System Setup

Set up necessary data (topology, basis state, and system configuration) on a record for WESTPA simulation

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
  • 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
  • Simulation Step Size (ps) (step_size) type: decimal: The size of each simulation step in picoseconds.
    Default: 0.002
  • Temperature (temperature) type: decimal: Temperature (Kelvin)
    Default: 308.0
  • Log Verbosity (verbosity) type: string: verbose level
    Default: debug
    Choices: info, warning, error, debug, ddebug

Field parameters

  • Basis State Field (bstate_field) type: Field Type: NumPy.NpzFile: Field containing data for a single basis state.
    Default: Basis State
  • Dry Molecule Field (dry_molecule_field) type: Field Type: Chem.Mol: Field containing the unsolvated molecule.
    Default: Dry Molecule
  • 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:
  • Integrator Field (OpenMM) (integrator_field) type: Field Type: OpenMM.Integrator: Field containing the OpenMM integrator.
    Default: Integrator (OpenMM)
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Molecule with Membrane Field (membrane_molecule_field) type: Field Type: Chem.Mol: Field containing the solvated molecule and the membrane.
    Default: Molecule with Membrane
  • Molecule ID Field (mol_id_field) type: Field Type: String: Field containing the identification number of the molecule.
    Default: Molecule ID
  • 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
  • Primary Molecule Field (primary_molecule_field) type: Field Type: Chem.Mol: Field containing the primary molecule.
  • Solvated Molecule Field (solvated_molecule_field) type: Field Type: Chem.Mol: Field containing the solvated molecule.
    Default: Solvated Molecule
  • Sytem Field (OpenMM) (system_field) type: Field Type: OpenMM.System: Field containing the OpenMM system.
    Default: System (OpenMM)
  • Temperature Field (temperature_field) type: Field Type: Float: Field containing the temperature under which the permeability simulation was run.
    Default: Temperature
  • Topology Field (OEMol) (topology_field) type: Field Type: Chem.Mol: Field containing an OEMol representing the topology.
    Default: Topology (OEMol)

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