Modernize Python tutorials

.github/workflows/linux.yml

@@ -38,9 +38,10 @@ jobs:
     - name: Run Python
       run: |
         cd GuidedTutorials/MultiFab/
-        python main.py
+        python3 main.py
         cd ../HeatEquation/Source/
-        python main.py
+        python3 main.py ../Exec/inputs
+        mpiexec -n 2 python3 main.py ../Exec/inputs
 
   # Build all tutorials
   tutorials_omp:
@@ -69,9 +70,9 @@ jobs:
     - name: Run Python
       run: |
         cd GuidedTutorials/MultiFab/
-        python main.py
+        python3 main.py
         cd ../HeatEquation/Source/
-        python main.py
+        python3 main.py ../Exec/inputs
 
   tutorials_clang:
     name: Clang SP Particles DP Mesh Debug [tutorials]
@@ -104,9 +105,9 @@ jobs:
     - name: Run Python
       run: |
         cd GuidedTutorials/MultiFab/
-        python main.py
+        python3 main.py
         cd ../HeatEquation/Source/
-        python main.py
+        python3 main.py ../Exec/inputs
 
   # Build all tutorials w/o MPI
   tutorials-nonmpi:
@@ -135,9 +136,9 @@ jobs:
     - name: Run Python
       run: |
         cd GuidedTutorials/MultiFab/
-        python main.py
+        python3 main.py
         cd ../HeatEquation/Source/
-        python main.py
+        python3 main.py ../Exec/inputs
 
   # Build all tutorials
   tutorials-nofortran:
@@ -164,9 +165,9 @@ jobs:
     - name: Run Python
       run: |
         cd GuidedTutorials/MultiFab/
-        python main.py
+        python3 main.py
         cd ../HeatEquation/Source/
-        python main.py
+        python3 main.py ../Exec/inputs
 
   # Build all tutorials with CUDA
   tutorials-cuda:

Docs/source/Python_Tutorial.rst

@@ -4,17 +4,44 @@
 Python
 ======
 
-These examples show how to use AMReX from Python.
+These examples show how to use AMReX from Python, via `pyAMReX <https://github.com/AMReX-Codes/pyamrex/>`__.
 AMReX applications can also be interfaced to Python with the same logic.
 
+Installation
+============
+
 In order to run the Python tutorials, you need to have pyAMReX installed.
-Please see `pyAMReX <https://github.com/AMReX-Codes/pyamrex/>`__ for more details.
+Please see the `pyAMReX documentation <https://pyamrex.readthedocs.io>`__ for installation details.
 
 Alternatively, you can build the ExampleCodes in this repository with ``-DTUTORIAL_PYTHON=ON`` added to the CMake configuration options,
-then install with ``cmake --build build --target pyamrex_pip_install``, and pyamrex will be installed for you.
+then install with ``cmake --build build --target pyamrex_pip_install``, and pyAMReX will be installed for you.
+
+Running
+=======
+
+Python tutorials are written so they run the same way as their C++ counterparts:
+command line arguments after the script name are forwarded to AMReX, so an
+:ref:`inputs file <amrex_docs:sec:basics:parmparse>` and ``key=value`` overrides can be passed as usual:
+
+.. code-block:: sh
+
+   python3 main.py inputs
+
+   # with runtime parameter override(s)
+   python3 main.py inputs nsteps=20
+
+   # MPI-parallel
+   mpiexec -n 2 python3 main.py inputs
+
+Tutorials
+=========
+
+Guided tutorials:
 
-Once pyAMReX is installed, you can run the following Guided Tutorial Examples:
+- :download:`MultiFab <../../GuidedTutorials/MultiFab/main.py>`: define, fill and plot a MultiFab
+- :download:`Heat Equation <../../GuidedTutorials/HeatEquation/Source/main.py>`: explicit heat equation solve with ghost cell exchanges and runtime parameters
+  (run with :download:`inputs <../../GuidedTutorials/HeatEquation/Exec/inputs>`)
 
