeleyLM format when using that format.

  • --lm-gen {kenlm (default), srilm, berkeleylm}, --buildlm-mem MEM, --witten-bell

    At the tuning step, an LM is built from the target side of the training data (unless --no-corpus-lm is specified). This controls which code is used to build it. The default is a KenLM’s lmplz, and is strongly recommended.

    If SRILM is used, it is called with the following arguments:

      $SRILM/bin/i686-m64/ngram-count -interpolate SMOOTHING -order 5 -text TRAINING-DATA -unk -lm lm.gz
    

    Where SMOOTHING is -kndiscount, or -wbdiscount if --witten-bell is passed to the pipeline.

    BerkeleyLM java class is also available. It computes a Kneser-Ney LM with a constant discounting (0.75) and no count thresholding. The flag --buildlm-mem can be used to control how much memory is allocated to the Java process. The default is “2g”, but you will want to increase it for larger language models.

    A language model built from the target side of the training data is placed at $RUNDIR/lm.gz.

Interlude: decoder arguments

Running the decoder is done in both the tuning stage and the testing stage. A critical point is that you have to give the decoder enough memory to run. Joshua can be very memory-intensive, in particular when decoding with large grammars and large language models. The default amount of memory is 3100m, which is likely not enough (especially if you are decoding with SAMT grammar). You can alter the amount of memory for Joshua using the --joshua-mem MEM argument, where MEM is a Java memory specification (passed to its -Xmx flag).

6. TUNING

Two optimizers are provided with Joshua: MERT and PRO (--tuner {mert,pro}). If Moses is installed, you can also use Cherry & Foster’s k-best batch MIRA (--tuner mira, recommended). Tuning is run till convergence in the $RUNDIR/tune directory.

When tuning is finished, each final configuration file can be found at either

$RUNDIR/tune/joshua.config.final

7. Testing

For each of the tuner runs, Joshua takes the tuner output file and decodes the test set. If you like, you can also apply minimum Bayes-risk decoding to the decoder output with --mbr. This usually yields about 0.3 - 0.5 BLEU points, but is time-consuming.

After decoding the test set with each set of tuned weights, Joshua computes the mean BLEU score, writes it to $RUNDIR/test/final-bleu, and cats it. It also writes a file $RUNDIR/test/final-times containing a summary of runtime information. That’s the end of the pipeline!

Joshua also supports decoding further test sets. This is enabled by rerunning the pipeline with a number of arguments:

  • --first-step TEST

    This tells the decoder to start at the test step.

  • --joshua-config CONFIG

    A tuned parameter file is required. This file will be the output of some prior tuning run. Necessary pathnames and so on will be adjusted.

8. ANALYSIS

If you have used the suggested layout, with a number of related runs all contained in a common directory with sequential numbers, you can use the script $JOSHUA/scripts/training/summarize.pl to display a summary of the mean BLEU scores from all runs, along with the text you placed in the run README file (using the pipeline’s --readme TEXT flag).

COMMON USE CASES AND PITFALLS

  • If the pipeline dies at the “thrax-run” stage with an error like the following:

    JOB FAILED (return code 1) 
    hadoop/bin/hadoop: line 47: 
    /some/path/to/a/directory/hadoop/bin/hadoop-config.sh: No such file or directory 
    Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/hadoop/fs/FsShell 
    Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.fs.FsShell 
    

    This occurs if the $HADOOP environment variable is set but does not point to a working Hadoop installation. To fix it, make sure to unset the variable:

    # in bash
    unset HADOOP
    

    and then rerun the pipeline with the same invocation.

  • Memory usage is a major consideration in decoding with Joshua and hierarchical grammars. In particular, SAMT grammars often require a large amount of memory. Many steps have been taken to reduce memory usage, including beam settings and test-set- and sentence-level filtering of grammars. However, memory usage can still be in the tens of gigabytes.

    To accommodate this kind of variation, the pipeline script allows you to specify both (a) the amount of memory used by the Joshua decoder instance and (b) the amount of memory required of nodes obtained by the qsub command. These are accomplished with the --joshua-mem MEM and --qsub-args ARGS commands. For example,

    pipeline.pl --joshua-mem 32g --qsub-args "-l pvmem=32g -q himem.q" ...
    

    Also, should Thrax fail, it might be due to a memory restriction. By default, Thrax requests 2 GB from the Hadoop server. If more memory is needed, set the memory requirement with the --hadoop-mem in the same way as the --joshua-mem option is used.

  • Other pitfalls and advice will be added as it is discovered.

FEEDBACK

Please email joshua_support@googlegroups.com with problems or suggestions.