MultiFab tutorial with pyamrex

.github/workflows/dependencies/dependencies.sh

@@ -13,4 +13,8 @@ sudo apt-get install -y --no-install-recommends\
     build-essential \
     g++ gfortran    \
     libopenmpi-dev  \
-    openmpi-bin
+    openmpi-bin     \
+    python3         \
+    python3-pip
+
+python3 -m pip install -U pip setuptools wheel

.github/workflows/dependencies/dependencies_clang6.sh

@@ -11,4 +11,8 @@ sudo apt-get update
 
 sudo apt-get install -y  \
     build-essential      \
-    clang gfortran
+    clang gfortran       \
+    python3              \
+    python3-pip
+
+python3 -m pip install -U pip setuptools wheel

.github/workflows/dependencies/dependencies_gcc10.sh

@@ -14,4 +14,8 @@ sudo apt-get install -y --no-install-recommends \
     build-essential    \
     g++-10 gfortran-10 \
     libopenmpi-dev     \
-    openmpi-bin
+    openmpi-bin        \
+    python3            \
+    python3-pip
+
+python3 -m pip install -U pip setuptools wheel

.github/workflows/dependencies/dependencies_nofortran.sh

@@ -17,4 +17,8 @@ sudo apt-get install -y --no-install-recommends\
     build-essential \
     g++             \
     libopenmpi-dev  \
-    openmpi-bin
+    openmpi-bin     \
+    python3         \
+    python3-pip
+
+python3 -m pip install -U pip setuptools wheel

.github/workflows/linux.yml

@@ -16,17 +16,21 @@ jobs:
     - name: Build & Install
       run: |
         cd ExampleCodes
-        mkdir build
-        cd build
-        cmake ..                        \
+        cmake -S . -B build             \
             -DCMAKE_BUILD_TYPE=Debug    \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
             -DAMReX_LINEAR_SOLVERS=ON   \
             -DAMReX_FORTRAN=ON          \
             -DAMReX_FORTRAN_INTERFACES=ON \
             -DAMReX_EB=ON                \
-            -DAMReX_PARTICLES=ON
-        make -j 2
+            -DAMReX_PARTICLES=ON        \
+            -DTUTORIAL_PYTHON=ON
+        cmake --build build -j 2
+        cmake --build build -j 2 --target pyamrex_pip_install
+    - name: Run Python
+      run: |
+        cd GuidedTutorials/MultiFab/
+        python main.py
 
   # Build all tutorials
   tutorials_cxx20:
@@ -40,22 +44,26 @@ jobs:
     - name: Build & Install
       run: |
         cd ExampleCodes
-        mkdir build
-        cd build
-        cmake ..                        \
+        cmake -S . -B build             \
             -DCMAKE_BUILD_TYPE=Debug    \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
             -DAMReX_OMP=ON              \
             -DAMReX_PARTICLES=ON        \
             -DAMReX_LINEAR_SOLVERS=ON   \
             -DAMReX_FORTRAN=ON          \
             -DAMReX_FORTRAN_INTERFACES=ON \
-            -DAMReX_EB=ON                \
+            -DAMReX_EB=ON               \
+            -DTUTORIAL_PYTHON=ON        \
             -DCMAKE_CXX_STANDARD=20     \
             -DCMAKE_C_COMPILER=$(which gcc-10)              \
             -DCMAKE_CXX_COMPILER=$(which g++-10)            \
             -DCMAKE_Fortran_COMPILER=$(which mpif90)
-        make -j 2
+        cmake --build build -j 2
+        cmake --build build -j 2 --target pyamrex_pip_install
+    - name: Run Python
+      run: |
+        cd GuidedTutorials/MultiFab/
+        python main.py
 
