Merge branch 'development' into topic-upstream-soa-named

AMReX-Codes · Nov 22, 2024 · d41d068 · d41d068
2 parents 50a26a2 + 66fc71f
commit d41d068
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diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -26,7 +26,7 @@ jobs:
     - name: Build & Install
       # mkl/rng/device/detail/mrg32k3a_impl.hpp has a number of sign-compare error
       # mkl/rng/device/detail/mrg32k3a_impl.hpp has missing braces in array-array initalization
-      env: {CXXFLAGS: "-fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-sign-compare -Wno-missing-braces"}
+      env: {CXXFLAGS: "-fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-unused-variable -Wno-shadow"}
       run: |
         set +e
         source /opt/intel/oneapi/setvars.sh
@@ -73,10 +73,8 @@ jobs:
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
     - name: Build & Install
-      # mkl/rng/device/detail/mrg32k3a_impl.hpp has a number of sign-compare error
-      # mkl/rng/device/detail/mrg32k3a_impl.hpp has missing braces in array-array initalization
       # /usr/include/c++/12/bits/stl_tempbuf.h has deprecated-declarations in 'get_temporary_buffer<std::pair<long, int>>'
-      env: {CXXFLAGS: "-fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-sign-compare -Wno-missing-braces -Wno-error=pass-failed -Wno-tautological-constant-compare -Wno-deprecated-declarations"}
+      env: {CXXFLAGS: "-fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-deprecated-declarations"}
       run: |
         set +e
         source /opt/intel/oneapi/setvars.sh

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -74,7 +74,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.9
+  rev: v0.7.3
   hooks:
     # Run the linter
     - id: ruff
@@ -94,7 +94,7 @@ repos:
 
 # Checks the manifest for missing files (native support)
 - repo: https://github.com/mgedmin/check-manifest
-  rev: "0.49"
+  rev: "0.50"
   hooks:
   - id: check-manifest
     # This is a slow hook, so only run this if --hook-stage manual is passed

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(pyAMReX VERSION 24.10)
+project(pyAMReX VERSION 24.11)
 
 include(${pyAMReX_SOURCE_DIR}/cmake/pyAMReXFunctions.cmake)
 

diff --git a/cmake/dependencies/AMReX.cmake b/cmake/dependencies/AMReX.cmake
@@ -67,7 +67,7 @@ macro(find_amrex)
         message(STATUS "Searching for pre-installed AMReX ...")
         # https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html#importing-amrex-into-your-cmake-project
         # not strictly required yet to compile pyAMReX: EB
-        find_package(AMReX 24.10 CONFIG REQUIRED COMPONENTS PARTICLES PIC)
+        find_package(AMReX 24.11 CONFIG REQUIRED COMPONENTS PARTICLES PIC)
         message(STATUS "AMReX: Found version '${AMReX_VERSION}'")
 
         if(AMReX_GPU_BACKEND STREQUAL CUDA)
@@ -86,7 +86,7 @@ option(pyAMReX_amrex_internal "Download & build AMReX" ON)
 set(pyAMReX_amrex_repo "https://github.com/AMReX-Codes/amrex.git"
     CACHE STRING
     "Repository URI to pull and build AMReX from if(pyAMReX_amrex_internal)")
-set(pyAMReX_amrex_branch "8df11b69a1169a1b7791a7a5e723feecd121b467"
+set(pyAMReX_amrex_branch "24.11"
     CACHE STRING
     "Repository branch for pyAMReX_amrex_repo if(pyAMReX_amrex_internal)")
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -72,9 +72,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "24.10"
+version = "24.11"
 # The full version, including alpha/beta/rc tags.
-release = "24.10"
+release = "24.11"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/setup.py b/setup.py
@@ -217,7 +217,7 @@ def build_extension(self, ext):
 setup(
     name="amrex",
     # note PEP-440 syntax: x.y.zaN but x.y.z.devN
-    version="24.10",
+    version="24.11",
     packages=["amrex"],
     # Python sources:
     package_dir={"": "src"},

diff --git a/src/Base/BoxArray.cpp b/src/Base/BoxArray.cpp
@@ -129,13 +129,15 @@ void init_BoxArray(py::module &m) {
     //! \brief Apply surroundingNodes(Box,int) to each Box in
     //! BoxArray.  See the documentation of Box for details.
     BoxArray& surroundingNodes (int dir);
+*/
 
