Merge branch 'main' into brendt/iso-tv-norm

docs/source/include/examplenotes.rst

@@ -9,7 +9,7 @@ which should be installed via conda:
 
 ::
 
-   conda install -c astra-toolbox astra-toolbox
+   conda install astra-toolbox
    pip install -r examples/examples_requirements.txt  # Installs other example requirements
 
 The dependencies can also be installed individually as required.

docs/source/notes.rst

@@ -2,15 +2,6 @@
 Notes
 *****
 
-No GPU/TPU Warning
-==================
-
-JAX currently issues a warning when used on a platform without a
-GPU. To disable this warning, set the environment variable
-``JAX_PLATFORM_NAME=cpu`` before running Python. This warning is
-suppressed by SCICO for JAX versions after 0.3.23, making use of
-the environment variable unnecessary.
-
 
 Debugging
 =========
@@ -44,6 +35,26 @@ can be enabled in one of two ways:
 
 For more information, see the `JAX notes on double precision <https://jax.readthedocs.io/en/latest/notebooks/Common_Gotchas_in_JAX.html#double-64bit-precision>`_.
 
+Device Control
+==============
+
+Use of the CPU device can be forced even when GPUs are present by setting the
+environment variable ``JAX_PLATFORM_NAME=cpu`` before running Python. This also
+serves to disable the warning that older versions of JAX issued when running
+on a platform without a GPU, but this should no longer be necessary for any
+JAX versions supported by SCICO.
+
+By default, JAX views a multi-core CPU as a single device. Primarily for testing
+purposes, it may be useful to instruct JAX to emulate multiple CPU devices, by
+setting the environment variable ``XLA_FLAGS='--xla_force_host_platform_device_count=<n>'``,
+where ``<n>`` is an integer number of devices. For more detail see the relevant
+`section of the JAX docs <https://jax.readthedocs.io/en/latest/jax-101/06-parallelism.html#aside-hosts-and-devices-in-jax>`__.
+
+By default, JAX will preallocate a large chunk of GPU memory on startup. This
+behavior can be controlled using environment variables ``XLA_PYTHON_CLIENT_PREALLOCATE``,
+``XLA_PYTHON_CLIENT_MEM_FRACTION``, and ``XLA_PYTHON_CLIENT_ALLOCATOR``, as described in
+the relevant `section of the JAX docs <https://jax.readthedocs.io/en/latest/gpu_memory_allocation.html>`__.
+
 
 Random Number Generation
 ========================
@@ -129,7 +140,8 @@ SCICO, while the other two depend on external packages.
 The :class:`.xray.svmbir.XRayTransform` class is implemented
 via an interface to the `svmbir
 <https://svmbir.readthedocs.io/en/latest/>`__ package. The
-:class:`.xray.astra.XRayTransform` class is implemented via an
+:class:`.xray.astra.XRayTransform2D` and
+:class:`.xray.astra.XRayTransform3D` classes are implemented via an
 interface to the `ASTRA toolbox
 <https://www.astra-toolbox.com/>`__. This toolbox does provide some
 GPU acceleration support, but efficiency is expected to be lower than

misc/availgpu.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+# Determine which GPUs available for use and recommend CUDA_VISIBLE_DEVICES
+# setting if any are already in use.
+
+# pylint: disable=missing-module-docstring
+
+
+import GPUtil
+
+print("GPU utlizitation")
+GPUtil.showUtilization()
+
+devIDs = GPUtil.getAvailable(
+    order="first", limit=65536, maxLoad=0.1, maxMemory=0.1, includeNan=False
+)
+
+Ngpu = len(GPUtil.getGPUs())
+if len(devIDs) == Ngpu:
+    print(f"All {Ngpu} GPUs available for use")
+else:
+    print(f"Only {len(devIDs)} of {Ngpu} GPUs available for use")
+    print("To avoid attempting to use GPUs already in use, run the command")
+    print(f"    export CUDA_VISIBLE_DEVICES={','.join(map(str, devIDs))}")

scico/flax/examples/data_generation.py

@@ -221,7 +221,7 @@ def generate_ct_data(
     # Normalize sinogram
     sino = sino / size
 
-    # Compute filter back-project in parallel.
+    # Compute filtered back projection in parallel.
     afbp_map = lambda v: jnp.atleast_3d(A.fbp(v.squeeze()))
     start_time = time()
     fbpshd = jax.pmap(lambda i: jax.lax.map(afbp_map, sinoshd[i]))(jnp.arange(nproc))

scico/linop/xray/astra.py

@@ -17,7 +17,7 @@
 not available.
 """
 
-from typing import List, Optional, Tuple
+from typing import List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 
@@ -33,12 +33,28 @@
     else:
         raise e
 
+try:
+    from collections import Iterable  # type: ignore
+except ImportError:
+    import collections
+
+    # Monkey patching required because latest astra release uses old module path for Iterable
+    collections.Iterable = collections.abc.Iterable  # type: ignore
 
 from scico.typing import Shape
 
 from .._linop import LinearOperator
 
 
+def set_astra_gpu_index(idx: Union[int, Sequence[int]]):
+    """Set the index/indices of GPU(s) to be used by astra.
+
+    Args:
+        idx: Index or indices of GPU(s).
+    """
+    astra.set_gpu_index(idx)
+
+
 class XRayTransform2D(LinearOperator):
     r"""2D parallel beam X-ray transform based on the ASTRA toolbox.
 
