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 withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: 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 withDefault: 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-evaluatedDefault: 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 secondsDefault: 60Choices: 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 CPUDefault: 32 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: 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 levelDefault: debugChoices: 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 fieldDefault: 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 reportDefault: 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 addressDefault: 64
- Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 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-evaluatedDefault: 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 withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: 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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network