     //! Apply Box::enclosedCells() to each Box in the BoxArray.
-    BoxArray& enclosedCells ();
-
-    //! Apply Box::enclosedCells(int) to each Box in the BoxArray.
-    BoxArray& enclosedCells  (int dir);
+    .def("enclosed_cells",
+            py::overload_cast<>(&BoxArray::enclosedCells))
+    .def("enclosed_cells",
+            py::overload_cast<int>(&BoxArray::enclosedCells))
 
+/*
     //! Apply Box::convert(IndexType) to each Box in the BoxArray.
     BoxArray& convert (IndexType typ);
 

diff --git a/src/Base/CMakeLists.txt b/src/Base/CMakeLists.txt
@@ -33,6 +33,7 @@ foreach(D IN LISTS AMReX_SPACEDIM)
         Utility.cpp
         Vector.cpp
         Version.cpp
+        VisMF.cpp
     )
 
     if (AMReX_MPI)

diff --git a/src/Base/IntVect.cpp b/src/Base/IntVect.cpp
@@ -28,8 +28,10 @@ namespace
         py::class_< iv_type > py_iv(m, iv_name.c_str());
         py_iv
             .def("__repr__",
-                 [iv_name](const iv_type&) {
-                     return "<amrex." + iv_name + ">";
+                 [iv_name](const iv_type& iv) {
+                     std::stringstream s;
+                     s << iv;
+                     return "<amrex." + iv_name + s.str() + ">";
                  }
             )
             .def("__str",

diff --git a/src/Base/VisMF.cpp b/src/Base/VisMF.cpp
@@ -0,0 +1,46 @@
+/* Copyright 2024 The AMReX Community
+ *
+ * Authors: David Grote
+ * License: BSD-3-Clause-LBNL
+ */
+#include "pyAMReX.H"
+
+#include <AMReX_VisMF.H>
+#include <AMReX_MultiFab.H>
+
+void init_VisMF(py::module &m)
+{
+    py::class_< amrex::VisMF > py_VisMF(m, "VisMF");
+
+    py_VisMF
+        .def_static("Write",
+           [](const amrex::FabArray<amrex::FArrayBox> &mf, const std::string& name) {
+               return amrex::VisMF::Write(mf, name);
+           },
+           py::arg("mf"), py::arg("name"),
+           "Writes a Multifab to the specified file")
+        .def_static("Read",
+           [](const std::string &name) {
+               amrex::MultiFab mf;
+               if (amrex::VisMF::Exist(name)) {
+                   amrex::VisMF::Read(mf, name);
+               } else {
+                   throw std::runtime_error("MultiFab file " + name + " couldn't be found!");
+               }
+               return mf;
+               },
+           py::return_value_policy::move,
+           py::arg("name"),
+           "Reads a MultiFab from the specified file")
+        .def_static("Read",
+           [](const std::string &name, amrex::MultiFab &mf) {
+               if (amrex::VisMF::Exist(name)) {
+                   amrex::VisMF::Read(mf, name);
+               } else {
+                   throw std::runtime_error("MultiFab file " + name + " couldn't be found!");
+               }
+               },
+           py::arg("name"), py::arg("mf"),
+           "Reads a MultiFab from the specified file into the given MultiFab. The BoxArray on the disk must match the BoxArray * in mf")
+        ;
+}
diff --git a/src/amrex/extensions/MultiFab.py b/src/amrex/extensions/MultiFab.py
@@ -314,13 +314,19 @@ def _process_index(self, index):
         # If only one slice or integer passed in, it was not wrapped in a tuple
         index = [index]
     elif isinstance(index, tuple):
-        index = list(index)
-        for i in range(len(index)):
-            if index[i] == Ellipsis:
-                index = (
-                    index[:i] + (dims + 2 - len(index)) * [slice(None)] + index[i + 1 :]
-                )
-                break
+        if len(index) == 0:
+            # The empty tuple specifies all valid and ghost cells
+            index = [index]
+        else:
+            index = list(index)
+            for i in range(len(index)):
+                if index[i] == Ellipsis:
+                    index = (
+                        index[:i]
+                        + (dims + 2 - len(index)) * [slice(None)]
+                        + index[i + 1 :]
+                    )
+                    break
     else:
         raise Exception("MultiFab.__getitem__: unexpected index type")
 