@@ -108,11 +124,16 @@ def __init__(
                     "Please see the astra documentation for details."
                 )
 
-        dev0 = jax.devices()[0]
-        if dev0.platform == "cpu" or device == "cpu":
-            self.device = "cpu"
-        elif dev0.platform == "gpu" and device in ["gpu", "auto"]:
-            self.device = "gpu"
+        if device in ["cpu", "gpu"]:
+            # If cpu or gpu selected, attempt to comply (no checking to
+            # confirm that a gpu is available to astra).
+            self.device = device
+        elif device == "auto":
+            # If auto selected, use cpu or gpu depending on the default
+            # jax device (for simplicity, no checking whether gpu is
+            # available to astra when one is not available to jax).
+            dev0 = jax.devices()[0]
+            self.device = dev0.platform
         else:
             raise ValueError(f"Invalid device specified; got {device}.")
 
@@ -280,10 +301,6 @@ def __init__(
         self.input_shape: tuple = input_shape
         self.vol_geom = astra.create_vol_geom(input_shape[1], input_shape[2], input_shape[0])
 
-        dev0 = jax.devices()[0]
-        if dev0.platform == "cpu":
-            raise ValueError("No CPU algorithm for 3D projection and GPU not available.")
-
         # Wrap our non-jax function to indicate we will supply fwd/rev mode functions
         self._eval = jax.custom_vjp(self._proj)
         self._eval.defvjp(lambda x: (self._proj(x), None), lambda _, y: (self._bproj(y),))  # type: ignore

scico/optimize/_ladmm.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2021-2023 by SCICO Developers
+# Copyright (C) 2021-2024 by SCICO Developers
 # All rights reserved. BSD 3-clause License.
 # This file is part of the SCICO package. Details of the copyright and
 # user license can be found in the 'LICENSE' file distributed with the
@@ -11,7 +11,7 @@
 # see https://www.python.org/dev/peps/pep-0563/
 from __future__ import annotations
 
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Tuple, Union
 
 import scico.numpy as snp
 from scico.functional import Functional
@@ -149,7 +149,7 @@ def minimizer(self):
     def objective(
         self,
         x: Optional[Union[Array, BlockArray]] = None,
-        z: Optional[List[Union[Array, BlockArray]]] = None,
+        z: Optional[Union[Array, BlockArray]] = None,
     ) -> float:
         r"""Evaluate the objective function.
 

scico/optimize/_padmm.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2022-2023 by SCICO Developers
+# Copyright (C) 2022-2024 by SCICO Developers
 # All rights reserved. BSD 3-clause License.
 # This file is part of the SCICO package. Details of the copyright and
 # user license can be found in the 'LICENSE' file distributed with the
@@ -11,7 +11,7 @@
 # see https://www.python.org/dev/peps/pep-0563/
 from __future__ import annotations
 
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Tuple, Union
 
 import scico.numpy as snp
 from scico import cvjp, jvp
@@ -144,7 +144,7 @@ def minimizer(self):
     def objective(
         self,
         x: Optional[Union[Array, BlockArray]] = None,
-        z: Optional[List[Union[Array, BlockArray]]] = None,
+        z: Optional[Union[Array, BlockArray]] = None,
     ) -> float:
         r"""Evaluate the objective function.
 
@@ -289,7 +289,7 @@ def __init__(
     def norm_primal_residual(
         self,
         x: Optional[Union[Array, BlockArray]] = None,
-        z: Optional[List[Union[Array, BlockArray]]] = None,
+        z: Optional[Union[Array, BlockArray]] = None,
     ) -> float:
         r"""Compute the :math:`\ell_2` norm of the primal residual.
 
@@ -507,7 +507,7 @@ def __init__(
     def norm_primal_residual(
         self,
         x: Optional[Union[Array, BlockArray]] = None,
-        z: Optional[List[Union[Array, BlockArray]]] = None,
+        z: Optional[Union[Array, BlockArray]] = None,
     ) -> float:
         r"""Compute the :math:`\ell_2` norm of the primal residual.
 

scico/test/linop/xray/test_astra.py

@@ -129,15 +129,6 @@ def test_jit_in_DiagonalStack():
     H.T @ snp.zeros(H.output_shape, dtype=snp.float32)
 
 
-@pytest.mark.skipif(jax.devices()[0].platform != "cpu", reason="checking CPU behavior")
-def test_3D_on_CPU():
-    x = snp.zeros((4, 5, 6))
-    with pytest.raises(ValueError):
-        A = XRayTransform3D(
-            x.shape, det_count=[6, 6], det_spacing=[1.0, 1.0], angles=snp.linspace(0, snp.pi, 10)
-        )
-
-
 @pytest.mark.skipif(jax.devices()[0].platform != "gpu", reason="checking GPU behavior")
 def test_3D_on_GPU():
     x = snp.zeros((4, 5, 6))