Merge branch 'master' into dp/pyREGCOIL

.gitignore

@@ -20,4 +20,6 @@ tests/benchmarks/.benchmarks/
 *.output
 *.pdf
 *.pyc
+*.swp
+*.swo
 .pymon

CHANGELOG.md

@@ -20,12 +20,22 @@ New Features
 - Changes ``ToroidalFlux`` objective to default using a 1D loop integral of the vector potential
 to compute the toroidal flux when possible, as opposed to a 2D surface integral of the magnetic field dotted with ``n_zeta``.
 - Allow specification of Nyquist spectrum maximum modenumbers when using ``VMECIO.save`` to save a DESC .h5 file as a VMEC-format wout file
+- Added and tested infinite-n ideal-ballooning stability solver implemented as a part of the BallooningStability Objective. DESC can use reverse-mode AD to now optimize equilibria against infinite-n ideal ballooning modes.
+- Add ``jac_chunk_size`` to ``ObjectiveFunction`` and ``_Objective`` to control the above chunk size for the ``fwd`` mode Jacobian calculation
+  - if ``None``, the chunk size is equal to ``dim_x``, so no chunking is done
+  - if an ``int``, this is the chunk size to be used.
+  - if ``"auto"`` for the ``ObjectiveFunction``, will use a heuristic for the maximum ``jac_chunk_size`` needed to fit the jacobian calculation on the available device memory, according to the formula: ``max_jac_chunk_size = (desc_config.get("avail_mem") / estimated_memory_usage - 0.22)  / 0.85  * self.dim_x`` with ``estimated_memory_usage = 2.4e-7 * self.dim_f * self.dim_x + 1``
+- the ``ObjectiveFunction`` ``jac_chunk_size`` is used if ``deriv_mode="batched"``, and the ``_Objective`` ``jac_chunk_size`` will be used if ``deriv_mode="blocked"``
+
 
 Bug Fixes
 
 - Fixes bugs that occur when saving asymmetric equilibria as wout files
 - Fixes bug that occurs when using ``VMECIO.plot_vmec_comparison`` to compare to an asymmetric wout file
 
+Deprecations
+
+- ``deriv_mode="looped"`` in ``ObjectiveFunction`` is deprecated and will be removed in a future version in favored of ``deriv_mode="batched"`` with ``jac_chunk_size=1``,
 
