Class SingularityConnector

Specialization of SlurmConnector that, in addition to supporting ssh/slurm jobs, connects a given singularity container to the HPC environment.

Hierarchy (view full)

SlurmConnector
- SingularityConnector

Constructors

`Protected` constructor

new SingularityConnector(maintainer, connector, is_cvmfs?): SingularityConnector
Parameters
- maintainer: default
  maintainer that this connector was created for
- connector: SSHConnector
  sshconnector this connector should use
- is_cvmfs: boolean = false
  whether this connector is cvmfs
Returns SingularityConnector
Inherited from SlurmConnector.constructor
- Defined in src/connectors/SlurmConnector.ts:39

Properties

isContainer

isContainer: boolean = true

`Protected` is_cvmfs

is_cvmfs: boolean

properties

`Protected` maintainer

maintainer: default

parent pointer

`Protected` modules

modules: string[] = []

`Protected` remoteDataFolderPath

remoteDataFolderPath: string

`Protected` remoteExecutableFolderPath

remoteExecutableFolderPath: string

`Protected` remoteResultFolderPath

remoteResultFolderPath: string

slurm_id

slurm_id: string

`Protected` sshConnector

sshConnector: SSHConnector

config

`Protected` template

template: string

`Private` volumeBinds

volumeBinds: Record<string, string> = {}

Methods

`Private` _getJobENV

_getJobENV(): string[]
Returns job environment

Returns string[]
jobENV - jobenvironment variables
- Defined in src/connectors/SingularityConnector.ts:250

`Private` _getVolumeBindCMD

_getVolumeBindCMD(manifest?): string
Returns volumeBinds
Parameters
- manifest: null | executableManifest = null
  manifest containing volumeBinds
Returns string
volumeBinds
- Defined in src/connectors/SingularityConnector.ts:200

cancel

cancel(): Promise<void>
cancels the job

Returns Promise<void>
Inherited from SlurmConnector.cancel
- Defined in src/connectors/SlurmConnector.ts:312

createKernelInit

createKernelInit(manifest): Promise<void>
Creates a bash script using kernelConfig
Parameters
- manifest: executableManifest
  manifest to create a kenrl for
Returns Promise<void>
Throws
if unable to create file by ssh
- Defined in src/connectors/SingularityConnector.ts:293

execCommandWithinImage

execCommandWithinImage(image, cmd, config): void
Executes specified command within specified image
Parameters
- image: string
  docker image
- cmd: string
  command to be executed
- config: slurm
  slurm configuration
Returns void
- Defined in src/connectors/SingularityConnector.ts:51

execExecutableManifestWithinImage

execExecutableManifestWithinImage(manifest, config): Promise<void>
Executes specified manifest within image
Parameters
- manifest: executableManifest
  manifest that needs toe be executed
- config: slurm
  slurm configuration
Returns Promise<void>
Throws
- thrown when container cannot be resolved
- Defined in src/connectors/SingularityConnector.ts:68

getContainerCVMFSFolderPath

getContainerCVMFSFolderPath(providedPath?): string
Get Container CVMFS folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
Inherited from SlurmConnector.getContainerCVMFSFolderPath
- Defined in src/connectors/SlurmConnector.ts:424

getContainerDataFolderPath

getContainerDataFolderPath(providedPath?): string
Get Container data folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
Inherited from SlurmConnector.getContainerDataFolderPath
- Defined in src/connectors/SlurmConnector.ts:434

getContainerExecutableFolderPath

getContainerExecutableFolderPath(providedPath?): string
Get Container executable folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
Inherited from SlurmConnector.getContainerExecutableFolderPath
- Defined in src/connectors/SlurmConnector.ts:414

getContainerResultFolderPath

getContainerResultFolderPath(providedPath?): string
Get Container result folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
Inherited from SlurmConnector.getContainerResultFolderPath
- Defined in src/connectors/SlurmConnector.ts:444

getRemoteDataFolderPath

getRemoteDataFolderPath(providedPath?): null | string
gets remote data folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns null | string
command execution output
Inherited from SlurmConnector.getRemoteDataFolderPath
- Defined in src/connectors/SlurmConnector.ts:390

getRemoteExecutableFolderPath

getRemoteExecutableFolderPath(providedPath?): string
gets remote executable folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
command execution output
Inherited from SlurmConnector.getRemoteExecutableFolderPath
- Defined in src/connectors/SlurmConnector.ts:378

getRemoteResultFolderContent

getRemoteResultFolderContent(): Promise<string[]>
Get remote results folder content

Returns Promise<string[]>
file content
Inherited from SlurmConnector.getRemoteResultFolderContent
- Defined in src/connectors/SlurmConnector.ts:454

getRemoteResultFolderPath

getRemoteResultFolderPath(providedPath?): string
gets remote result folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
command execution output
Inherited from SlurmConnector.getRemoteResultFolderPath
- Defined in src/connectors/SlurmConnector.ts:402

getSSHConnection

getSSHConnection(): SSHConnector
Returns SSHConnector
the ssh connection this connector uses
Inherited from SlurmConnector.getSSHConnection
- Defined in src/connectors/SlurmConnector.ts:659

getSlurmStderr

getSlurmStderr(): Promise<void>
gets SlurmStderr and emit it as a log in the maintainer

Returns Promise<void>
Inherited from SlurmConnector.getSlurmStderr
- Defined in src/connectors/SlurmConnector.ts:349

getSlurmStdout

getSlurmStdout(): Promise<void>
gets SlurmStdOut and emit it as a log in the maintainer

