Clustering Report

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
  • Floe Report Name (floe_report_name) type: string:
    Default: Cluster Report
  • 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
  • None (is_large_scale) type: boolean:
    Default: False
  • Is Sphere Exclusion (is_sphere_exclusion) type: boolean:
    Default: False
  • 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
  • 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
  • Similarity Measure (similarity_measure_type) type: string: The similarity measure used to 2D similarity calculation.
    Default: Tanimoto
    Choices: Cosine, Dice, Euclid, Manhattan, Tanimoto, Tversky
  • Sort Order (sort_order) type: string: The sort order for the hitlist scores.
    Default: Descending
    Choices: Descending, Ascending
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • None (use_hitlist) type: boolean:
    Default: False
  • None (use_matrix_input_file) type: boolean:
    Default: False
  • Use Score (use_rank) type: boolean:
    Default: False

Field parameters

  • None (bin_field) type: Field Type: IntVec:
    Default: bin_field
  • 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
  • Cluster Method Field (cluster_method_field) type: Field Type: String: Field name for passing the clustering method to the floe report.
    Default: Cluster Method
  • Cluster Parameters Field (cluster_parameters_field) type: Field Type: String: Field name for passing the cluster parameters to the Floe report.
    Default: Parameters
  • 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 (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
  • None (method_field) type: Field Type: String:
    Default: method
  • None (mol_field) type: Field Type: Chem.Mol:
  • Hit Score Field (rank_field) type: Field Type: Float: The name for the field that will contain the hitlist score.
    Default: Score
  • None (score_total_field) type: Field Type: Float:
    Default: score_total
  • None (x_field) type: Field Type: Int:
    Default: x

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