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contributors:team_4_page [2015/06/01 06:44] emfeal |
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Note that the parallel version of ABySS requires two things in particular: | Note that the parallel version of ABySS requires two things in particular: | ||
- | * The use of a parallel environment which can be selected using a qsub option. | + | * The use of a [[parallel environment]] (PE) which can be selected using a qsub option. |
* The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | * The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
- | The parallel environment option in the script above: | + | The PE option in the script above: |
<code> | <code> | ||
#$ -pe mpi 10 | #$ -pe mpi 10 | ||
</code> | </code> | ||
- | The //mpi// designates the choice of a [[parallel environment]] that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command: | + | The //mpi// designates the choice of a PE that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command: |
<code> | <code> | ||
qconf -spl | qconf -spl | ||
</code> | </code> | ||
- | Selecting the proper parallel environment is critical to ensure the success of a parallelized ABySS job. By using the command: | + | Selecting the proper PE is critical to ensure the success of a parallelized ABySS job. By using the command: |
<code> | <code> | ||
qconf -sp PE_NAME | qconf -sp PE_NAME | ||
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accounting_summary TRUE | accounting_summary TRUE | ||
</code> | </code> | ||
- | For using ABySS with openmpi, there are two settings in particular which should be noted: | + | For using ABySS with openmpi, there are three settings in particular which should be noted: |
* slots: indicates maximum number of slots that can be designated with the PE | * slots: indicates maximum number of slots that can be designated with the PE | ||
* allocation_rule: indicates the form of scheduling to be used to allocate slots to nodes | * allocation_rule: indicates the form of scheduling to be used to allocate slots to nodes |