Difference between revisions of "Applications/BayesTraits"
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| + | ===Multi-Batch Jobs=== | ||
| + | The following job script will automatically run 3 identical BayesTrait jobs in an array, so that three outputs can be compared. It takes care of separating the jobs, running them and then bringing the outputs together. | ||
| + | |||
| + | <pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;"> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -J BayesTrait_array | ||
| + | #SBATCH -N 1 | ||
| + | #SBATCH -n 28 | ||
| + | #SBATCH -o %N.%j.%a.out | ||
| + | #SBATCH -e %N.%j.%a.err | ||
| + | #SBATCH -pcompute | ||
| + | #SBATCH --exclusive | ||
| + | #SBATCH --array 1-3 | ||
| + | |||
| + | module add bayesTraits/3.0/intel-2017 | ||
| + | |||
| + | # Create 3 sub-directories inside which each job will run | ||
| + | RUNDIR=`pwd` | ||
| + | mkdir $SLURM_ARRAY_TASK_ID | ||
| + | cd $SLURM_ARRAY_TASK_ID | ||
| + | |||
| + | # Update here to set command, tree and data files | ||
| + | COMMAND_FILE=MCcSM_RJHPexp05_WCLCBNoZero_command.txt | ||
| + | TREE_FILE=FritzHARD_WCLCBNoZero.trees | ||
| + | DATA_FILE=MCcSM_RJHPexp05_WCLCBNoZero.txt | ||
| + | |||
| + | # Make a 'copy' of the command, tree and data files in the job sub-directories | ||
| + | ln -s ../$COMMAND_FILE . | ||
| + | ln -s ../$TREE_FILE . | ||
| + | ln -s ../$DATA_FILE . | ||
| + | |||
| + | BayesTraitsV3 $TREE_FILE $DATA_FILE < $COMMAND_FILE | ||
| + | |||
| + | cd $RUNDIR | ||
| + | |||
| + | # Copy the output files from each of the 3 run directories into a files called run_1_<data_file>.log.txt | ||
| + | cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Log.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Log.txt | ||
| + | cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Schedule.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Schedule.txt | ||
| + | </pre> | ||
| + | |||
| + | The job is submitted in the same way as a standard batch job. | ||
==Further Information== | ==Further Information== | ||
Revision as of 12:00, 10 May 2019
Contents
Application Details
- Description: BayesTraits
- Version: 3.0.0 (supplied compiled binaries)
- Modules: bayes/3.0.0 (apps)
- Licence: Free (http://www.evolution.rdg.ac.uk/index.html)
Usage Examples
Interactive Session
[user@login01 ~]$ interactive salloc: Granted job allocation 409670 Job ID 409670 connecting to c128, please wait... [username@c128 ~]$ module add bayesTrait/3.0.0 [username@c128 ~]$ BayesTraitsV3 /trinity/clustervision/CentOS/7/apps/bayesTraits/3.0.0/Mammal.trees bob.tress BayesTraits V3.0 (Mar 2 2017) Mark Pagel and Andrew Meade www.evolution.reading.ac.uk
Batch Session
#!/bin/bash #SBATCH -J BayesTrait # Job Name #SBATCH -N 1 # Number of Nodes to use #SBATCH -n 28 # Number of CPUs #SBATCH -o %N.%j.%a.out # Output file name #SBATCH -e %N.%j.%a.err # Error file name #SBATCH -p compute # Partition to run on #SBATCH --exclusive # Instructs SLURM to not run any other job in the node(s) selected module add bayesTraits/3.0.0 BayesTraitsV3 Mammal.trees bob.tress < command.txt
[user@login01 ~]$ sbatch bayestrait-test.job Submitted batch job 409671
Multi-Batch Jobs
The following job script will automatically run 3 identical BayesTrait jobs in an array, so that three outputs can be compared. It takes care of separating the jobs, running them and then bringing the outputs together.
#!/bin/bash
#SBATCH -J BayesTrait_array
#SBATCH -N 1
#SBATCH -n 28
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH -pcompute
#SBATCH --exclusive
#SBATCH --array 1-3
module add bayesTraits/3.0/intel-2017
# Create 3 sub-directories inside which each job will run
RUNDIR=`pwd`
mkdir $SLURM_ARRAY_TASK_ID
cd $SLURM_ARRAY_TASK_ID
# Update here to set command, tree and data files
COMMAND_FILE=MCcSM_RJHPexp05_WCLCBNoZero_command.txt
TREE_FILE=FritzHARD_WCLCBNoZero.trees
DATA_FILE=MCcSM_RJHPexp05_WCLCBNoZero.txt
# Make a 'copy' of the command, tree and data files in the job sub-directories
ln -s ../$COMMAND_FILE .
ln -s ../$TREE_FILE .
ln -s ../$DATA_FILE .
BayesTraitsV3 $TREE_FILE $DATA_FILE < $COMMAND_FILE
cd $RUNDIR
# Copy the output files from each of the 3 run directories into a files called run_1_<data_file>.log.txt
cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Log.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Log.txt
cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Schedule.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Schedule.txt
The job is submitted in the same way as a standard batch job.
Further Information
|