HPC RSE: improving the parallel scaling of Python

.github/workflows/build.yml

@@ -1,5 +1,4 @@
-name: C/C++ CI
-
+name: "Python: continuous integration tests"
 on:
   push:
     branches:
@@ -11,58 +10,47 @@ on:
       - "main"
 env:
   PYTHON: ${{ github.workspace }}
-
 jobs:
-  greeting_job:
+  greeting:
+    name: Greeting job
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: "Print out environment variables"
       run: |
-        echo "WORKSPACE IS $GITHUB_WORKSPACE $PYTHON"
-        $PYTHON/bin/Setup_Py_Dir
+        echo "WORKSPACE IS $GITHUB_WORKSPACE"
+        echo "PYTHON ENV VARIABLE IS: $PYTHON"
 
-  build:
+  build_and_test:
+    name: Build Python and run tests
     runs-on: ubuntu-latest
+    needs: greeting
     steps:
     - uses: actions/checkout@v3
-    - name: configure
+    #- name: "Installing build dependencies"
+    #  run: sudo apt update && apt install -y build-essential cmake
+
+    - name: Configuring Python
       run: ./configure
-    - name: make gh_workflow_install
+    - name: Build GH Workflow version of Python
       run: make gh_workflow_install
 
-  run:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-    - uses: actions/checkout@v3
     - uses: actions/setup-python@v3
       with:
         python-version: '3.x' # Version range
-
-    - name: Install dependencies
+    - name: Install Python (the language) dependencies
       run: |
         python -m pip install --upgrade pip
         pip install wheel
         cd $PYTHON/examples/gh-workflow/
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
-    - name: compile helper programs and setup
-      run: |
-        cd $PYTHON/source/
-        make clean
-        make CC=gcc INDENT=no all
-        make clean
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/Setup_Py_Dir
+#    - name: Compile programs, again
+#      run: |
+#        cd $PYTHON/source
+#        make CC=gcc INDENT=no all
 
-    - name: balmer test
-      run: |
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/py -f -v 1 balmer_test
-        python $PYTHON/py_progs/balmer_decrement.py balmer_test
-
-    - name: read in parameter files
+    - name: Checking Python compiled and can read in inputs correctly
       run: |
         cd $PYTHON/examples/gh-workflow/
         $PYTHON/bin/Setup_Py_Dir
@@ -76,3 +64,14 @@ jobs:
         $PYTHON/bin/py -i ngc5548
         $PYTHON/bin/py -i lamp_post
         $PYTHON/bin/py -i cv_standard_import
+
+    - name: Running unit tests
+      run: |
+        cd $PYTHON/source/tests
+        make check CC=gcc
+
+    - name: Running Balmer test case
+      run: |
+        cd $PYTHON/examples/gh-workflow/
+        $PYTHON/bin/py -f -v 1 balmer_test
+        python $PYTHON/py_progs/balmer_decrement.py balmer_test

CMakeLists.txt

@@ -14,15 +14,16 @@ project(Python LANGUAGES C)
 
 # The C standard is being set to 90. The compiler is being set to mpicc
 
-set(CMAKE_C_STANDARD 90)
+set(CMAKE_C_STANDARD 99)
 set(CMAKE_C_COMPILER mpicc)
+set(CMAKE_CXX_COMPILER mpixx)
 include_directories(include)
 link_directories(lib)
 add_definitions(-DMPI_ON)
 
 # Set the Python version, which is going to be appended to source/version.h
 
-set(PYTHON_VERSION 87b)
+set(PYTHON_VERSION 87g)
 message(STATUS "Python version : ${PYTHON_VERSION}")
 
