contributors:team_4_page
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contributors:team_4_page [2015/05/11 08:31] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 08:37] emfeal [Running ABySS] |
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| Line 85: | Line 85: | ||
| <code> | <code> | ||
| #!/bin/sh | #!/bin/sh | ||
| - | # | ||
| #$ -N team4 | #$ -N team4 | ||
| #$ -cwd | #$ -cwd | ||
| Line 93: | Line 92: | ||
| #$ -V | #$ -V | ||
| #$ -l mem_free=15g | #$ -l mem_free=15g | ||
| - | # | ||
| ABYSSRUNDIR=/campusdata/BME235/bin | ABYSSRUNDIR=/campusdata/BME235/bin | ||
| - | |||
| export PATH=$PATH:/opt/openmpi/bin:/campusdata/BME235/bin/ | export PATH=$PATH:/opt/openmpi/bin:/campusdata/BME235/bin/ | ||
| export LD_LIBRARY_PATH=/opt/openmpi/lib/:$LD_LIBRARY_PATH | export LD_LIBRARY_PATH=/opt/openmpi/lib/:$LD_LIBRARY_PATH | ||
| - | |||
| ABYSSRUN=$ABYSSRUNDIR/abyss-pe | ABYSSRUN=$ABYSSRUNDIR/abyss-pe | ||
| - | |||
| $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | ||
| </code> | </code> | ||
| - | A qsub option of import which is vital to successfully run a parallel ABySS job on the cluster is the use of a parallel environment. The PE designated in the script above: | + | Something to note is that using the parallel version of ABySS on the cluster requires the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: |
| <code> | <code> | ||
| #$ -pe mpi 10 | #$ -pe mpi 10 | ||
| </code> | </code> | ||
| - | The //-pe// designates the parallel environment qsub option. The //mpi// designates the choice of a parallel environment that is installed on the system. The 10 indicates the number of processes you wish the job to be parallelized over. To see which PE's are installed on the system, use the command: | + | 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: |
| <code> | <code> | ||
| qconf -spl | qconf -spl | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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