-- :download:`MultiFab <../../GuidedTutorials/MultiFab/main.py>`
-- :download:`Heat Equation <../../GuidedTutorials/HeatEquation/Source/main.py>`
+Example codes:
 
+- :download:`MPMD Case-2 <../../ExampleCodes/MPMD/Case-2/main.py>`: a Python app coupled to a C++ app via AMReX MPMD (see :ref:`tutorials_mpmd`)

ExampleCodes/MPMD/Case-2/main.py

@@ -1,15 +1,17 @@
+import sys
+
 from mpi4py import MPI
 
 import amrex.space3d as amr
 
 # Initialize amrex::MPMD to establish communication across the two apps
 # However, leverage MPMD_Initialize_without_split
 # so that communication split can be performed using mpi4py.MPI
-amr.MPMD_Initialize_without_split([])
+amr.MPMD_Initialize_without_split(sys.argv[1:])
 # Leverage MPI from mpi4py to perform communication split
 app_comm_py = MPI.COMM_WORLD.Split(amr.MPMD_AppNum(), amr.MPMD_MyProc())
 # Initialize AMReX
-amr.initialize_when_MPMD([], app_comm_py)
+amr.initialize_when_MPMD(sys.argv[1:], app_comm_py)
 
 amr.Print(f"Hello world from pyAMReX version {amr.__version__}\n")
 # Create a MPMD Copier that gets the BoxArray information from the other (C++) app

GuidedTutorials/HeatEquation/Source/main.py

@@ -8,6 +8,8 @@
 # License: BSD-3-Clause-LBNL
 # Authors: Revathi Jambunathan, Edoardo Zoni, Olga Shapoval, David Grote, Axel Huebl
 
+import sys
+
 import amrex.space3d as amr
 
 
@@ -96,8 +98,8 @@ def main(n_cell, max_grid_size, nsteps, plot_int, dt):
     # Loop over boxes
     for mfi in phi_old:
         bx = mfi.validbox()
-        # phiOld is indexed in reversed order (z,y,x) and indices are local
-        phiOld = xp.array(phi_old.array(mfi), copy=False)
+        # phiOld is indexed in reversed order (n,z,y,x) and indices are local
+        phiOld = phi_old.array(mfi).to_xp(copy=False, order="C")
         # set phi = 1 + e^(-(r-0.5)^2)
         x = (xp.arange(bx.small_end[0],bx.big_end[0]+1,1) + 0.5) * dx[0]
         y = (xp.arange(bx.small_end[1],bx.big_end[1]+1,1) + 0.5) * dx[1]
@@ -121,8 +123,8 @@ def main(n_cell, max_grid_size, nsteps, plot_int, dt):
         # new_phi = old_phi + dt * Laplacian(old_phi)
         # Loop over boxes
         for mfi in phi_old:
-            phiOld = xp.array(phi_old.array(mfi), copy=False)
-            phiNew = xp.array(phi_new.array(mfi), copy=False)
+            phiOld = phi_old.array(mfi).to_xp(copy=False, order="C")
+            phiNew = phi_new.array(mfi).to_xp(copy=False, order="C")
             hix = phiOld.shape[3]
             hiy = phiOld.shape[2]
             hiz = phiOld.shape[1]
@@ -157,20 +159,38 @@ def main(n_cell, max_grid_size, nsteps, plot_int, dt):
 