   tutorials_clang:
     name: [email protected] C++14 SP Particles DP Mesh Debug [tutorials]
@@ -68,9 +76,7 @@ jobs:
     - name: Build & Install
       run: |
         cd ExampleCodes
-        mkdir build
-        cd build
-        cmake ..                                      \
+        cmake -S . -B build             \
             -DCMAKE_BUILD_TYPE=Debug                  \
             -DCMAKE_VERBOSE_MAKEFILE=ON               \
             -DAMReX_MPI=OFF                           \
@@ -81,11 +87,17 @@ jobs:
             -DAMReX_EB=ON                 \
             -DAMReX_PRECISION=DOUBLE                  \
             -DAMReX_PARTICLES_PRECISION=SINGLE        \
+            -DTUTORIAL_PYTHON=ON          \
             -DCMAKE_CXX_STANDARD=14                   \
             -DCMAKE_C_COMPILER=$(which clang)         \
             -DCMAKE_CXX_COMPILER=$(which clang++)     \
             -DCMAKE_Fortran_COMPILER=$(which gfortran)
-        make -j 2
+        cmake --build build -j 2
+        cmake --build build -j 2 --target pyamrex_pip_install
+    - name: Run Python
+      run: |
+        cd GuidedTutorials/MultiFab/
+        python main.py
 
   # Build all tutorials w/o MPI
   tutorials-nonmpi:
@@ -99,18 +111,22 @@ jobs:
     - name: Build & Install
       run: |
         cd ExampleCodes
-        mkdir build
-        cd build
-        cmake ..                        \
+        cmake -S . -B build             \
             -DCMAKE_BUILD_TYPE=Debug    \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
             -DAMReX_MPI=OFF             \
             -DAMReX_LINEAR_SOLVERS=ON     \
             -DAMReX_FORTRAN=ON          \
             -DAMReX_FORTRAN_INTERFACES=ON \
             -DAMReX_EB=ON                 \
-            -DAMReX_PARTICLES=ON
-        make -j 2
+            -DAMReX_PARTICLES=ON         \
+            -DTUTORIAL_PYTHON=ON
+        cmake --build build -j 2
+        cmake --build build -j 2 --target pyamrex_pip_install
+    - name: Run Python
+      run: |
+        cd GuidedTutorials/MultiFab/
+        python main.py
 
   # Build all tutorials
   tutorials-nofortran:
@@ -124,16 +140,20 @@ jobs:
     - name: Build & Install
       run: |
         cd ExampleCodes
-        mkdir build
-        cd build
-        cmake ..                        \
+        cmake -S . -B build             \
             -DCMAKE_BUILD_TYPE=Debug    \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
             -DAMReX_LINEAR_SOLVERS=ON     \
             -DAMReX_EB=ON                 \
             -DAMReX_PARTICLES=ON       \
-            -DAMReX_FORTRAN=OFF
-        make -j 2
+            -DAMReX_FORTRAN=OFF        \
+            -DTUTORIAL_PYTHON=ON
+        cmake --build build -j 2
+        cmake --build build -j 2 --target pyamrex_pip_install
+    - name: Run Python
+      run: |
+        cd GuidedTutorials/MultiFab/
+        python main.py
 
   # Build all tutorials with CUDA 11.0.2 (recent supported)
   tutorials-cuda11:

Docs/source/Python_Tutorial.rst

@@ -0,0 +1,17 @@
+.. _tutorials_python:
+
+======
+Python
+======
+
+These examples show how to use AMReX from Python.
+AMReX applications can also be interfaced to Python with the same logic.
+
+In order to build the Python tutorials, add ``-DTUTORIAL_PYTHON=ON`` to the CMake configuration options.
+Then install with ``cmake --build build --target pyamrex_pip_install``.
+
+Examples:
+
+- ``GuidedTutorials/MultiFab/main.py``
+
+Please see `pyAMReX <https://github.com/AMReX-Codes/pyamrex/>`__ for more details.

Docs/source/index.rst

@@ -50,6 +50,7 @@ sorted by the following categories:
 - :ref:`Linear Solvers<tutorials_linearsolvers>`  -- Examples of several linear solvers.
 - :ref:`MUI<tutorials_mui>`  -- Incorporates the MxUI/MUI (Multiscale Universal interface) frame into AMReX.
 - :ref:`Particles<tutorials_particles>`  -- Basic usage of AMReX's particle data structures.
+- :ref:`Python<tutorials_python>`  -- Using AMReX and interfacing with AMReX applications form Python - via `pyAMReX <https://github.com/AMReX-Codes/pyamrex/>`__
 - :ref:`SDC<tutorials_sdc>`  -- Example usage of a "Multi-Implicit" Spectral Deferred Corrections (MISDC) integrator
   to solve a scalar advection-diffusion-reaction equation.
 - :ref:`SENSEI<tutorials_sensei>`  -- In situ data analysis and visualization through a unified interface.
@@ -71,6 +72,7 @@ sorted by the following categories:
    ML_Tutorial
    MUI_Tutorial
    Particles_Tutorial
+   Python_Tutorial
    SDC_Tutorial
    SENSEI_Tutorial
    SUNDIALS_Tutorial
@@ -95,6 +97,8 @@ sorted by the following categories:
 
