Macos cpp17 into Periodic Boundaries merge (#362)

* Move to ROOT 6.30.02 and C++17. ROOT 6.30.02 provided for macOS arm64 and i386 and ubuntu-22.04. * Drop requirement that ROOT is compiled with C++17. Let's see if we can use ROOT C++14 with BDM compiled with C++17. Initial tests showed ROOT C++14 still work. * Add macos 14 runners (beta, #356) * Add SHA for Root Arm XCode 14.1 * Add back ROOT C++17 compilation check as it must match to BDM C++17 flag. * Require ROOT 6.30/02 for all platforms for move to C++17. For CI we will provide ROOT 6.30/02 for CentOS7, Ubuntu 20.04,22.04 and macOS 12,13,14. * Update the SHA for ROOT for Ubuntu 20.04. * Fix filenames of ROOT tar files. * Update checkout and cache github actions to v4. * Update github actions checkout and cache to v4. * On centos-7 one needs devtoolset-10 for a working c++17 compiler. * Use xcode 14.2 on macOS 12, change pyenv cache key for centOS7. * Support Xcode 14.2. * Missing some run-time libs, hope they come from devtools-8. * Test only macos-13. * Fix cache test. * Don't use the latest checkout and cache actions as they need a node that is not supported. * Work around a brew issue. * Move from devtoolset-8 to devtoolset-10. * Check macos-14 CI. * Added ROOT 6.30.02 for macos-13 with Xcode 15.2. This version can also be used on macos-14 with Xcode 15.2. * Use XCode 15.2 on macOS 13 for macOS System CI * On CentOS7 use cache@v2 node is too old for cache@v4. * For CentOS7 need also previous version of chechout action. * Add minor changes moving to C++17 (#360) * Update demo Cmake * Update Doc * Remove experimental file system * Replace if statement with std::clamp (cpp17) * Automatic detection of cache line size * Add todo * Turn off numa for notebooks Loading BDM into rootcling results in picking up the wrong numa header and returns a fatal error in the resource manager's constructor * Don't build notebooks on ubuntu 20.04; 22.04 only * Disable notebooks with a warning if using float --------- Co-authored-by: Fons Rademakers <[email protected]> Co-authored-by: Tobias Duswald <[email protected]> Co-authored-by: Ahmad Hesam <[email protected]>
BioDynaMo · Feb 19, 2024 · 91d10b9 · 91d10b9
1 parent 93d1ded
commit 91d10b9
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diff --git a/.github/workflows/centos-ci.yml b/.github/workflows/centos-ci.yml
@@ -22,7 +22,7 @@ jobs:
         yum -y update
         yum -y install centos-release-scl epel-release
         yum -y install man wget environment-modules libXt-devel libXext-devel ninja-build make \
-          devtoolset-8-gcc* numactl-devel openmpi3-devel freeglut-devel \
+          devtoolset-10-gcc* numactl-devel openmpi3-devel freeglut-devel \
           scl-utils which xorg-x11-server-Xvfb fontconfig mesa-dri-drivers
         yum -y install @development zlib-devel bzip2 bzip2-devel readline-devel sqlite \
           sqlite-devel openssl-devel xz xz-devel libffi-devel findutils lapack-devel blas-devel
@@ -85,7 +85,7 @@ jobs:
         eval "$(pyenv init --path)"
         eval "$(pyenv init -)"
         pyenv shell 3.9.1
-        . scl_source enable devtoolset-8 || true
+        . scl_source enable devtoolset-10 || true
         . /etc/profile.d/modules.sh || true
         module load mpi
         cmake -G Ninja \

diff --git a/.github/workflows/centos-system-ci.yml b/.github/workflows/centos-system-ci.yml
@@ -118,7 +118,7 @@ jobs:
         eval "$(pyenv init --path)"
         eval "$(pyenv init -)"
         pyenv shell 3.9.1
-        . scl_source enable devtoolset-8 || true
+        . scl_source enable devtoolset-10 || true
         . /etc/profile.d/modules.sh || true
         module load mpi
         cmake \
@@ -140,7 +140,7 @@ jobs:
     #     eval "$(pyenv init --path)"
     #     eval "$(pyenv init -)"
     #     pyenv shell 3.9.1
-    #     . scl_source enable devtoolset-8 || true
+    #     . scl_source enable devtoolset-10 || true
     #     . /etc/profile.d/modules.sh || true
     #     module load mpi
     #     cmake \

