WESTPA Run Reader

Construct the Run object and emit segment data.

Calculation Parameters

  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • Starting Iteration (first_iter) type: integer: Starting iteration to be used for extracting segments from. Leave empty to start from the first iteration that is available.
    , Min: 1
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Last Iteration (last_iter) type: integer: Last iteration to be used for extracting segments from. Leave empty to stop at the last iteration that is available.
    , Min: 1
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Project Name (project) type: string:
    Default: WESTPA
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Log Verbosity (verbosity) type: string: The level of logging verbosity.
    Default: debug
    Choices: error, warning, info, debug, ddebug

Field parameters

  • Collection Field (collection_field) type: Field Type: LinkedResource: Field containing the collection (link) that stores the WESTPA project configurations and MD trajectory data.
    Default: Collection
  • Initial Point State (XML) Field (init_point_field) type: Field Type: CompressedBlob: Field containing the initial point state file in the XML format.
    Default: Initial Point State (XML)
  • Init Shard Field (init_shard_field) type: Field Type: LinkedShard: Field containing the init shard (link) that stores the WESTPA project configurations.
    Default: Init Shard
  • Segment Iteration Number Field (iteration_number_field) type: Field Type: Int:
    Default: Segment Iteration Number
  • Log Field (log_field) type: Field Type: String: Message log field
    Default: Log Field
  • Segment Index Field (segment_index_field) type: Field Type: Int:
    Default: Segment Index
  • Segment Progress Coordinate Field (segment_pcoord_field) type: Field Type: NumpyArray:
    Default: Segment Progress Coordinate
  • Segment Weight Field (segment_weight_field) type: Field Type: Float:
    Default: Segment Weight
  • Segment Shard Field (shard_field) type: Field Type: LinkedShard: Field containing the shard (link) that can be used or created by this cube.
    Default: Segment Shard
  • HDF5 Data (west.h5) Field (west_h5_field) type: Field Type: CompressedBlob: Field containing the WESTPA data (west.h5).
    Default: HDF5 Data (west.h5)

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network