Distribute pyspi jobs across a PBS cluster

This repository contains scripts for distributing pyspi jobs across a PBS-type cluster. Each job will contain one Calculator object that is associated with one multivariate time series (MTS).

The scripts allow the user to specify a directory containing the MTS files, with each sample's time series stored in a separate binary NumPy (.npy) file (as shown in simple_demo.ipynb). Within this directory, the user needs to also include a YAML configuration file like that included in the repo specifying the relative location of each .npy file (and, optionally, the name, dim_order, and any relevant labels). See simple_demo.ipynb for code to automatically populate a sample.yaml file.

Usage

Follow the pyspi documentation to install and set up pyspi on your cluster. We recommend installing into a new conda environment.
Organize all MTS .npy files into a user-specified data directory.
Create the sample.yaml file and store it in the same user-specified data directory as your MTS .npy files.
Activate your conda environment where pyspi is installed:

conda activate pyspi_environment

Submit the jobs from the command line using distribute_jobs.py (see below for usage).

distribute_jobs.py works by taking in a data directory, compute file, and sample YAML (see below), iterating over each MTS NumPy array, and submitting a separate pbs job per sample. The pbs file is automatically generated from this script and submitted via qsub. distribute_jobs.py includes several command-line options for user configuration, all of which are optional:

--data_dir: Data directory in which all samples' MTS NumPy files are stored.
--calc_file_name: Name of the .pkl output file for each sample. The default is calc.pkl.
--compute_file: The file path for python script that actually runs pyspi. Default is pyspi_compute.py in the directory where this script is located.
--sample_yaml: The file path to the sample YAML configuration file (see below for generation details). The default is sample.yaml.
--pyspi_config: If desired, the file path to a user-generated YAML configuration file specifying a subset of SPIs to compute. Omitting this argument computes all 283 SPIs.
--walltime_hrs: Maximum walltime allowed for a given job, in hours. The default is 6.
--cpu: The number of CPUs requested per job. The default is 2.
--mem: The amount of memory requested per job, in GB. The default is 20.
--overwrite_pkl: Including this flag means that existing pyspi results for a given sample will be overwritten if found.
--pbs-notify: When pbs should email user; a=abort, b=begin, e=end. The default is 'a'.
--user_email: Email address where pbs should notify user.
--table_only: Optional flag to only save the calc.table results for each sample rather than the full Calculator object.

Accessing results

The results will be stored in the user-specified data directory under the same name as the numpy files; e.g., if you have the file example_data/Dataset_0.npy in your YAML file, then there will be a new folder called example_data/Dataset_0 with a calc.pkl file inside that contains the calculator (or the SPI results table).

You can access the results using the dill package:

import dill

with open('calc.pkl','rb') as f:
  calc = dill.load(f)

Then you can view the contents as per the standard pyspi documentation, e.g.,

calc.table
calc.table['cov_EmpiricalCovariance]

Check out simple_demo.ipynb for a more in-depth walkthrough of this process.

Automatically generate sample YAML configuration file

If you have many samples, you may wish to automatically populate your sample YAML configuration file. As shown in simple_demo.ipynb, if you have a dictionary containing your MTS where each key is the name of the dataset and the value is the MTS array, you can automatically populate your sample.yaml file as follows:

# Define the YAML file
yaml_file = "example_data/sample.yaml"

# Use ps dimension order to indicate that processes are the rows while timepoints are the columns
dim_order = "ps"

# Iterate over the keys and values of the dictionary
for key, value in MTS_datasets.items():
    # Define template string and fill in variables
    yaml_string = "{{file: example_data/{key}.npy, name: {key}, dim_order: {dim_order}, labels: [{key}]}}\n"
    yaml_string_formatted = f"{yaml_string.format(key=key, dim_order=dim_order)}"

    # Append line to file
    with open(yaml_file, "a") as f:
        f.write(yaml_string_formatted)

anniegbryant/pyspi-distribute

Distribute pyspi jobs across a PBS cluster

Usage

Accessing results

Automatically generate sample YAML configuration file