Permeability Report

Collects basic simulation information and generates a floe 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
  • 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
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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
  • Display RED Rates (red) type: boolean: Plot permeability evolution estimated using the Rate from Event Durations (RED) scheme (if available)
    Default: False
  • Floe Report (report_out) type: string: The title for the output floe report.
  • 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: verbose level
    Default: debug
    Choices: info, warning, error, debug, ddebug

Field parameters

  • Collection Field (collection_field) type: Field Type: Orion.Collection: Field containing the link to the collection associated with the record.
    Default: Collection
  • Compartment Boundary (z) Field (compartment_boundary_field) type: Field Type: Float: Field containing the definition for the donor and acceptor compartment.
    Default: Compartment Boundary (z)
  • Log Experimental Permeability Field (exp_permeability_field) type: Field Type: FloatVec: Field containing the experimentally measured permeability and their variance (or standard deviation) in log-scale.
    Default: Log Experimental Permeability
  • Experiment Type Field (exp_type_field) type: Field Type: String: Field containing the type of the permeability experiment.
    Default: Experiment Type
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Molecule Name Field (mol_name_field) type: Field Type: String: Field containing the name of the molecule.
    Default: Molecule Name
  • Molecule SMILES Field (mol_smiles_field) type: Field Type: String: Field containing the SMILES string for the primary molecule.
    Default: Molecule SMILES
  • Log Estimated Permeability Evolution Field (permeabilities_field) type: Field Type: NumPy.NDArray: Field containing the evolution of permeability estimates and their confidence interval (upper and lower bounds) in log-scale.
    Default: Log Estimated Permeability Evolution
  • Coordinate for Inverse Probability Distribution Field (prob_evol_coord_field) type: Field Type: FloatVec: Field containing the coordinate for the inverse probability distribution.
    Default: Coordinate for Inverse Probability Distribution
  • Evolution of the Inverse Probability Distribution Field (prob_evol_field) type: Field Type: NumPy.NDArray: Field containing the evolution of the inverse probabbility distribution along z.
    Default: Evolution of the Inverse Probability Distribution
  • Log Estimated Permeability Evolution Field (red_permeabilities_field) type: Field Type: NumPy.NDArray: Field containing the evolution of permeability estimates and their confidence interval (upper and lower bounds) in log-scale.
    Default: Log Estimated Permeability Evolution
  • Primary Molecule Field (traj_field) type: Field Type: Chem.Mol: Field containing the primary molecule.
  • Weight Field (weight_field) type: Field Type: Float: Field containing the weight of the terminal walker.
    Default: Weight

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
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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