diff --git a/.github/workflows/gitpod.yml b/.github/workflows/gitpod.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: 'LukasBreitwieser/gitpod-vnc'
           ref: master

diff --git a/.github/workflows/macos-ci.yml b/.github/workflows/macos-ci.yml
@@ -14,38 +14,39 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-12, macos-13]
+        os: [macos-12, macos-13, macos-14]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: Make sure Xcode 14.1 is used on macOS 12 as the default /Application/Xcode.app
+    - name: Make sure Xcode 14.2 is used on macOS 12 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_14.1.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_14.2.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
       if: matrix.os == 'macos-12'
 
-    - name: Make sure Xcode 13.1 is used on macOS 11 as the default /Application/Xcode.app
+    - name: Make sure Xcode 15.2 is used on macOS 13 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_13.1.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_15.2.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
-      if: matrix.os == 'macos-11'
+      if: matrix.os == 'macos-13'
 
     - name: Install dependencies
       run: |
+        export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
         brew install libomp open-mpi [email protected] wget cmake ninja qt@5 libgit2
 
     - name: Checkout BioDynaMo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     # - name: Cache Third Party Packages
-    #   uses: actions/cache@v2
+    #   uses: actions/cache@v4
     #   with:
     #     path: build/third_party
     #     key: ${{ runner.os }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}

diff --git a/.github/workflows/macos-system-ci.yml b/.github/workflows/macos-system-ci.yml
@@ -21,26 +21,26 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-12, macos-13]
+        os: [macos-12, macos-13, macos-14]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: Make sure Xcode 14.1 is used on macOS 12 as the default /Application/Xcode.app
+    - name: Make sure Xcode 14.2 is used on macOS 12 as the default /Application/Xcode.app
       shell: zsh {0}
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_14.1.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_14.2.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
       if: matrix.os == 'macos-12'
-
-    - name: Make sure Xcode 13.1 is used on macOS 11 as the default /Application/Xcode.app
+    
+    - name: Make sure Xcode 15.2 is used on macOS 13 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_13.1.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_15.2.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
-      if: matrix.os == 'macos-11'
+      if: matrix.os == 'macos-13'
 
     - name: Set GHA_BRANCH_NAME
       run: |
@@ -67,7 +67,7 @@ jobs:
         find /tmp -iname biodynamo -type d || true
 
     - name: Checkout BioDynaMo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -84,7 +84,7 @@ jobs:
         fi
 
     # - name: Cache Third Party Packages
-    #   uses: actions/cache@v2
+    #   uses: actions/cache@v4
     #   with:
     #     path: build/third_party
     #     key: ${{ runner.os }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}

diff --git a/.github/workflows/repository-checks.yml b/.github/workflows/repository-checks.yml
@@ -19,7 +19,7 @@ jobs:
         sudo apt install clang-format
 
     - name: Checkout BioDynaMo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Run clang-format code style check
       run: |

diff --git a/.github/workflows/singularity-integration.yml b/.github/workflows/singularity-integration.yml
@@ -19,7 +19,7 @@ jobs:
       image: quay.io/singularity/singularity:v3.9.0
       options: "--privileged --workdir /data"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Add root user to subuid and subgid...
         run: |

diff --git a/.github/workflows/sonar-source.yml b/.github/workflows/sonar-source.yml
@@ -19,7 +19,7 @@ jobs:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
       - name: Download BioDynaMo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Install sonar-scanner and build-wrapper

diff --git a/.github/workflows/ubuntu-ci.yml b/.github/workflows/ubuntu-ci.yml
@@ -52,7 +52,7 @@ jobs:
         echo "OSVERS=$ID-$VERSION" >> $GITHUB_ENV
 
     - name: Cache pyenv
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: pyenv-cache
       with:
         path: ~/.pyenv
@@ -71,12 +71,12 @@ jobs:
         pyenv shell 3.9.1
 
     - name: Checkout BioDynaMo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Cache Third Party Packages
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: build/third_party
         key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}

diff --git a/.github/workflows/ubuntu-system-ci.yml b/.github/workflows/ubuntu-system-ci.yml
@@ -64,7 +64,7 @@ jobs:
         find /tmp -iname biodynamo -type d || true
 