Returns Promise<void>
Inherited from SlurmConnector.getSlurmStdout
- Defined in src/connectors/SlurmConnector.ts:336

getStatus

getStatus(): Promise<string>
checks job status

Returns Promise<string>
job status (RETRY, UNKNOWN, or a slurm job status)
Inherited from SlurmConnector.getStatus
- Defined in src/connectors/SlurmConnector.ts:268

getUsage

getUsage(): Promise<Record<string, null | number>>
Get job usage

Returns Promise<Record<string, null | number>>
- usage dictionary
Inherited from SlurmConnector.getUsage
- Defined in src/connectors/SlurmConnector.ts:514

isCommunityAccount

isCommunityAccount(): boolean
Returns boolean
whether or not this connection is via a community account
Inherited from SlurmConnector.isCommunityAccount
- Defined in src/connectors/SlurmConnector.ts:628

pause

pause(): Promise<void>
pauses the job

Returns Promise<void>
Inherited from SlurmConnector.pause
- Defined in src/connectors/SlurmConnector.ts:320

`Protected` prepare

prepare(cmd, config): void
Creates slurm string with specified configuation. Saves it to this.template.
Parameters
- cmd: string
  command that needs to be executed
- config: slurm
  slurm configuration
Returns void
Inherited from SlurmConnector.prepare
- Defined in src/connectors/SlurmConnector.ts:99

registerContainerVolumeBinds

registerContainerVolumeBinds(volumeBinds): void
Registers volumeBinds
Parameters
- volumeBinds: Record<string, string>
  volumeBinds that need to be registered
Returns void
- Defined in src/connectors/SingularityConnector.ts:187

registerModules

registerModules(modules): void
Registers all of the specified modules
Parameters
- modules: string[]
  Array of strings
Returns void
Inherited from SlurmConnector.registerModules
- Defined in src/connectors/SlurmConnector.ts:78

resume

resume(): Promise<void>
resumes the job

Returns Promise<void>
Inherited from SlurmConnector.resume
- Defined in src/connectors/SlurmConnector.ts:328

runImage

runImage(image, config): void
Runs singularity image
Parameters
- image: string
  singularity image
- config: slurm
  slurm configuration
Returns void
- Defined in src/connectors/SingularityConnector.ts:166

setRemoteDataFolderPath

setRemoteDataFolderPath(path): void
Parameters
- path: string
  remote data folder path
Returns void
Inherited from SlurmConnector.setRemoteDataFolderPath
- Defined in src/connectors/SlurmConnector.ts:644

setRemoteExecutableFolderPath

setRemoteExecutableFolderPath(path): void
Parameters
- path: string
  remote executable folder path
Returns void
Inherited from SlurmConnector.setRemoteExecutableFolderPath
- Defined in src/connectors/SlurmConnector.ts:636

setRemoteResultFolderPath

setRemoteResultFolderPath(path): void
Parameters
- path: string
  remote result folder path
Returns void
Inherited from SlurmConnector.setRemoteResultFolderPath
- Defined in src/connectors/SlurmConnector.ts:652

submit

submit(): Promise<void>
Submit the slurm job.

Returns Promise<void>
Throws
when job cannot be submitted or ssh commands fail
Inherited from SlurmConnector.submit
- Defined in src/connectors/SlurmConnector.ts:166

`Static` build

build(maintainer, is_cvmfs?): Promise<undefined | SingularityConnector>
Public interface for constructing a singularity connector
Parameters
- maintainer: default
  maintainer this cnonector is for
- is_cvmfs: boolean = false
  whether or not this is cvmfs
Returns Promise<undefined | SingularityConnector>
the connector, or undefined if construction was unsuccessful
Overrides SlurmConnector.build
- Defined in src/connectors/SingularityConnector.ts:26

Class SingularityConnector

Hierarchy (view full)

Index

Constructors

Properties

Methods

Constructors

Protected constructor

Parameters

Returns SingularityConnector

Properties

isContainer

Protected is_cvmfs

Protected maintainer

Protected modules

Protected remoteDataFolderPath

Protected remoteExecutableFolderPath

Protected remoteResultFolderPath

slurm_id

Protected sshConnector

Protected template

Private volumeBinds

Methods

Private _getJobENV

Returns string[]

Private _getVolumeBindCMD

Parameters

Returns string

cancel

Returns Promise<void>

createKernelInit

Parameters

Returns Promise<void>

Throws

execCommandWithinImage

Parameters

Returns void

execExecutableManifestWithinImage

Parameters

Returns Promise<void>

Throws

getContainerCVMFSFolderPath

Parameters

Returns string

getContainerDataFolderPath

Parameters

Returns string

getContainerExecutableFolderPath

Parameters

Returns string

getContainerResultFolderPath

Parameters

Returns string

getRemoteDataFolderPath

Parameters

Returns null | string

getRemoteExecutableFolderPath

Parameters

Returns string

getRemoteResultFolderContent

Returns Promise<string[]>

getRemoteResultFolderPath

Parameters

Returns string

getSSHConnection

Returns SSHConnector

getSlurmStderr

Returns Promise<void>

getSlurmStdout

Returns Promise<void>

getStatus

Returns Promise<string>

getUsage

Returns Promise<Record<string, null | number>>

isCommunityAccount

Returns boolean

pause

Returns Promise<void>

Protected prepare

Parameters

`Protected` constructor

`Protected` is_cvmfs

`Protected` maintainer

`Protected` modules

`Protected` remoteDataFolderPath

`Protected` remoteExecutableFolderPath

`Protected` remoteResultFolderPath

`Protected` sshConnector

`Protected` template

`Private` volumeBinds

`Private` _getJobENV

`Private` _getVolumeBindCMD

`Protected` prepare

`Static` build