 
 v0.12.1

desc/batching.py

@@ -0,0 +1,322 @@
+"""Utility functions for the ``batched_vectorize`` function."""
+
+import functools
+from typing import Callable, Optional
+
+from desc.backend import jax, jnp
+
+if jax.__version_info__ >= (0, 4, 16):
+    from jax.extend import linear_util as lu
+else:
+    from jax import linear_util as lu
+
+from jax._src.numpy.vectorize import (
+    _apply_excluded,
+    _check_output_dims,
+    _parse_gufunc_signature,
+    _parse_input_dimensions,
+)
+
+# The following section of this code is derived from the NetKet project
+# https://github.com/netket/netket/blob/9881c9fb217a2ac4dc9274a054bf6e6a2993c519/
+# netket/jax/_chunk_utils.py
+#
+# The original copyright notice is as follows
+# Copyright 2021 The NetKet Authors - All rights reserved.
+# Licensed under the Apache License, Version 2.0 (the "License");
+
+
+def _treeify(f):
+    def _f(x, *args, **kwargs):
+        return jax.tree_util.tree_map(lambda y: f(y, *args, **kwargs), x)
+
+    return _f
+
+
+@_treeify
+def _unchunk(x):
+    return x.reshape((-1,) + x.shape[2:])
+
+
+@_treeify
+def _chunk(x, chunk_size=None):
+    # chunk_size=None -> add just a dummy chunk dimension,
+    #  same as np.expand_dims(x, 0)
+    if x.ndim == 0:
+        raise ValueError("x cannot be chunked as it has 0 dimensions.")
+    n = x.shape[0]
+    if chunk_size is None:
+        chunk_size = n
+
+    n_chunks, residual = divmod(n, chunk_size)
+    if residual != 0:
+        raise ValueError(
+            "The first dimension of x must be divisible by chunk_size."
+            + f"\n        Got x.shape={x.shape} but chunk_size={chunk_size}."
+        )
+    return x.reshape((n_chunks, chunk_size) + x.shape[1:])
+
+
+####
+
+# The following section of this code is derived from the NetKet project
+# https://github.com/netket/netket/blob/9881c9fb217a2ac4dc9274a054bf6e6a2993c519/
+# netket/jax/_scanmap.py
+
+
+def scan_append(f, x):
+    """Evaluate f element by element in x while appending the results.
+
+    Parameters
+    ----------
+    f: a function that takes elements of the leading dimension of x
+    x: a pytree where each leaf array has the same leading dimension
+
+    Returns
+    -------
+    a (pytree of) array(s) with leading dimension same as x,
+    containing the evaluation of f at each element in x
+    """
+    carry_init = True
+
+    def f_(carry, x):
+        return False, f(x)
+
+    _, res_append = jax.lax.scan(f_, carry_init, x, unroll=1)
+    return res_append
+
+
+# TODO in_axes a la vmap?
+def _scanmap(fun, scan_fun, argnums=0):
+    """A helper function to wrap f with a scan_fun."""
+
+    def f_(*args, **kwargs):
+        f = lu.wrap_init(fun, kwargs)
+        f_partial, dyn_args = jax.api_util.argnums_partial(
+            f, argnums, args, require_static_args_hashable=False
+        )
+        return scan_fun(lambda x: f_partial.call_wrapped(*x), dyn_args)
+
+    return f_
+
+
+# The following section of this code is derived from the NetKet project
+# https://github.com/netket/netket/blob/9881c9fb217a2ac4dc9274a054bf6e6a2993c519/
+# netket/jax/_vmap_chunked.py
+
+
+def _eval_fun_in_chunks(vmapped_fun, chunk_size, argnums, *args, **kwargs):
+    n_elements = jax.tree_util.tree_leaves(args[argnums[0]])[0].shape[0]
+    n_chunks, n_rest = divmod(n_elements, chunk_size)
+
+    if n_chunks == 0 or chunk_size >= n_elements:
+        y = vmapped_fun(*args, **kwargs)
+    else:
+        # split inputs
+        def _get_chunks(x):
+            x_chunks = jax.tree_util.tree_map(
+                lambda x_: x_[: n_elements - n_rest, ...], x
+            )
+            x_chunks = _chunk(x_chunks, chunk_size)
+            return x_chunks
+
+        def _get_rest(x):
+            x_rest = jax.tree_util.tree_map(
+                lambda x_: x_[n_elements - n_rest :, ...], x
+            )
+            return x_rest
+
+        args_chunks = [
+            _get_chunks(a) if i in argnums else a for i, a in enumerate(args)
+        ]
+        args_rest = [_get_rest(a) if i in argnums else a for i, a in enumerate(args)]
+
+        y_chunks = _unchunk(
+            _scanmap(vmapped_fun, scan_append, argnums)(*args_chunks, **kwargs)
+        )
+
+        if n_rest == 0:
+            y = y_chunks
+        else:
+            y_rest = vmapped_fun(*args_rest, **kwargs)
+            y = jax.tree_util.tree_map(
+                lambda y1, y2: jnp.concatenate((y1, y2)), y_chunks, y_rest
+            )
+    return y
+
+
+def _chunk_vmapped_function(
+    vmapped_fun: Callable,
+    chunk_size: Optional[int],
+    argnums=0,
+) -> Callable:
+    """Takes a vmapped function and computes it in chunks."""
+    if chunk_size is None:
+        return vmapped_fun
+
+    if isinstance(argnums, int):
+        argnums = (argnums,)
+    return functools.partial(_eval_fun_in_chunks, vmapped_fun, chunk_size, argnums)
+
+
+def _parse_in_axes(in_axes):
+    if isinstance(in_axes, int):
+        in_axes = (in_axes,)
+
+    if not set(in_axes).issubset((0, None)):
+        raise NotImplementedError("Only in_axes 0/None are currently supported")
+
+    argnums = tuple(
+        map(lambda ix: ix[0], filter(lambda ix: ix[1] is not None, enumerate(in_axes)))
+    )
+    return in_axes, argnums
+
+
+def vmap_chunked(
+    f: Callable,
+    in_axes=0,
+    *,
+    chunk_size: Optional[int],
+) -> Callable:
+    """Behaves like jax.vmap but uses scan to chunk the computations in smaller chunks.
+
+    Parameters
+    ----------
+    f: The function to be vectorised.
+    in_axes: The axes that should be scanned along. Only supports `0` or `None`
+    chunk_size: The maximum size of the chunks to be used. If it is `None`,
+        chunking is disabled
+
+
+    Returns
+    -------