@@ -463,7 +469,7 @@ def _get_intersect_slice(self, mfi, index, with_internal_ghosts):
         return None, None
 
 
-def __getitem__(self, index):
+def __getitem__(self, index, with_internal_ghosts=False):
     """Returns slice of the MultiFab using global indexing, as a numpy array.
     This uses numpy array indexing, with the indexing relative to the global array.
     The slice ranges can cross multiple blocks and the result will be gathered into a single
@@ -484,13 +490,18 @@ def __getitem__(self, index):
     ----------
     index : the index using numpy style indexing
         Index of the slice to return.
+    with_internal_ghosts : bool, optional
+        Whether to include internal ghost cells. When true, data from ghost cells may be used that
+        overlaps valid cells.
     """
-    index = _process_index(self, index)
+    index4 = _process_index(self, index)
 
     # Gather the data to be included in a list to be sent to other processes
     datalist = []
     for mfi in self:
-        block_slices, global_slices = _get_intersect_slice(self, mfi, index, False)
+        block_slices, global_slices = _get_intersect_slice(
+            self, mfi, index4, with_internal_ghosts
+        )
         if global_slices is not None:
             # Note that the array will always have 4 dimensions.
             device_arr = _get_field(self, mfi)
@@ -522,11 +533,29 @@ def __getitem__(self, index):
             raise Exception("MultiFab.__getitem__ requires mpi4py")
         all_datalist = comm_world.allgather(datalist)
 
-    # Create the array to be returned
-    result_shape = tuple([max(0, ii.stop - ii.start) for ii in index])
+    # The shape of the array to be returned
+    result_shape = tuple([max(0, ii.stop - ii.start) for ii in index4])
+
+    # If the boxes do not fill the domain, then include the internal ghost
+    # cells since they may cover internal regions not otherwise covered by valid cells.
+    # If the domain is not completely covered, __getitem__ is done twice, the first time
+    # including internal ghost cells, and the second time without. The second time is needed
+    # to ensure that in places where ghost cells overlap with valid cells, that the data
+    # from the valid cells is used.
+    # The domain is complete if the number of cells in the box array is the same as
+    # the number of cells in the minimal box.
+    cell_centered_box_array = self.box_array().enclosed_cells()
+    domain_complete = (
+        cell_centered_box_array.numPts == cell_centered_box_array.minimal_box().numPts()
+    )
+
+    if domain_complete or with_internal_ghosts:
+        result_global = None
+    else:
+        # First get the data including the internal ghost cells
+        result_global = self.__getitem__(index, with_internal_ghosts=True)
 
     # Now, copy the data into the result array
-    result_global = None
     for datalist in all_datalist:
         for global_slices, f_arr in datalist:
             if result_global is None:
@@ -540,7 +569,12 @@ def __getitem__(self, index):
 
     # Remove dimensions of length 1, and if all dimensions
     # are removed, return a scalar (that's what the [()] does)
-    return result_global.squeeze()[()]
+    if with_internal_ghosts:
+        # Return the data without the squeeze so that the result can be used in the loop
+        # above again.
+        return result_global
+    else:
+        return result_global.squeeze()[()]
 
 
 def __setitem__(self, index, value):

diff --git a/src/amrex/space1d/__init__.pyi b/src/amrex/space1d/__init__.pyi
@@ -30,6 +30,7 @@ amrex
    StructOfArrays
    Utility
    Vector
+   VisMF
 
 """
 
