Merge remote-tracking branch 'upstream' into bugFixes

Author: wilfonba

.github/workflows/ci.yml

@@ -88,7 +88,10 @@ jobs:
           /bin/bash mfc.sh test -j $(nproc) $OPT1 $OPT2
         env:
           OPT1: ${{ matrix.mpi == 'mpi' && '--test-all' || '' }}
-          OPT2: ${{ matrix.debug == 'debug' && '-% 75' || '' }}
+          OPT2: ${{ matrix.debug == 'debug' && '-% 20' || '' }}
+
+      - name: Ensure empty diff
+        run:  git diff --exit-code tests/
 
   docker:
     name:    Github | Docker
@@ -100,6 +103,9 @@ jobs:
     - name: Test
       run:  sudo ./mfc.sh docker ./mfc.sh test -j $(nproc) -a
 
+    - name: Ensure empty diff
+      run:  git diff --exit-code tests/
+
   self:
     name: Georgia Tech | Phoenix (NVHPC)
     if: github.repository == 'MFlowCode/MFC'
@@ -125,8 +131,10 @@ jobs:
           mv misc/run-phoenix-release-${{ matrix.device }}.sh ./
           sbatch run-phoenix-release-${{ matrix.device }}.sh
 
+      - name: Ensure empty diff
+        run:  exit $(git status --porcelain tests/ | wc -l)
+
       - name: Print
         if: always()
         run: |
           cat test.out
-

.github/workflows/lint.yml

@@ -0,0 +1,19 @@
+name: Lint
+
+on:
+  push:
+
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  docs:
+    name:    Lint Toolchain
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Lint the toolchain
+      run: ./mfc.sh lint

.github/workflows/pretty.yml

@@ -0,0 +1,21 @@
+name: Pretty
+
+on:
+  push:
+
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  docs:
+    name:    Code formatting
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Check formatting
+      run: |
+        ./mfc.sh format
+        git diff --exit-code

.github/workflows/spelling.yml

@@ -0,0 +1,15 @@
+name: Spell Check
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  run:
+    name: Spell Check
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Spell Check
+      uses: crate-ci/typos@master

.gitignore

@@ -28,6 +28,7 @@ __pycache__
 
 docs/*/initial*
 docs/*/result*
+docs/documentation/*-example.png
 docs/documentation/examples.md
 
 examples/*batch/*/

.typos.toml

@@ -0,0 +1,19 @@
+[default]
+extend-ignore-identifiers-re = [
+    "AttributeID.*Supress.*",
+]
+
+[default.extend-identifiers]
+AttributeIDSupressMenu = "AttributeIDSupressMenu"
+
+[default.extend-words]
+INOUT = "INOUT"
+WRONLY = "WRONLY"
+nd = "nd"
+# Childs = "Childs"
+# myu = "myu"
+
+
+
+[files]
+extend-exclude = ["docs/documentation/references*", "tests/"]

CMakeLists.txt

@@ -65,7 +65,18 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
     endif()
 elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_ID STREQUAL "PGI"))
     if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 21.7)
-        message(FATAL_ERROR "${__err_msg}ERROR: NVHPC v21.7 or newer is required to build MFC.")
+        message(FATAL_ERROR "${__err_msg}ERROR: When using NVHPC, v21.7 or newer is required to build MFC.")
+    endif()
+    if (MAKE_BUILD_TYPE STREQUAL "Debug")
+        if (MFC_OpenACC)
+            if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.0)
+                message(FATAL_ERROR "${__err_msg}ERROR: When using NVHPC, v23.0 or newer is required to build MFC with Debug and GPU options.")
+            endif()
+        else()
+            if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.8)
+                message(FATAL_ERROR "${__err_msg}ERROR: Debug is not working with NVHPC 23.X and older and CPU options at present.")
+            endif()
+        endif()
     endif()
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_C_COMPILER_ID STREQUAL "AppleClang")
     message(FATAL_ERROR "${__err_msg}ERROR: MFC does not support the Apple Clang compilers. Please consult the documentation.")
@@ -145,7 +156,7 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
     endif()
 
