map2map

Neural network emulators to transform field/map data

Installation
Usage

Installation

Install in editable mode

pip install -e .

Usage

The command is m2m.py in your $PATH after installation. Take a look at the examples in scripts/*.slurm. For all command line options look at map2map/args.py or do m2m.py -h.

Data

Put each field in one npy file. Structure your data to start with the channel axis and then the spatial dimensions, e.g. (2, 64, 64) for a 2D vector field of size 64^2 and (1, 32, 32, 32) for a 3D scalar field of size 32^3. Specify the data path with glob patterns.

During training, pairs of input and target fields are loaded. Both input and target data can consist of multiple fields, which are then concatenated along the channel axis.

Data cropping

If the size of a pair of input and target fields is too large to fit in a GPU, we can crop part of them to form pairs of samples. Each field can be cropped multiple times, along each dimension. See --crop, --crop-start, --crop-stop, and --crop-step. The total sample size is the number of input and target pairs multiplied by the number of cropped samples per pair.

Data padding

Here we are talking about two types of padding. We differentiate the padding during convolution from our explicit data padding, and refer to the former as conv-padding.

Convolution preserves translational invariance, but conv-padding breaks it, except for the periodic conv-padding, which is not feasible at runtime for large 3D fields. Therefore we recommend convolution without conv-padding. By doing this, the output size will be smaller than the input size, and thus smaller than the target size if it equals the input size, making loss computation inefficient.

To solve this, we can pad the input before feeding it into the model. The pad size should be adjusted so that the output size equals or approximates the target size. One should be able to calculate the proper pad size given the model. Padding works for cropped samples, or samples with periodic boundary condition.

Data loading, sampling, and page caching

The difference in speed between disks and GPUs makes training an IO-bound job. Stochastic optimization exacerbates the situation, especially for large 3D data with multiple crops per field. In this case, we can use the --div-data option to divide field files among GPUs, so that each node only need to load part of all data if there are multiple nodes. Data division is shuffled every epoch. Crops within each field can be further randomized within a distance relative to the field, controlled by --div-shuffle-dist. Setting it to 0 turn off this randomization, and setting it to N limits the shuffling within a distance of N files. With both --div-data and --div-shuffle-dist, each GPU only need to work on about N files at a time, with those files kept in the Linux page cache. This is especially useful when the amount of data exceeds the CPU memory size.

Data normalization

Input and target (output) data can be normalized by functions defined in map2map2/data/norms/. Also see Customization.

Model

Find the models in map2map/models/. Modify the existing models, or write new models somewhere and then follow Customization.

class Net(nn.Module):
    def __init__(self, in_chan, out_chan, mid_chan=32, kernel_size=3,
                 negative_slope=0.2, **kwargs):
        super().__init__()

        self.conv1 = nn.Conv2d(in_chan, mid_chan, kernel_size)
        self.act = nn.LeakyReLU(negative_slope)
        self.conv2 = nn.Conv2d(mid_chan, out_chan, kernel_size)

    def forward(self, x):
        x = self.conv1(x)
        x = self.act(x)
        x = self.conv2(x)
        return x

The model __init__ requires two positional arguments, the number of input and output channels. Other hyperparameters can be specified as keyword arguments, including the scale_factor useful for super-resolution tasks. Note that the **kwargs is necessary for compatibility.

Training

Files generated

*.out: job stdout and stderr
state_{i}.pt: training state after the i-th epoch including the model state
checkpoint.pt: symlink to the latest state
runs/: directories of tensorboard logs

Tracking

Install tensorboard and launch it by

tensorboard --logdir PATH --samples_per_plugin images=IMAGES --port PORT

Use . as PATH in the training directory, or use the path to some parent directory for tensorboard to search recursively for multiple jobs.
Show IMAGES images, or all of them by setting it to 0.
Pick a free PORT. For remote jobs, do ssh port forwarding.

Customization

Models, criteria, optimizers and data normalizations can be customized without modifying map2map. They can be implemented as callbacks in a user directory which is then passed by --callback-at. The default locations are searched first before the callback directory. So be aware of name collisions.

The default locations are

models: map2map/models/
criteria: torch.nn
optimizers: torch.optim
normalizations: map2map/data/norms/

This approach is good for experimentation. For example, one can play with a model Bar in path/to/foo.py, by calling m2m.py with --model foo.Bar --callback-at path/to.

License

eelregit/map2map

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