Pmac¶
Template ID: pmac
Quickstart¶
Take note below how to configure the template. This quickstart only includes the fields you absolutely require. This will write a new configuration to ~/.janis.conf
. See configuring janis for more information.
janis init pmac
# or to find out more information
janis init pmac --help
OR you can insert the following lines into your template:
template:
id: pmac
Fields¶
Optional
ID | Type | Default | Documentation |
---|---|---|---|
intermediate_execution_dir | <class ‘str’> | Computation directory | |
container_dir | <class ‘str’> | /config/binaries/singularity/containers_devel/janis/ | [OPTIONAL] Override the directory singularity containers are stored in |
queues | typing.Union[str, typing.List[str]] | prod_med,prod | The queue to submit jobs to |
singularity_version | <class ‘str’> | 3.4.0 | The version of Singularity to use on the cluster |
send_job_emails | <class ‘bool’> | False | Send Slurm job notifications using the provided email |
catch_slurm_errors | <class ‘bool’> | True | Fail the task if Slurm kills the job (eg: memory / time) |
singularity_build_instructions | <class ‘str’> | Sensible default for PeterMac template | |
max_cores | <class ‘int’> | 40 | Override maximum number of cores (default: 32) |
max_ram | <class ‘int’> | 256 | Override maximum ram (default 508 [GB]) |
max_workflow_time | <class ‘int’> | 20100 | The walltime of the submitted workflow “brain” |
janis_memory_mb | <class ‘int’> | ||
email_format | <class ‘str’> | (null, “molpath”) | |
log_janis_job_id_to_stdout | <class ‘bool’> | False | This is already logged to STDERR, but you can also log the “Submitted batch job d” to stdout with this option set to true. |
submission_sbatch | <class ‘str’> | sbatch | |
submission_node | typing.Union[str, NoneType] | papr-expanded02, | Request a specific node with ‘–nodelist <nodename>’ |