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, 09:39, 16 October 2014
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| You will not need to set or know about most of the settings, however, there are | | You will not need to set or know about most of the settings, however, there are |
| some things you'll want to know about to make using GotCloud as simple to use as possible. | | some things you'll want to know about to make using GotCloud as simple to use as possible. |
| + | |
| + | '''Configure Your Batch Environment''' |
| + | |
| + | GotCloud supports two options to allow you to submit the work from the aligner and umake |
| + | to run on your local cluster. |
| + | There are many different types of clusters and the details of their interfaces vary for each installation. |
| + | As distributed GotCloud contacts support for these: |
| + | |
| + | * MOSIX |
| + | * SGE (Sun Grid Engine) |
| + | ** Used by StarCluster |
| + | * SLURM |
| + | * PBS (Portable Batch System) |
| + | |
| + | You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options |
| + | to that cluster system with the option '''-batchopt'''. |
| + | * Alternatively, you can set them using BATCH_TYPE and BATCH_OPTS in the configuration file. |
| + | For example, here are examples of invocations of the aligner using these batch systems: |
| + | |
| + | <code> |
| + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"''' |
| + | |
| + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"''' |
| + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"''' |
| + | |
| + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype sge''' |
| + | </code> |
| + | |
| + | The interface to actually submit a job to a cluster is coded in '''scripts/runcluster.pl''' |
| + | (probably installed in ''/usr/local/gotcloud''). |
| + | You may need to (and should) modify this code to work with your particular cluster system, |
| + | whether it be to handle options in some manner or add an entirely new batchtype. |