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 | + | 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]. |
To use mothur, you can use the <code>module</code> command: | To use mothur, you can use the <code>module</code> command: | ||
| − | non-MPI version | + | For non-MPI version |
| − | MPI version | + | <code>module load mothur/1.39.5</code> |
| + | |||
| + | For MPI version, you also need to load openmpi: | ||
| + | |||
| + | <code>module load mothur/1.39.5_mpi openmpi/gnu/2.0.2</code> | ||
| + | |||
| + | Then you can start Mothur typing: | ||
| + | |||
| + | <code>mothur</code> | ||
| + | |||
| + | You can either run mothur interactively on compute nodes or submit the calculation to the compute nodes. | ||
Latest revision as of 11:16, 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.