v1.2.0 release candidate

.clang-format

@@ -106,6 +106,8 @@ IncludeCategories:
     Priority: 4
   - Regex: '^"engines\/.*\.h"'
     Priority: 4
+  - Regex: '^"checkpoint\/.*\.h"'
+    Priority: 4
   - Regex: '^"output\/.*\.h"'
     Priority: 4
   - Regex: '^"archetypes\/.*\.h"'

.github/workflows/actions.yml

@@ -1,26 +1,44 @@
 name: Unit tests
 
 on:
-  pull_request:
-    branches:
-      - '**rc'
-      - 'master'
+  push:
 
 jobs:
+  check-commit:
+    runs-on: ubuntu-latest
+    outputs:
+      run_tests: ${{ steps.check_message.outputs.run_tests }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Check commit message
+        id: check_message
+        run: |
+          if git log -1 --pretty=%B | grep -q "RUNTEST"; then
+            echo "run_tests=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "run_tests=false" >> "$GITHUB_OUTPUT"
+          fi
   tests:
+    needs: check-commit
+    if: needs.check-commit.outputs.run_tests == 'true'
     strategy:
       fail-fast: false
       matrix:
-        device: [amd-gpu, nvidia-gpu]
+        device: [cpu, amd-gpu, nvidia-gpu]
         precision: [double, single]
-        exclude: 
+        mpi: [serial, parallel]
+        exclude: # my AMD GPU doesn't support fp64 atomics : (
         - device: amd-gpu 
           precision: double
-        # my AMD GPUs doesn't support fp64 atomics : (
+        - device: amd-gpu
+          mpi: parallel
+        - device: nvidia-gpu
+          mpi: parallel
     runs-on: [self-hosted, "${{ matrix.device }}"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v4
       - name: Configure
         run: |
           if [ "${{ matrix.device }}" = "nvidia-gpu" ]; then
@@ -34,6 +52,8 @@ jobs:
             fi
           elif [ "${{ matrix.device }}" = "amd-gpu" ]; then
             FLAGS="-D Kokkos_ENABLE_HIP=ON -D Kokkos_ARCH_AMD_GFX1100=ON"
+          elif [ "${{ matrix.mpi }}" = "parallel" ]; then
+            FLAGS="-D mpi=ON"
           fi
           cmake -B build -D TESTS=ON -D output=ON -D precision=${{ matrix.precision }} $FLAGS
       - name: Compile

.gitignore

@@ -51,6 +51,10 @@ venv/
 # CMake testing files
 Testing/
 
+tags
+.clangd
 .schema.json
 *_old/
 action-token
+*.vim
+ignore-*

.gitmodules

@@ -1,13 +1,9 @@
-[submodule "extern/toml11"]
-	path = extern/toml11
-	url = https://github.com/ToruNiina/toml11.git
 [submodule "extern/plog"]
 	path = extern/plog
 	url = https://github.com/SergiusTheBest/plog.git
 [submodule "extern/adios2"]
 	path = extern/adios2
 	url = https://github.com/ornladios/ADIOS2.git
-	branch = master
 [submodule "extern/Kokkos"]
 	path = extern/Kokkos
 	url = https://github.com/kokkos/kokkos.git

.taplo.toml

@@ -0,0 +1,6 @@
+[formatting]
+  align_entries    = true
+  indent_tables    = true
+  indent_entries   = true
+  trailing_newline = true
+  align_comments   = true

CMakeLists.txt

@@ -1,19 +1,22 @@
+# cmake-lint: disable=C0103,C0111,E1120,R0913,R0915
+
 cmake_minimum_required(VERSION 3.16)
 cmake_policy(SET CMP0110 NEW)
 
 set(PROJECT_NAME entity)
 
 project(
   ${PROJECT_NAME}
-  VERSION 1.1.1
+  VERSION 1.2.0
   LANGUAGES CXX C)
 add_compile_options("-D ENTITY_VERSION=\"${PROJECT_VERSION}\"")
-execute_process(COMMAND
-  bash -c "git diff --quiet src/ && echo $(git rev-parse HEAD) || echo $(git rev-parse HEAD)-mod"
+set(hash_cmd "git diff --quiet src/ && echo $(git rev-parse HEAD) ")
+string(APPEND hash_cmd "|| echo $(git rev-parse HEAD)-mod")
+execute_process(
+  COMMAND bash -c ${hash_cmd}
   WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
   OUTPUT_VARIABLE GIT_HASH
-  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
-)
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 message(STATUS "Git hash: ${GIT_HASH}")
 add_compile_options("-D ENTITY_GIT_HASH=\"${GIT_HASH}\"")
 
