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, 18:09, 23 October 2014
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| | === Running on a Cluster === | | === Running on a Cluster === |
| − | To run on the Cluster, the following settings need to be added to the configuration file:
| + | See [[#Cluster Configuration|Cluster Configuration]] settings for information on how to run on a cluster. |
| − | BATCH_TYPE = batch_type
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| − | BATCH_OPTS = options to your batch system, as you would normally specify them
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| − | Alternatively, <code>--batchtype</code> and <code>--batchopts</code> can be specified on the command line.
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| − | Valid values for BATCH_TYPE are: mosix, sge, sgei, slurm, slurmi, pbs, local
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| − | * If you are at UM and are using flux, you can specify either <code>flux</code> or <code>pbs</code>.
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| − | * <code>sgei</code> and <code>slurmi</code> run in interactive mode.
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| − | * For any BATCH_TYPEs that run in batch mode, GotCloud generates a script that will wait until the step is complete before returning.
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| − | ** In a sense, it "fakes" interactive mode for all batch types since it will not proceed until a command is finished.
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| − | Here's the same configuration file we used above but now made to run on a cluster computer with MOSIX.
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| − | === Example Configuration File ===
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| − | CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
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| − | BAM_INDEX = /path/freeze5/freeze5.bam.index
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| − | OUT_DIR = /path/freeze5/output
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| − | REF = /path/reference/hs37d5.fa
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| − | INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19
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| − | HM3_VCF = /path/reference/hapmap3_r3_b37.sites.vcf.gz
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| − | DBSNP_VCF = /path/reference/dbsnp_135.b37.sites.vcf.gz
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| − | BATCH_TYPE = mosix ### Specify MOSIX as the batch system
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| − | BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes
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| | == Results == | | == Results == |
