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MrBayes: Difference between revisions
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{{Command|module spider mrbayes}} | {{Command|module spider mrbayes}} | ||
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For more on finding and selecting a version of MrBayes using <code>module</code> commands see [[Utiliser_des_modules/en|Using modules]] | For more on finding and selecting a version of MrBayes using <code>module</code> commands see [[Utiliser_des_modules/en|Using modules]] | ||
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The example uses an input file (<code>primates.nex</code>) distributed with MrBayes. | The example uses an input file (<code>primates.nex</code>) distributed with MrBayes. | ||
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{{File | {{File | ||
|name=submit-mrbayes-seq.sh | |name=submit-mrbayes-seq.sh | ||
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Like the previous example it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | Like the previous example it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | ||
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{{File | {{File | ||
|name=submit-mrbayes-parallel.sh | |name=submit-mrbayes-parallel.sh | ||
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Like the previous examples it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | Like the previous examples it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | ||
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{{File | {{File | ||
|name=submit-mrbayes-gpu.sh | |name=submit-mrbayes-gpu.sh | ||
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If you need very long runs of MrBayes, we suggest you break up the work into several small jobs rather than one very long job. Long jobs have are more likely to be interrupted a hardware failure or a maintenance outage. Fortunately, MrBayes has a mechanism for creating checkpoints, in which progress can be saved from one job and continued in a subsequent job. | If you need very long runs of MrBayes, we suggest you break up the work into several small jobs rather than one very long job. Long jobs have are more likely to be interrupted a hardware failure or a maintenance outage. Fortunately, MrBayes has a mechanism for creating checkpoints, in which progress can be saved from one job and continued in a subsequent job. | ||
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Here is an example of how to split a calculation into two Slurm jobs which will run one after the other. Create two files, <code>job1.nex</code> and <code>job2.nex</code>, as shown below. Notice that the key difference between them is the presence of the <code>append</code> keyword in the second. | Here is an example of how to split a calculation into two Slurm jobs which will run one after the other. Create two files, <code>job1.nex</code> and <code>job2.nex</code>, as shown below. Notice that the key difference between them is the presence of the <code>append</code> keyword in the second. | ||
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directive and the <code>$SLURM_ARRAY_TASK_ID</code> variable used here. | directive and the <code>$SLURM_ARRAY_TASK_ID</code> variable used here. | ||
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{{File | {{File | ||
|name=submit-mrbayes-cp.sh | |name=submit-mrbayes-cp.sh | ||
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cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | ||
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srun mb job${SLURM_ARRAY_TASK_ID}.nex | srun mb job${SLURM_ARRAY_TASK_ID}.nex | ||
}} | }} | ||