 if __name__ == '__main__':
     # Initialize AMReX
-    amr.initialize([])
-
-    # TODO Implement parser
-    # Simulation parameters
-    # number of cells on each side of the domain
-    n_cell = 32
-    # size of each box (or grid)
-    max_grid_size = 16
-    # total steps in simulation
-    nsteps = 1000
-    # how often to write a plotfile
-    plot_int = 100
+    # Command line arguments are forwarded, e.g., an inputs file:
+    #   python3 main.py ../Exec/inputs
+    amr.initialize(sys.argv[1:])
+
+    # **********************************
+    # SIMULATION PARAMETERS
+
+    # ParmParse is a way of reading inputs from the inputs file
+    # pp.get means we require the inputs file to have it
+    # pp.query means we optionally need the inputs file to have it - but we must supply a default here
+    pp = amr.ParmParse()
+
+    # We need to get n_cell from the inputs file - this is the number of cells on each side of
+    #   a square (or cubic) domain.
+    n_cell = pp.get_int("n_cell")
+
+    # The domain is broken into boxes of size max_grid_size
+    max_grid_size = pp.get_int("max_grid_size")
+
+    # Default nsteps to 10, allow us to set it to something else in the inputs file
+    exists, nsteps = pp.query_int("nsteps")
+    if not exists:
+        nsteps = 10
+
+    # Default plot_int to -1, allow us to set it to something else in the inputs file
+    #  If plot_int < 0 then no plot files will be written
+    exists, plot_int = pp.query_int("plot_int")
+    if not exists:
+        plot_int = -1
+
     # time step
-    dt = 1e-5
+    dt = pp.get_real("dt")
 
     main(n_cell, max_grid_size, nsteps, plot_int, dt)
 

GuidedTutorials/MultiFab/main.py

@@ -8,6 +8,8 @@
 # License: BSD-3-Clause-LBNL
 # Authors: Revathi Jambunathan, Edoardo Zoni, Olga Shapoval, David Grote, Axel Huebl
 
+import sys
+
 import amrex.space3d as amr
 
 
@@ -34,7 +36,8 @@ def load_cupy():
 
 
 # Initialize AMReX
-amr.initialize([])
+# Command line arguments after the script name are forwarded to AMReX
+amr.initialize(sys.argv[1:])
 
 # CPU/GPU logic
 xp = load_cupy()
@@ -91,21 +94,23 @@ def load_cupy():
 for mfi in mf:
     bx = mfi.validbox()
     # Preferred way to fill array using fast ranged operations:
-    # - xp.array is indexed in reversed order (n,z,y,x),
-    #   .T creates a view into the AMReX (x,y,z,n) order
+    # - .to_xp() provides a NumPy (CPU) or CuPy (GPU) view into the
+    #   data, indexed in the AMReX (x,y,z,n) order ("F" order, default)
     # - indices are local (range from 0 to box size)
-    mf_array = xp.array(mf.array(mfi), copy=False).T
+    mf_array = mf.array(mfi).to_xp(copy=False)
     x = (xp.arange(bx.small_end[0], bx.big_end[0]+1)+0.5)*dx[0]
     y = (xp.arange(bx.small_end[1], bx.big_end[1]+1)+0.5)*dx[1]
     z = (xp.arange(bx.small_end[2], bx.big_end[2]+1)+0.5)*dx[2]
-    v = (x[xp.newaxis,xp.newaxis,:]
-       + y[xp.newaxis,:,xp.newaxis]*0.1
-       + z[:,xp.newaxis,xp.newaxis]*0.01)
     rsquared = ((z[xp.newaxis, xp.newaxis,          :] - 0.5)**2
               + (y[xp.newaxis,          :, xp.newaxis] - 0.5)**2
               + (x[         :, xp.newaxis, xp.newaxis] - 0.5)**2) / 0.01
     mf_array[:, :, :, 0] = 1. + xp.exp(-rsquared)
 
+# Inspect the data: reductions over all boxes (and MPI ranks)
+amr.Print(f"min(phi) = {mf.min(comp=0)}")
+amr.Print(f"max(phi) = {mf.max(comp=0)}")
+amr.Print(f"sum(phi) = {mf.sum(comp=0)}")
+
 # Plot MultiFab data
 plotfile = amr.concatenate(root="plt", num=1, mindigits=3)
 varnames = amr.Vector_string(["comp0"])