Merge Multiple Simulation DataΒΆ

In this section, we will cover how to merge multiple simulation data files into a single HDF5 file using the wepy.hdf5 module. This process is essential for combining the results of different simulation runs, making it easier to analyze the overall data.

When running multiple simulations, it is often useful to merge the resulting data files into a single file. This allows for a more streamlined analysis and management of the data. The following example demonstrates how to use the WepyHDF5 class to accomplish this task.

The following Python script shows how to initialize, clone, and link multiple HDF5 files containing simulation results.

import os.path as osp
from wepy.hdf5 import WepyHDF5

print('running...', flush=True)

# Define the base path where the merged file will be saved
BASE_PATH = '<simulation-base-path>'

# List of HDF5 files to be merged
hdf5_filenames = [
    'run1.h5',
    'run2.h5',
    'run3.h5',
    ...
]

# Initialization of a single HDF5 file
init_wepy_h5 = WepyHDF5(filename=hdf5_filenames[0], mode='r')

# Creating a clone (This has to be done every time you link all HDF5 files in as separate runs)
CLONE_FILENAME = osp.join(BASE_PATH, 'merge.h5')

with init_wepy_h5:
    wepy_file = init_wepy_h5.clone(path=CLONE_FILENAME, mode='w')

# The linking step
with wepy_file:
    for hdf5_filename in hdf5_filenames:
        wepy_file.link_file_runs(hdf5_filename)

The script performs the following steps:

  1. Initialization:

    • We start by importing the necessary modules and defining the base path where the merged file will be saved.

    • A list of HDF5 filenames is provided, which contains the paths to the individual simulation result files.

  2. Cloning:

    • We initialize a WepyHDF5 object with the first HDF5 file in read mode.

    • Using the clone method, we create a new HDF5 file that will serve as the merged output file.

  3. Linking:

    • We open the newly created HDF5 file in write mode.

    • Each of the HDF5 files listed in hdf5_filenames is linked to the new file using the link_file_runs method.

By following these steps, you can merge multiple HDF5 files into a single file, making it easier to handle and analyze your simulation data.

Merging simulation data is a crucial step in data analysis workflows, especially when dealing with multiple runs. The wepy.hdf5 module provides a straightforward way to achieve this, ensuring that you can efficiently combine and manage your simulation results.