 # Create the version.h file. During the configure process, the file version.h
@@ -69,6 +70,7 @@ endif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
 set(CUDA_SOURCE source/matrix_gpu.cu)
 
 set(PYTHON_SOURCE
+    ${CUDA_SOURCE}
     source/agn.c
     source/atomicdata.c
     source/atomicdata_init.c
@@ -173,15 +175,28 @@ set(PYTHON_SOURCE
     source/photon_gen_matom.c
     source/disk_photon_gen.c
     source/matrix_cpu.c
-    ${CUDA_SOURCE})
+    source/define_wind.c
+    source/communicate_wind.c
+    source/communicate_plasma.c
+    source/communicate_macro.c
+    source/communicate_spectra.c
+    source/janitor.c
+)
 
 set(PY_WIND_SOURCE source/py_wind_ion.c source/py_wind_macro.c
-                   source/py_wind_sub.c source/py_wind_write.c)
+                   source/py_wind_sub.c source/py_wind_write.c
+        source/define_wind.c
+        source/communicate_wind.c
+        source/communicate_spectra.c)
 
-set(WINDSAVE2TABLE_SOURCE source/windsave2table_sub.c)
+set(WINDSAVE2TABLE_SOURCE source/windsave2table_sub.c
+        source/define_wind.c
+        source/communicate_wind.c)
 
 set(RAD_HYDRO_SOURCE source/rad_hydro_files.c)
 
+set(MODIFY_WIND_SOURCE source/modify_wind.c)
+
 set(INSPECT_WIND_SOURCE source/inspect_wind.c)
 
 set(OPTICAL_DEPTH_SOURCE
@@ -192,10 +207,13 @@ set(TEST_SOURCE
     source/tests/unit_test_main.c
     source/tests/tests/test_matrix.c
     source/tests/tests/test_compton.c
-    ${PYTHON_SOURCE})
-
-#${CUDA_SOURCE})
-
+    ${PYTHON_SOURCE}
+        source/define_wind.c
+        source/tests/tests/test_define_wind.c
+        source/communicate_wind.c
+        source/tests/unit_test_model.c
+        source/tests/tests/test_run_mode.c
+)
 
 # Create the executables for each program, and link the required libraries
 
@@ -212,6 +230,22 @@ add_executable(windsave2table source/windsave2table.c ${PYTHON_SOURCE}
                               ${WINDSAVE2TABLE_SOURCE})
 target_link_libraries(windsave2table gsl gslcblas m)
 
+# rad_hydro_files
+add_executable(rad_hydro_files ${PYTHON_SOURCE} ${RAD_HYDRO_SOURCE})
+target_link_libraries(rad_hydro_files gsl gslcblas m)
+
+# modify_wind
+add_executable(modify_wind ${PYTHON_SOURCE} ${MODIFY_WIND_SOURCE})
+target_link_libraries(modify_wind gsl gslcblas m)
+
+# inspect_wind
+add_executable(inspect_wind ${PYTHON_SOURCE} ${INSPECT_WIND_SOURCE})
+target_link_libraries(inspect_wind gsl gslcblas m)
+
+# py_optd
+add_executable(py_optd ${PYTHON_SOURCE} ${OPTICAL_DEPTH_SOURCE})
+target_link_libraries(py_optd gsl gslcblas m)
+
 # test
 add_executable(py_unit_test ${TEST_SOURCE})
 target_link_libraries(py_unit_test m gsl gslcblas cunit)

Makefile.in

@@ -68,7 +68,6 @@ endif
 MAKE_PYTHON = \
 	cd $(PYTHON)/source; \
 	make CC=$(CMAKE) INDENT=no all \
-	$(MAKE_CHECK)
 
 # Compile and install the libraries and Python
 install:

docs/sphinx/source/developer/tests.rst

@@ -140,7 +140,7 @@ implementation. If you need to create your own assertion, these should be kept i
       /* Use the following assertion to compare the value of the "correct" values (vector_x)
          against the output from `solve_matrix` (test_vector_x) */
 
-      CU_CHECK_DOUBLE_ARRAY_EQ_FATAL(test_vector_x, vector_x, vector_size, EPSILON);  /* Custom from assert.h */
+      CU_ASSERT_DOUBLE_ARRAY_EQUAL_FATAL(test_vector_x, vector_x, vector_size, EPSILON);  /* Custom from assert.h */
 
       free(matrix_a);
       free(vector_b);

examples/regress/commands.txt

@@ -9,3 +9,4 @@ py -ignore_partial_cells agn_simple.pf
 # py cv_vert.pf
 # py star.pf
 # py two.pf
+# py cv_standard_import.pf