Configuration
Kuristo’s behavior can be customized using a configuration file named config.yaml.
Kuristo searches for this file in a .kuristo directory, starting from the current working directory and moving up through parent directories until it finds the first match.
The available configuration options are listed below.
Basic options
base:General settings section.
base.workflow-filenameName of files that contain workflow descriptions. These files are looked for when Kuristo executes workflows from a location.
Default value:
kuristo.yamlbase.console-widthMaximum width for console output, in characters.
Default value:
100
Logging options
log:Logging settings section.
log.dir-nameDirectory where logs will be stored.
log.historyNumber of recent runs to keep. Older runs are automatically deleted when this limit is exceeded. Tagged runs are protected from deletion and do not count toward this limit. Use the
tagcommand to protect important results (e.g., versions, baselines).Default value:
5log.cleanupCurrently, does nothing.
Resources
resources:Resource allocation settings.
resources.num-coresMaximum number of CPU cores available for parallel job execution. Kuristo will not attempt to run more than this many cores in parallel.
Default value: System CPU count (determined automatically)
Runner
runner:Main runner settings.
runner.mpi-launcherMPI command used to launch jobs.
Default value:
mpirunCan be overridden with the
KURISTO_MPI_LAUNCHERenvironment variable:KURISTO_MPI_LAUNCHER=mpiexec kuristo run tests/
Batch
batch:Batch submission settings.
batch.backendWhich batch system to use (e.g., slurm).
batch.default-accountCurrently, does nothing.
batch.partitionCluster partition or queue to submit jobs to.
Example
This example shows how to setup kuristo for a slurm queue, submitting into
a default partition.
The MPI launcher is set to mpiexec.
And we want to keep 10 previous runs.
log:
history: 10
runner:
mpi-launcher: mpiexec
batch:
backend: slurm
partition: default