Using MPI-HMMER on Big Red at IU

On this page:

• Introduction
• Using the hmmerjob script to submit parallel hmmsearch jobs
• Using the hmmerjob script to submit parallel hmmpfam jobs
• Using non-parallel HMMER programs

Introduction

HMMER is a suite of programs that you can use to create and query hidden Markov models that describe molecular sequences. A parallel port of HMMER known as MPI-HMMER is available on Big Red at Indiana University. It contains all the HMMER programs, but only hmmpfam and hmmsearch have been parallelized.

MPI-HMMER is installed in the directory /N/soft/linux-sles9-ppc64/hmmer-2.3.2-MPI-0.92. Documentation for HMMER programs is available as man pages. You can also visit the MPI-HMMER page for more information.

Using the hmmerjob script to submit parallel hmmsearch jobs

The hmmerjob script is written to submit both hmmpfam and hmmsearch jobs. Use the hmmpfam and hmmsearch options with hmmerjob just as you would with serial versions of these programs. If you use only the hmmpfam and hmmsearch options, a job will be submitted that uses four processes for up to two hours in the NORMAL queue on Big Red. You can use other options to change those settings.

The form of the hmmerjob command using hmmpsearch is:

Replace items in brackets with your chosen values. The -CPUS option specifies the number of processes to start, -wallhours the length of time the job may run, and -queue the name of the queue that is to receive the job. The SERIAL, NORMAL, LONG, and DEBUG queues are available; see Big Red usage policies.

To run a simple hmmsearch with models in models.hmm and sequences in experiment56.fa in the NORMAL queue using 512 processes for 8 hours, the command is:

When you run hmmerjob, you'll receive a message that your job has been submitted to the queue. You will receive mail when the job finishes. You can check the status of your job by using the llq command.

Output from the job is stored in a file with a name of the form hmmerjob.999999.0.out, where the nines are replaced by other digits that represent the job ID. Errors and debugging output are stored in a separate file with a name of the form hmmerjob.999999.err.

Using the hmmerjob script to submit parallel hmmpfam jobs

Because hmmpfam is more I/O intensive than hmmsearch, it is better to index the HMM database first. This step is required only the first time you use a particular database. You can reuse the resulting .ssi file in subsequent searches.

First, add the SoftEnv key (softkey):

Then index the HMM database:

Replace /path/to/HMM/database with the path to the database you will be using.

The form of the hmmerjob command using hmmpfam is:

The rules for using hmmpfam are the same as those described above for hmmsearch. For example, suppose you would like to compare all the sequences in a file named unknowns.fa with all the models in models.hmm and select matches that have an E score of 1 or better, using four processes for up to two hours. The command would be:

To run the same job using 64 processes for up to 72 hours, you would use:

Using non-parallel HMMER programs

The serial (single-process) HMMER programs are also available on Big Red. The simplest way to use them is to put them on your path by using the +mpi-hmmer softkey. To permanently make HMMER available at the command prompt, run the commands:

You should then be able to run serial HMMER programs, and all HMMER manual pages should be available to you by calling the man command, e.g., man hmmbuild . If you need to run serial HMMER programs in batch jobs, the simplest way to do so is to use the serialjob script. A manual page for it is available on Big Red.

This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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