Generate Heads for 2D Directed Sphere Exclusion

This cube generates the heads used for directed sphere exclusion so that the sphere exclusion clustering itself can happen in parallel.

Calculation Parameters

  • None (batch_size) type: integer:
    Default: 10000
  • None (batch_size_floor) type: integer:
    Default: 400
  • 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
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • None (head_percentage) type: decimal: Fraction of batch size to find as cluster heads.
    Default: 0.03
  • 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
  • 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
  • None (num_clusters_per_cycle_floor) type: integer:
    Default: 20
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • None (sim_cutoff) type: decimal:
    Default: 0.2
  • Similarity Measure (sim_type) type: string: The similarity measure used to 2D similarity calculation.
    Default: OETanimoto
    Choices: OECosine, OEDice, OEEuclid, OEManhattan, OETanimoto
  • Sort Order (sort_order) type: string: The sort order for the hitlist scores.
    Default: Descending
    Choices: Descending, Ascending
  • None (sphere_exclusion_radius) type: decimal:
    Default: 0.05
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • None (starting_batch_percentage) type: decimal:
    Default: 0.1
  • None (target_num_clusters) type: integer:
  • Use Score (use_rank) type: boolean:
    Default: False

Field parameters

  • Fingerprint X Vector Field (cluster_fingerprint_field) type: Field Type: Chem.FingerPrintVec:
    Default: fp_x
  • None (cluster_head_index_field) type: Field Type: Int:
    Default: cluster_head_index
  • Cluster ID Field (cluster_id_field) type: Field Type: String: The name for the field that will contain the unique cluster ID.
    Default: Cluster ID
  • None (count_field) type: Field Type: Int:
    Default: count
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Fingerprint Field (fingerprint_field) type: Field Type: Chem.FingerPrint: Tag name for the field that stores fingerprints.
    Default: Fingerprint
  • None (finished_field) type: Field Type: String:
    Default: finished
  • UUID (id_field) type: Field Type: String: The field to store unique identifiers for mols
    Default: UUID
  • None (is_core) type: Field Type: Bool:
    Default: is_core
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Hit Score Field (rank_field) type: Field Type: Float: The name for the field that will contain the hitlist score.
    Default: Score

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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • 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