 .. _`Particles`: Particles_Tutorial.html
 
+.. _`Python`: Python_Tutorial.html
+
 .. _`SDC`: SDC_Tutorial.html
 
 .. _`SENSEI`: SENSEI_Tutorial.html

ExampleCodes/CMakeLists.txt

@@ -14,17 +14,34 @@ set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake )
 # If AMReX_DIR is passed then we link to the library found there. Otherwise
 # the sources are fetched and compiled from the repo pointed to by AMReX_GIT_REPO
 #
-set ( AMReX_GIT_REPO "https://github.com/AMReX-Codes/amrex.git/"
-    CACHE STRING "The URL identifying the repo to fetchg AMReX from" )
+set ( AMReX_GIT_REPO "https://github.com/AMReX-Codes/amrex.git"
+    CACHE STRING "The URL identifying the repo to fetch AMReX from" )
 
 #
 # Fetch and compile AMReX or link to an existing CMake build install of libamrex.
 # If AMReX_DIR is passed then we link to the library found there. Otherwise
-# the sources are fetched and compiled from the repo pointed to by AMReX_GIT_REPO
+# the sources are fetched and compiled from the repo pointed to by pyAMReX_GIT_REPO
+#
+set ( pyAMReX_GIT_REPO "https://github.com/AMReX-Codes/pyamrex.git"
+    CACHE STRING "The URL identifying the repo to fetch pyAMReX from" )
+option(TUTORIAL_PYTHON OFF)
+
+#
+# Fetch and compile AMReX or link to an existing CMake build install of libamrex.
+# If AMReX_DIR is passed then we link to the library found there. Otherwise
+# the sources are fetched and compiled from the repo pointed to by SUNDIALS_GIT_REPO
 #
 set ( SUNDIALS_GIT_REPO "https://github.com/LLNL/sundials.git"
     CACHE STRING "The URL identifying the repo to fetch SUNDIALS from" )
 
+#
+# For Python, we need AMReX as a a sahred library, otherwise we cannot share all
+# its global variables between multiple Python modules
+#
+if(TUTORIAL_PYTHON)
+    set(AMReX_BUILD_SHARED_LIBS ON CACHE BOOL "Build AMReX shared library" FORCE)
+endif()
+
 if( NOT DEFINED AMReX_DIR )
    #
    # Fetch amrex repo
@@ -174,6 +191,33 @@ else()
    endif()
 endif()
 
+if(TUTORIAL_PYTHON)
+    if(DEFINED pyAMReX_DIR)
+       add_subdirectory(${pyAMReX_DIR})
+    else()
+       #
+       # Fetch pyAMReX repo
+       #
+       message(STATUS "Fetching from ${pyAMReX_GIT_REPO} branch ${pyAMReX_GIT_BRANCH}" )
+
+       set(pyAMReX_GIT_BRANCH "development" CACHE STRING "The pyAMReX branch to checkout")
+       set(pyAMReX_INSTALL  "NO" CACHE INTERNAL "Disable install target for pyAMReX")
+
+       include(FetchContent)
+       #set(FETCHCONTENT_QUIET OFF)  # Verbose ON
+
+       FetchContent_Declare( fetchedpyamrex
+           GIT_REPOSITORY ${pyAMReX_GIT_REPO}
+           GIT_TAG        ${pyAMReX_GIT_BRANCH}
+           )
+
+       if(NOT fetchedpyamrex_POPULATED)
+           FetchContent_Populate(fetchedpyamrex)
+           add_subdirectory(${fetchedpyamrex_SOURCE_DIR} ${fetchedpyamrex_BINARY_DIR})
+       endif()
+    endif()
+endif()
+
 #
 # List of subdirectories to search for CMakeLists.
 # For now, we do not include MUI, SDC, SWFFT