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-        add_compile_options(-C -g -traceback -Mchkptr -Mchkstk -Minform=inform -Mbounds)
+        add_compile_options(-C -g -O0 -traceback -Mchkptr -Mchkstk -Minform=inform -Mbounds)
     endif()
 endif()
 
@@ -229,6 +240,8 @@ macro(HANDLE_SOURCES target useCommon)
     set(${target}_DIR "${CMAKE_SOURCE_DIR}/src/${target}")
     set(common_DIR    "${CMAKE_SOURCE_DIR}/src/common")
 
+    string(TOUPPER ${target} ${target}_UPPER)
+
     # Gather src/[<target>,common]/*.f90
     file(GLOB ${target}_F90s CONFIGURE_DEPENDS "${${target}_DIR}/*.f90")
     set(${target}_SRCs ${${target}_F90s})
@@ -245,9 +258,9 @@ macro(HANDLE_SOURCES target useCommon)
     endif()
 
     # Locate src/[<target>,common]/include/*.fpp
-    if (EXISTS "${${target}_DIR}/include")
-        file(GLOB ${target}_incs CONFIGURE_DEPENDS "${${target}_DIR}/include/*.fpp")
-    endif()
+    file(GLOB ${target}_incs CONFIGURE_DEPENDS "${${target}_DIR}/include/*.fpp"
+                                               "${CMAKE_CURRENT_BINARY_DIR}/include/*.fpp")
+
     if (${useCommon})
         file(GLOB common_incs CONFIGURE_DEPENDS "${common_DIR}/include/*.fpp")
         list(APPEND ${target}_incs ${common_incs})
@@ -261,11 +274,14 @@ macro(HANDLE_SOURCES target useCommon)
         add_custom_command(
             OUTPUT   ${f90}
             COMMAND  ${FYPP_EXE} -m re
-                                 -I "${common_DIR}"
-                                 -I "${common_DIR}/include"
+                                 -I "${CMAKE_CURRENT_BINARY_DIR}/include"
                                  -I "${${target}_DIR}/include"
+                                 -I "${common_DIR}/include"
+                                 -I "${common_DIR}"
                                  -D MFC_${CMAKE_Fortran_COMPILER_ID}
+                                 -D MFC_${${target}_UPPER}
                                  -D MFC_COMPILER="${CMAKE_Fortran_COMPILER_ID}"
+                                 -D MFC_CASE_OPTIMIZATION=False
                                  --line-numbering
                                  --no-folding
                                  "${fpp}" "${f90}"
@@ -317,10 +333,10 @@ function(MFC_SETUP_TARGET)
             "${CMAKE_SOURCE_DIR}/src/${ARGS_TARGET}/include")
     endif()
 
-    string(TOUPPER "${ARGS_TARGET}" ARGS_TARGET_UPPER)
+    string(TOUPPER "${ARGS_TARGET}" ${ARGS_TARGET}_UPPER)
     target_compile_definitions(
         ${ARGS_TARGET} PRIVATE MFC_${CMAKE_Fortran_COMPILER_ID}
-                               MFC_${ARGS_TARGET_UPPER}
+                               MFC_${${ARGS_TARGET}_UPPER}
     )
 
     if (MFC_MPI AND ARGS_MPI)
@@ -430,6 +446,20 @@ if (MFC_SYSCHECK)
 endif()
 
 if (MFC_DOCUMENTATION)
+    # Files in examples/ are used to generate docs/documentation/examples.md
+    file(GLOB_RECURSE examples_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/examples/*")
+
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples.sh;${examples_DOCs}"
+        COMMAND "bash" "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples.sh" 
+                       "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMENT "Generating examples.md"
+        VERBATIM
+    )
+
+    file(GLOB common_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/*")
+
     # GEN_DOCS: Given a target name (herein <target>), this macro sets up a
     # target, <target>_docs, that generates documentation for <target> using
     # Doxygen. It is then added as a dependency of the documentation target.
@@ -456,13 +486,20 @@ if (MFC_DOCUMENTATION)
             "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in"
             "${CMAKE_CURRENT_BINARY_DIR}/${target}-Doxyfile" @ONLY)
 
