Bureaucrats, cc_docs_admin, cc_staff
2,879
edits
MrBayes: Difference between revisions
copy editing
(Marked this version for translation) |
(copy editing) |
||
| Line 8: | Line 8: | ||
{{Command|module spider mrbayes}} | {{Command|module spider mrbayes}} | ||
== | == Examples == <!--T:3--> | ||
=== Sequential === <!--T:4--> | === Sequential === <!--T:4--> | ||
1. | The following job script uses only one CPU core (<code>--cpus-per-task=1</code>). | ||
The example uses an input file (<code>primates.nex</code>) distributed with MrBayes. | |||
{{File | {{File | ||
|name=submit-mrbayes-seq.sh | |name=submit-mrbayes-seq.sh | ||
| Line 24: | Line 26: | ||
<!--T:5--> | <!--T:5--> | ||
module load mrbayes/3.2.7 | module load mrbayes/3.2.7 | ||
cd $SCRATCH | cd $SCRATCH | ||
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | ||
<!--T:8--> | <!--T:8--> | ||
mb primates.nex | mb primates.nex | ||
}} | }} | ||
<!--T:9--> | <!--T:9--> | ||
The job script can be submitted with | |||
{{Command|sbatch submit-mrbayes-seq.sh}} | {{Command|sbatch submit-mrbayes-seq.sh}} | ||
=== Parallel === <!--T:10--> | === Parallel === <!--T:10--> | ||
MrBayes | MrBayes can be run on multiple cores, on multiple nodes, and on GPUs. | ||
==== MPI ==== <!--T:11--> | ==== MPI ==== <!--T:11--> | ||
The following job script will use 8 CPU cores in total, on one or more nodes. | |||
Like the previous example it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | |||
{{File | {{File | ||
|name=submit-mrbayes-parallel.sh | |name=submit-mrbayes-parallel.sh | ||
| Line 58: | Line 56: | ||
<!--T:12--> | <!--T:12--> | ||
module load mrbayes/3.2.7 | module load mrbayes/3.2.7 | ||
cd $SCRATCH | cd $SCRATCH | ||
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | ||
<!--T:15--> | <!--T:15--> | ||
srun mb primates.nex | srun mb primates.nex | ||
}} | }} | ||
<!--T:16--> | <!--T:16--> | ||
The job script can be submitted with | |||
{{Command|sbatch submit-mrbayes-parallel.sh}} | {{Command|sbatch submit-mrbayes-parallel.sh}} | ||
==== GPU ==== <!--T:17--> | ==== GPU ==== <!--T:17--> | ||
The following job script will use a GPU. | |||
Like the previous examples it uses an input file (<code>primates.nex</code>) distributed with MrBayes. | |||
{{File | {{File | ||
|name=submit-mrbayes-gpu.sh | |name=submit-mrbayes-gpu.sh | ||
| Line 90: | Line 84: | ||
<!--T:18--> | <!--T:18--> | ||
module load gcc cuda/12 mrbayes/3.2.7 | module load gcc cuda/12 mrbayes/3.2.7 | ||
cd $SCRATCH | cd $SCRATCH | ||
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex . | ||
<!--T:21--> | <!--T:21--> | ||
srun mb primates.nex | srun mb primates.nex | ||
}} | }} | ||
<!--T:22--> | <!--T:22--> | ||
The job script can be submitted with | |||
{{Command|sbatch submit-mrbayes-gpu.sh}} | {{Command|sbatch submit-mrbayes-gpu.sh}} | ||
== Checkpointing == <!--T:23--> | == Checkpointing == <!--T:23--> | ||
For users needing very long runs of MrBayes, | For users needing 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 built-in mechanism for creating checkpoints, where progress can be saved from one job and continued in a subsequent job. | ||
<!--T:24--> | <!--T:24--> | ||