pipeline.hpc
pipeline.hpc
Classes for working with different HPC clusters.
Use ccbr_tools.pipeline.hpc.get_hpc to retrieve an HPC Cluster instance, which contains default attributes for supported clusters.
Classes
| Name | Description |
|---|---|
| Biowulf | The Biowulf cluster – child of ccbr_tools.pipeline.hpc.Cluster |
| Cluster | Base class for an HPC cluster - evaluates to None |
| FRCE | The FRCE cluster – child of ccbr_tools.pipeline.hpc.Cluster |
Biowulf
pipeline.hpc.Biowulf(self)The Biowulf cluster – child of ccbr_tools.pipeline.hpc.Cluster
Attributes
| Name | Type | Description |
|---|---|---|
| name | str |
The name of the cluster. |
| modules | dict |
A dictionary mapping module names to their corresponding commands. |
| singularity_sif_dir | str |
The directory path for Singularity SIF files. |
| env_vars | str |
A string representing the environment variables to be set on the cluster. |
Cluster
pipeline.hpc.Cluster(self)Base class for an HPC cluster - evaluates to None
Attributes
| Name | Type | Description |
|---|---|---|
| name | str |
The name of the cluster. |
| modules | dict |
A dictionary containing the modules installed on the cluster. The keys are the module names and the values are the corresponding versions. |
| singularity_sif_dir | str |
The directory where Singularity SIF files are stored. |
| env_vars | str |
A string representing the environment variables to be set on the cluster. |
FRCE
pipeline.hpc.FRCE(self)The FRCE cluster – child of ccbr_tools.pipeline.hpc.Cluster
Attributes
| Name | Type | Description |
|---|---|---|
| name | str |
The name of the cluster. |
| modules | dict |
A dictionary mapping module names to their corresponding commands. |
| singularity_sif_dir | str |
The directory path for Singularity SIF files. |
| env_vars | str |
A string representing the environment variables to be set on the cluster. |
Functions
| Name | Description |
|---|---|
| get_hpc | Returns an instance of the High-Performance Computing (HPC) cluster based on the specified HPC name. |
get_hpc
pipeline.hpc.get_hpc(debug=False)Returns an instance of the High-Performance Computing (HPC) cluster based on the specified HPC name.
If the HPC is not known or supported, an instance of the base Cluster class is returned.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| debug | bool |
If True, uses debug as the HPC name. Defaults to False. |
False |
Returns
| Name | Type | Description |
|---|---|---|
| cluster | Cluster | An instance of the HPC cluster. |
Examples
>>> get_hpc()
>>> get_hpc(debug=True)