@@ -25,100 +28,80 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/defaults.cmake)
 
 # defaults
 set(DEBUG
-  ${default_debug}
-  CACHE BOOL "Debug mode")
+    ${default_debug}
+    CACHE BOOL "Debug mode")
 
 set(precision
-  ${default_precision}
-  CACHE STRING "Precision")
+    ${default_precision}
+    CACHE STRING "Precision")
 set(pgen
-  ${default_pgen}
-  CACHE STRING "Problem generator")
+    ${default_pgen}
+    CACHE STRING "Problem generator")
 
 set(gui
-  ${default_gui}
-  CACHE BOOL "Use GUI [nttiny]")
+    ${default_gui}
+    CACHE BOOL "Use GUI [nttiny]")
 set(output
-  ${default_output}
-  CACHE BOOL "Enable output")
+    ${default_output}
+    CACHE BOOL "Enable output")
 set(mpi
-  ${default_mpi}
-  CACHE BOOL "Use MPI")
+    ${default_mpi}
+    CACHE BOOL "Use MPI")
 
 # -------------------------- Compilation settings -------------------------- #
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if(${DEBUG} STREQUAL "OFF")
   set(CMAKE_BUILD_TYPE
-    Release
-    CACHE STRING "CMake build type")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNDEBUG")
+      Release
+      CACHE STRING "CMake build type")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNDEBUG "
+                      "-Wno-unused-local-typedefs -Wno-unknown-cuda-version")
 else()
   set(CMAKE_BUILD_TYPE
-    Debug
-    CACHE STRING "CMake build type")
+      Debug
+      CACHE STRING "CMake build type")
   set(CMAKE_CXX_FLAGS
-    "${CMAKE_CXX_FLAGS} -DDEBUG -Wall -Wextra -Wno-unknown-pragmas")
+      "${CMAKE_CXX_FLAGS} -DDEBUG -Wall -Wextra -Wno-unknown-pragmas")
 endif()
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-local-typedefs")
-
 # options
 set(precisions
-  "single" "double"
-  CACHE STRING "Precisions")
+    "single" "double"
+    CACHE STRING "Precisions")
 
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/config.cmake)
 
 # ------------------------- Third-Party Tests ------------------------------ #
 set(BUILD_TESTING
-  OFF
-  CACHE BOOL "Build tests")
+    OFF
+    CACHE BOOL "Build tests")
 
 # ------------------------ Third-party dependencies ------------------------ #
-include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/kokkosConfig.cmake)
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/dependencies.cmake)
 
-find_or_fetch_dependency(Kokkos FALSE)
-find_or_fetch_dependency(plog TRUE)
-find_or_fetch_dependency(toml11 TRUE)
+find_or_fetch_dependency(Kokkos FALSE QUIET)
+find_or_fetch_dependency(plog TRUE QUIET)
 set(DEPENDENCIES Kokkos::kokkos)
 include_directories(${plog_SRC}/include)
-include_directories(${toml11_SRC})
 
 # -------------------------------- Main code ------------------------------- #
 set_precision(${precision})
 
 # MPI
 if(${mpi})
-  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/MPIConfig.cmake)
+  find_or_fetch_dependency(MPI FALSE REQUIRED)
+  include_directories(${MPI_CXX_INCLUDE_PATH})
+  add_compile_options("-D MPI_ENABLED")
   set(DEPENDENCIES ${DEPENDENCIES} MPI::MPI_CXX)
 endif()
 
