Path Ensemble Writer

Saves trajectories and their importance weights to a

tar archive.

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
• Tar Archive Name (filename) type: string: Name of the tar archive to create.

  Default: paths.tar
• 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
• 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
• Save Topology (save_topology) type: boolean: Save the molecular topology as a separate file

  (“topology.pdb”). | Default: False

• 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
• Trajectory File Extension (traj_file_ext) type: string: File format in which to store trajectory data.

  Default: .h5

  Choices: .arc, .dcd, .binpos, .xtc, .trr, .hdf5, .h5, .ncdf, .netcdf, .nc, .pdb.gz, .pdb, .lh5, .crd, .mdcrd, .inpcrd, .restrt, .rst7, .ncrst, .lammpstrj, .dtr, .stk, .gro, .xyz.gz, .xyz, .tng, .xml, .mol2, .hoomdxml, .gsd, .rst

Field parameters

• Trajectory Field (traj_field) type: Field Type: Blob: Field containing the trajectory in MDTraj HDF5 format.

  Default: Trajectory
• Weight Field (weight_field) type: Field Type: Float: Field containing the trajectory weight.

  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
• 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