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Difference between revisions of "Mothur"

From Montana Tech High Performance Computing

 
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[https://www.mothur.org Mothur] is an opensource, expandable bioinformatics software for the microbial ecology community.
 
[https://www.mothur.org Mothur] is an opensource, expandable bioinformatics software for the microbial ecology community.
  
There are two versions of mothur installed. One is the MPI-enabled version and a non-MPI version. If you just need to use a single compute node, you will want to use the non-MPI version; for multi-node parallelization, you will want to use the MPI version.
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There are two installations of mothur, both are of version 1.39.5. One is the MPI-enabled version and another is a non-MPI version. If you just need to use a single compute node, you will want to use the non-MPI version; for multi-node parallelization (more than 32 processes), you will want to use the MPI version. Using the MPI version for a single node multi-threading parallelization will result in slower performance [https://www.mothur.org/wiki/Makefile_options#MPI_Version].
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To use mothur, you can use the <code>module</code> command:
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For non-MPI version
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    <code>module load mothur/1.39.5</code>
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For MPI version, you also need to load openmpi: 
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    <code>module load mothur/1.39.5_mpi openmpi/gnu/2.0.2</code>
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Then you can start Mothur typing:
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    <code>mothur</code>
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You can either run mothur interactively on compute nodes or submit the calculation to the compute nodes.

Latest revision as of 12:16, 25 April 2018

Mothur is an opensource, expandable bioinformatics software for the microbial ecology community.

There are two installations of mothur, both are of version 1.39.5. One is the MPI-enabled version and another is a non-MPI version. If you just need to use a single compute node, you will want to use the non-MPI version; for multi-node parallelization (more than 32 processes), you will want to use the MPI version. Using the MPI version for a single node multi-threading parallelization will result in slower performance [1].

To use mothur, you can use the module command:

For non-MPI version

   module load mothur/1.39.5

For MPI version, you also need to load openmpi:

   module load mothur/1.39.5_mpi openmpi/gnu/2.0.2

Then you can start Mothur typing:

   mothur

You can either run mothur interactively on compute nodes or submit the calculation to the compute nodes.