@@ -261,6 +262,7 @@ from amrex.space1d.amrex_1d_pybind import (
     Vector_Long,
     Vector_Real,
     Vector_string,
+    VisMF,
     XDim3,
     begin,
     coarsen,
@@ -508,6 +510,7 @@ __all__ = [
     "Vector_Real",
     "Vector_int",
     "Vector_string",
+    "VisMF",
     "XDim3",
     "amrex_1d_pybind",
     "begin",
@@ -553,4 +556,4 @@ def d_decl(x, y, z):
 
 __author__: str = "Axel Huebl, Ryan T. Sandberg, Shreyas Ananthan, David P. Grote, Revathi Jambunathan, Edoardo Zoni, Remi Lehe, Andrew Myers, Weiqun Zhang"
 __license__: str = "BSD-3-Clause-LBNL"
-__version__: str = "24.10-8-g8df11b69a116"
+__version__: str = "24.11"
diff --git a/src/amrex/space1d/amrex_1d_pybind/__init__.pyi b/src/amrex/space1d/amrex_1d_pybind/__init__.pyi
@@ -30,6 +30,7 @@ amrex
    StructOfArrays
    Utility
    Vector
+   VisMF
 
 """
 
@@ -261,6 +262,7 @@ __all__ = [
     "Vector_Real",
     "Vector_int",
     "Vector_string",
+    "VisMF",
     "XDim3",
     "begin",
     "coarsen",
@@ -4935,6 +4937,10 @@ class BoxArray:
     @typing.overload
     def coarsenable(self, arg0: IntVect1D, arg1: IntVect1D) -> bool: ...
     def define(self, arg0: Box) -> None: ...
+    @typing.overload
+    def enclosed_cells(self) -> BoxArray: ...
+    @typing.overload
+    def enclosed_cells(self, arg0: int) -> BoxArray: ...
     def get(self, arg0: int) -> Box: ...
     def ix_type(self) -> IndexType: ...
     @typing.overload
@@ -4959,7 +4965,7 @@ class BoxArray:
     def size(self) -> int: ...
 
 class Config:
-    amrex_version: typing.ClassVar[str] = "24.10-8-g8df11b69a116"
+    amrex_version: typing.ClassVar[str] = "24.11"
     gpu_backend = None
     have_eb: typing.ClassVar[bool] = False
     have_gpu: typing.ClassVar[bool] = False
@@ -6276,7 +6282,7 @@ class MultiFab(FabArray_FArrayBox):
         """
         dst = src + a*dst
         """
-    def __getitem__(self, index):
+    def __getitem__(self, index, with_internal_ghosts=False):
         """
         Returns slice of the MultiFab using global indexing, as a numpy array.
             This uses numpy array indexing, with the indexing relative to the global array.
@@ -6298,6 +6304,9 @@ class MultiFab(FabArray_FArrayBox):
             ----------
             index : the index using numpy style indexing
                 Index of the slice to return.
+            with_internal_ghosts : bool, optional
+                Whether to include internal ghost cells. When true, data from ghost cells may be used that
+                overlaps valid cells.
 
         """
     @typing.overload
@@ -18043,6 +18052,25 @@ class Vector_string:
         """
     def size(self) -> int: ...
 
+class VisMF:
+    @staticmethod
+    @typing.overload
+    def Read(name: str) -> MultiFab:
+        """
+        Reads a MultiFab from the specified file
+        """
+    @staticmethod
+    @typing.overload
+    def Read(name: str, mf: MultiFab) -> None:
+        """
+        Reads a MultiFab from the specified file into the given MultiFab. The BoxArray on the disk must match the BoxArray * in mf
+        """
+    @staticmethod
+    def Write(mf: FabArray_FArrayBox, name: str) -> int:
+        """
+        Writes a Multifab to the specified file
+        """
+
 class XDim3:
     x: float
     y: float
@@ -18351,5 +18379,5 @@ def write_single_level_plotfile(
 
 __author__: str = "Axel Huebl, Ryan T. Sandberg, Shreyas Ananthan, David P. Grote, Revathi Jambunathan, Edoardo Zoni, Remi Lehe, Andrew Myers, Weiqun Zhang"
 __license__: str = "BSD-3-Clause-LBNL"
-__version__: str = "24.10-8-g8df11b69a116"
+__version__: str = "24.11"
 IntVect = IntVect1D