 # Output
 if(${output})
-  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/adios2Config.cmake)
-  find_or_fetch_dependency(adios2 FALSE)
-  if (NOT DEFINED ENV{HDF5_ROOT})
-    set(USE_CUSTOM_HDF5 OFF)
-    if (DEFINED ENV{CONDA_PREFIX})
-      execute_process(COMMAND bash -c "conda list | grep \"hdf5\" -q"
-        RESULT_VARIABLE HDF5_INSTALLED)
-      if (HDF5_INSTALLED EQUAL 0)
-        set(HDF5_ROOT $ENV{CONDA_PREFIX})
-      else()
-        set(USE_CUSTOM_HDF5 ON)
-      endif()
-    else()
-      set(USE_CUSTOM_HDF5 ON)
-    endif()
-    if (USE_CUSTOM_HDF5)
-      message(FATAL_ERROR "HDF5_ROOT is not set. Please set it to the root of the HDF5 installation")
-    endif()
-  endif()
-  find_package(HDF5 REQUIRED)
-
+  find_or_fetch_dependency(adios2 FALSE QUIET)
+  add_compile_options("-D OUTPUT_ENABLED")
   if(${mpi})
     set(DEPENDENCIES ${DEPENDENCIES} adios2::cxx11_mpi)
   else()
@@ -131,14 +114,18 @@ link_libraries(${DEPENDENCIES})
 if(TESTS)
   # ---------------------------------- Tests --------------------------------- #
   include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/tests.cmake)
+elseif(BENCHMARK)
+  # ------------------------------ Benchmark --------------------------------- #
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/benchmark.cmake)
 else()
   # ----------------------------------- GUI ---------------------------------- #
   if(${gui})
-    find_or_fetch_dependency(nttiny FALSE)
+    find_or_fetch_dependency(nttiny FALSE QUIET)
   endif()
 
   # ------------------------------- Main source ------------------------------ #
   set_problem_generator(${pgen})
   add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/src src)
-  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/report.cmake)
 endif()
+
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/report.cmake)

README.md

@@ -10,21 +10,29 @@ Our [detailed documentation](https://entity-toolkit.github.io/) includes everyth
 
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-## Core developers (alphabetical)
+## Lead developers
 
-👀 __Yangyang Cai__ {[@StaticObserver](https://github.com/StaticObserver): GRPIC}
+☕ __Hayk Hakobyan__ {[@haykh](https://github.com/haykh)}
 
-💁‍♂️ __Alexander Chernoglazov__ {[@SChernoglazov](https://github.com/SChernoglazov): PIC}
+🥔 __Jens Mahlmann__ {[@jmahlmann](https://github.com/jmahlmann)}
 
-🍵 __Benjamin Crinquand__ {[@bcrinquand](https://github.com/bcrinquand): GRPIC, cubed-sphere}
+💁‍♂️ __Alexander Chernoglazov__ {[@SChernoglazov](https://github.com/SChernoglazov)}
+
+🧋 __Alisa Galishnikova__ {[@alisagk](https://github.com/alisagk)}
+
+🐬 __Sasha Philippov__ {[@sashaph](https://github.com/sashaph)}
 
-🧋 __Alisa Galishnikova__ {[@alisagk](https://github.com/alisagk): GRPIC}
+## Contributors (alphabetical)
 
-☕ __Hayk Hakobyan__ {[@haykh](https://github.com/haykh): framework, PIC, GRPIC, cubed-sphere}
+🎸 __Ludwig Böss__ {[@LudwigBoess](https://github.com/LudwigBoess): PIC, framework}
+
+👀 __Yangyang Cai__ {[@StaticObserver](https://github.com/StaticObserver): GRPIC}
+
+🍵 __Benjamin Crinquand__ {[@bcrinquand](https://github.com/bcrinquand): GRPIC, cubed-sphere}
 
-🥔 __Jens Mahlmann__ {[@jmahlmann](https://github.com/jmahlmann): framework, MPI, cubed-sphere}
+🚂 __Evgeny Gorbunov__ {[@Alcauchy](https://github.com/Alcauchy): PIC, framework}
 
-🐬 __Sasha Philippov__ {[@sashaph](https://github.com/sashaph): all-around}
+:radio: __Siddhant Solanki__ {[@sidruns30](https://github.com/sidruns30): framework}
 
 🤷 __Arno Vanthieghem__ {[@vanthieg](https://github.com/vanthieg): framework, PIC}
 

benchmark/benchmark.cpp

@@ -0,0 +1,17 @@
+#include "global.h"
+
+#include <iostream>
+#include <stdexcept>
+
+auto main(int argc, char* argv[]) -> int {
+  ntt::GlobalInitialize(argc, argv);
+  try {
+    // ...
+  } catch (const std::exception& e) {
+    std::cerr << "Error: " << e.what() << std::endl;
+    GlobalFinalize();
+    return 1;
+  }
+  GlobalFinalize();
+  return 0;
+}