+        set(opt_example_dependency "")
+        if (${target} STREQUAL documentation)
+            set(opt_example_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md")
+        endif()
+
+        file(GLOB_RECURSE ${target}_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}/*")
+        list(APPEND ${target}_DOCs "${common_DOCs}")
+
         add_custom_command(
             OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/${target}/html/index.html"
             DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/${target}-Doxyfile"
-                    "${${target}_SRCs}"
-            COMMAND  "bash" "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples.sh" 
-                            "${CMAKE_CURRENT_SOURCE_DIR}" && 
-                    "${DOXYGEN_EXECUTABLE}" "${target}-Doxyfile"
+                    "${opt_example_dependency}"
+                    "${${target}_SRCs}" "${${target}_DOCs}"
+            COMMAND "${DOXYGEN_EXECUTABLE}" "${target}-Doxyfile"
             WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
             COMMENT "${target}: Generating documentation"
         )
@@ -487,7 +524,7 @@ if (MFC_DOCUMENTATION)
     ExternalProject_Add(doxygen-awesome-css
         PREFIX            doxygen-awesome-css
         GIT_REPOSITORY    "https://github.com/jothepro/doxygen-awesome-css"
-        GIT_TAG           "df83fbf22cfff76b875c13d324baf584c74e96d0"
+        GIT_TAG           "df88fe4fdd97714fadfd3ef17de0b4401f804052"
         CONFIGURE_COMMAND ""
         BUILD_COMMAND     ""
         INSTALL_COMMAND   ""

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Computational Physics Group at Georgia Tech (Spencer Bryngelson)
+Copyright (c) 2021 Spencer Bryngelson, Tim Colonius
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

README.md

@@ -19,10 +19,11 @@
 <p align="justify">
   Welcome to the home of MFC!
   MFC simulates compressible multi-component and multi-phase flows, amongst other things. 
-  It scales ideally to tens of thousands of GPUs.
+  It scales ideally to tens of thousands of GPUs on NVIDIA- and AMD-GPU Machines, like OLCF Summit and Frontier.
+  As such, it is an exascale CFD codebase.
   MFC is written in Fortran and makes use of metaprogramming to keep the codebase readable.
-  Please contact the developers, like <a href="mailto:shb@gatech.edu">Spencer</a>, if you have questions.
-  We have an active Slack channel to help ease in new MFC users and support development.
+  Don't hesitate to get in touch with the developers, like <a href="mailto:shb@gatech.edu">Spencer</a>, if you have questions.
+  We have an active Slack channel to help ease new MFC users and support development.
 
   MFC has API and high-level documentation on [its website](https://mflowcode.github.io/).
   The latter is also available [here](docs/documentation/readme.md).

docs/documentation/authors.md

@@ -1,20 +1,3 @@
 ## Authors
 
-MFC was first developed by the Colonius research group at Caltech.
-Now it is developed and maintained by the groups of Professors <a href="https://comp-physics.group">Spencer Bryngelson</a>, <a href="https://colonius.caltech.edu/">Tim Colonius</a>, and <a href="https://vivo.brown.edu/display/mrodri97">Mauro Rodriguez</a> (alphabetical).
-
-We try to maintain a list of current and past developers:
-
-+ S. Bryngelson 
-+ T. Colonius 
-+ V. Coralic 
-+ H. Le Berre
-+ K. Maeda 
-+ J. Meng 
-+ F. O'Meally
-+ A. Radhakrishnan 
-+ J. Rodolfo Chreim
-+ M. Rodriguez 
-+ K. Schmidmayer 
-+ J. Spratt 
-+ B. Wilfong    
+Contributors to MFC since 2019 can be [viewed here](https://github.com/MFlowCode/MFC/graphs/contributors).