GuidedTutorials/MultiFab/main.py

@@ -0,0 +1,92 @@
+import numpy as np
+import amrex.space3d as amr
+
+# Initialize AMReX
+amr.initialize([])
+
+if amr.ParallelDescriptor.IOProcessor():
+    print(f"Hello world from pyAMReX version {amr.__version__}\n")
+
+# Goals:
+# * Define a MultiFab
+# * Fill a MultiFab with data
+# * Plot it
+
+# Parameters
+
+# Number of data components at each grid point in the MultiFab
+ncomp = 1
+# How many grid cells in each direction over the problem domain
+n_cell = 32
+# How many grid cells are allowed in each direction over each box
+max_grid_size = 16
+
+# BoxArray: abstract domain setup
+
+# Integer vector indicating the lower coordinate bounds
+dom_lo = amr.IntVect(0,0,0)
+# Integer vector indicating the upper coordinate bounds
+dom_hi = amr.IntVect(n_cell-1, n_cell-1, n_cell-1)
+# Box containing the coordinates of this domain
+domain = amr.Box(dom_lo, dom_hi)
+
+# Will contain a list of boxes describing the problem domain
+ba = amr.BoxArray(domain)
+
+# Chop the single grid into many small boxes
+ba.max_size(max_grid_size)
+
+# Distribution Mapping
+dm = amr.DistributionMapping(ba)
+
+# Define MultiFab
+mf = amr.MultiFab(ba, dm, ncomp, 0)
+mf.set_val(0.)
+
+# Geometry: physical properties for data on our domain
+real_box = amr.RealBox([0., 0., 0.], [1. , 1., 1.])
+
+coord = 0  # Cartesian
+is_per = [0, 0, 0] # periodicity
+geom = amr.Geometry(domain, real_box, coord, is_per)
+
+# Calculate cell sizes
+dx = geom.data().CellSize() # dx[0]=dx dx[1]=dy dx[2]=dz
+
+# Fill a MultiFab with data
+mf_val = 0.
+for mfi in mf:
+    bx = mfi.validbox()
+    # Preferred way to fill array using NumPy operations:
+    # - mf_array is indexed in reversed order (n,z,y,x)
+    # - indices are local (range from 0 to box size)
+    mf_array = np.array(mf.array(mfi), copy=False)
+    x = (np.arange(bx.small_end[0], bx.big_end[0]+1)+0.5)*dx[0]
+    y = (np.arange(bx.small_end[1], bx.big_end[1]+1)+0.5)*dx[1]
+    z = (np.arange(bx.small_end[2], bx.big_end[2]+1)+0.5)*dx[2]
+    v = (x[np.newaxis,np.newaxis,:]
+       + y[np.newaxis,:,np.newaxis]*0.1
+       + z[:,np.newaxis,np.newaxis]*0.01)
+    mf_array = 1. + np.exp(-v)
+    # Alternative way to fill array using standard for loop over box indices:
+    # - mf_array_ref is indexed in standard order (x,y,z,n)
+    # - indices are global
+    mf_array_ref = mf.array(mfi)
+    for i, j, k in bx:
+        x = (i+0.5)*dx[0]
+        y = (j+0.5)*dx[1]
+        z = (k+0.5)*dx[2]
+        v = x + y*0.1 + z*0.01
+        mf_array_ref[i,j,k,0] = 1. + np.exp(-v)
+    # Check that mf_array has been filled correctly, compare it with
+    # mf_array_ref (filled as Array4 and transformed to NumPy array)
+    mf_array_ref_np = np.array(mf_array_ref, copy=False)
+    assert np.allclose(mf_array, mf_array_ref_np, rtol=1e-16, atol=1e-16)
+
+# Plot MultiFab data
+plotfile = amr.concatenate(root="plt", num=1, mindigits=3)
+varnames = amr.Vector_string(["comp0"])
+amr.write_single_level_plotfile(plotfile, mf, varnames, geom, time=0., level_step=0)
+
+# Finalize AMReX
+amr.finalize()