+    f: A vectorised and chunked function
+    """
+    in_axes, argnums = _parse_in_axes(in_axes)
+    vmapped_fun = jax.vmap(f, in_axes=in_axes)
+    return _chunk_vmapped_function(vmapped_fun, chunk_size, argnums)
+
+
+def batched_vectorize(pyfunc, *, excluded=frozenset(), signature=None, chunk_size=None):
+    """Define a vectorized function with broadcasting and batching.
+
+    :func:`vectorize` is a convenience wrapper for defining vectorized
+    functions with broadcasting, in the style of NumPy's
+    `generalized universal functions
+    <https://numpy.org/doc/stable/reference/c-api/generalized-ufuncs.html>`_.
+    It allows for defining functions that are automatically repeated across
+    any leading dimensions, without the implementation of the function needing to
+    be concerned about how to handle higher dimensional inputs.
+
+    :func:`jax.numpy.vectorize` has the same interface as
+    :class:`numpy.vectorize`, but it is syntactic sugar for an auto-batching
+    transformation (:func:`vmap`) rather than a Python loop. This should be
+    considerably more efficient, but the implementation must be written in terms
+    of functions that act on JAX arrays.
+
+    Parameters
+    ----------
+    pyfunc: callable,function to vectorize.
+    excluded: optional set of integers representing positional arguments for
+    which the function will not be vectorized. These will be passed directly
+    to ``pyfunc`` unmodified.
+    signature: optional generalized universal function signature, e.g.,
+    ``(m,n),(n)->(m)`` for vectorized matrix-vector multiplication. If
+    provided, ``pyfunc`` will be called with (and expected to return) arrays
+    with shapes given by the size of corresponding core dimensions. By
+    default, pyfunc is assumed to take scalars arrays as input and output.
+    chunk_size: the size of the batches to pass to vmap. If None, defaults to
+    the largest possible chunk_size (like the default behavior of ``vectorize11)
+
+    Returns
+    -------
+    Batch-vectorized version of the given function.
+
+    """
+    if any(not isinstance(exclude, (str, int)) for exclude in excluded):
+        raise TypeError(
+            "jax.numpy.vectorize can only exclude integer or string arguments, "
+            "but excluded={!r}".format(excluded)
+        )
+    if any(isinstance(e, int) and e < 0 for e in excluded):
+        raise ValueError(f"excluded={excluded!r} contains negative numbers")
+
+    @functools.wraps(pyfunc)
+    def wrapped(*args, **kwargs):
+        error_context = (
+            "on vectorized function with excluded={!r} and "
+            "signature={!r}".format(excluded, signature)
+        )
+        excluded_func, args, kwargs = _apply_excluded(pyfunc, excluded, args, kwargs)
+
+        if signature is not None:
+            input_core_dims, output_core_dims = _parse_gufunc_signature(signature)
+        else:
+            input_core_dims = [()] * len(args)
+            output_core_dims = None
+
+        none_args = {i for i, arg in enumerate(args) if arg is None}
+        if any(none_args):
+            if any(input_core_dims[i] != () for i in none_args):
+                raise ValueError(
+                    f"Cannot pass None at locations {none_args} with {signature=}"
+                )
+            excluded_func, args, _ = _apply_excluded(excluded_func, none_args, args, {})
+            input_core_dims = [
+                dim for i, dim in enumerate(input_core_dims) if i not in none_args
+            ]
+
+        args = tuple(map(jnp.asarray, args))
+
+        broadcast_shape, dim_sizes = _parse_input_dimensions(
+            args, input_core_dims, error_context
+        )
+
+        checked_func = _check_output_dims(
+            excluded_func, dim_sizes, output_core_dims, error_context
+        )
+
+        # Rather than broadcasting all arguments to full broadcast shapes, prefer
+        # expanding dimensions using vmap. By pushing broadcasting
+        # into vmap, we can make use of more efficient batching rules for
+        # primitives where only some arguments are batched (e.g., for
+        # lax_linalg.triangular_solve), and avoid instantiating large broadcasted
+        # arrays.
+
+        squeezed_args = []
+        rev_filled_shapes = []
+
+        for arg, core_dims in zip(args, input_core_dims):
+            noncore_shape = arg.shape[: arg.ndim - len(core_dims)]
+
+            pad_ndim = len(broadcast_shape) - len(noncore_shape)
+            filled_shape = pad_ndim * (1,) + noncore_shape
+            rev_filled_shapes.append(filled_shape[::-1])
+
+            squeeze_indices = tuple(
+                i for i, size in enumerate(noncore_shape) if size == 1
+            )
+            squeezed_arg = jnp.squeeze(arg, axis=squeeze_indices)
+            squeezed_args.append(squeezed_arg)
+
+        vectorized_func = checked_func
+        dims_to_expand = []
+        for negdim, axis_sizes in enumerate(zip(*rev_filled_shapes)):
+            in_axes = tuple(None if size == 1 else 0 for size in axis_sizes)
+            if all(axis is None for axis in in_axes):
+                dims_to_expand.append(len(broadcast_shape) - 1 - negdim)
+            else:
+                # change the vmap here to chunked_vmap
+                vectorized_func = vmap_chunked(
+                    vectorized_func, in_axes, chunk_size=chunk_size
+                )
+        result = vectorized_func(*squeezed_args)
+
+        if not dims_to_expand:
+            return result
+        elif isinstance(result, tuple):
+            return tuple(jnp.expand_dims(r, axis=dims_to_expand) for r in result)
+        else:
+            return jnp.expand_dims(result, axis=dims_to_expand)
+
+    return wrapped