     - name: Checkout BioDynaMo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -78,7 +78,7 @@ jobs:
         fi
 
     - name: Cache pyenv
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: pyenv-cache
       with:
         path: ~/.pyenv
@@ -99,7 +99,7 @@ jobs:
         pyenv shell 3.9.1
 
     - name: Cache Third Party Packages
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: build/third_party
         key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
@@ -115,7 +115,8 @@ jobs:
         fi
 
     # Don't do this in the `Build BioDynaMo step`, because notebooks might time out in GHA
-    # runners, while waiting for other targets to be compiled
+    # runners, while waiting for other targets to be compiled. Run notebooks only
+    # if the event is a pull request, and on ubuntu-22.04.
     - name: Run notebooks
       shell: bash
       run: |
@@ -126,11 +127,13 @@ jobs:
         cmake \
           -Dnotebooks=ON \
           -Dsbml=OFF \
+          -Dnuma=OFF \
           -DCMAKE_BUILD_TYPE=Release \
           -Dreal_t=${{ env.REALT }} \
           -B build
         cmake --build build --parallel --config Release --target notebooks  -- -j1
-      if: github.event_name == 'pull_request'
+      if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-22.04'
+
 
     - name: Build BioDynaMo
       shell: bash

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -148,10 +148,6 @@ if(APPLE)
   foreach(_prefix /sw /opt/local)
     list(APPEND CMAKE_IGNORE_PATH ${_prefix}/bin ${_prefix}/include ${_prefix}/lib)
   endforeach()
-
-  # Silence std::experimental::filesystem warning on MacOS.
-  # Remove after update to c++17
-  add_definitions("-D_LIBCPP_NO_EXPERIMENTAL_DEPRECATION_WARNING_FILESYSTEM")
 endif()
 
 if(UNIX AND NOT APPLE)
@@ -167,6 +163,12 @@ if(real_t)
   add_definitions("-DBDM_REALT=${real_t}")
   add_definitions("-DBDM_CL_REALT=cl_${real_t}")
   set(BDM_CONFIG_REALT "${real_t}")
+  if(notebooks AND real_t STREQUAL "float")
+    # This if statement turns of the notebooks when we run with real_t=float.
+    # Currently, the notebooks do not support BDM with float for unknown reasons.
+    message(WARNING "Notebooks are not supported with real_t=float. Disabling notebooks.")
+    set(notebooks OFF)
+  endif()
 else()
   message(STATUS "Using default real_t (double)")
   set(BDM_CONFIG_REALT "float")
@@ -580,15 +582,12 @@ file(GLOB_RECURSE KERNELS "${CMAKE_SOURCE_DIR}/src/*.cu")
 filter_list(LIB_SOURCES "${LIB_SOURCES}" "paraview/*")
 filter_list(HEADERS "${HEADERS}" "paraview/*")
 
-# NB: Remove stdc++fs after switching to c++17  
-if (LINUX)
-  set(FS_LIB stdc++fs)
-endif()
 build_shared_library(biodynamo
                    SELECTION selection-libbiodynamo.xml
                    SOURCES ${LIB_SOURCES}
                    HEADERS ${HEADERS}
-                   LIBRARIES ${BDM_REQUIRED_LIBRARIES} ${ROOT_LIBRARIES} ${FS_LIB})
+                   LIBRARIES ${BDM_REQUIRED_LIBRARIES} ${ROOT_LIBRARIES})
+
 # libbiodynamo must be built before optimlib; otherwise optimlib could be missing during
 # the linking stage of libbiodynamo
 add_dependencies(biodynamo optim)
@@ -714,11 +713,12 @@ if (test)
                          ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/core/visualization/paraview/*.h
                          ${CMAKE_SOURCE_DIR}/test/unit/neuroscience/*.h)
-  # NB: Remove stdc++fs after switching to c++17  
+
   bdm_add_test_executable(biodynamo-unit-tests
                           SOURCES ${TEST_SOURCES}
                           HEADERS ${TEST_HEADERS}
-                          LIBRARIES ${REQUIRED_PARAVIEW_LIBRARIES} ${FS_LIB})
+                          LIBRARIES ${REQUIRED_PARAVIEW_LIBRARIES})
+
   #   separate test binaries - each source file is compiled into a separate binary
   # file(GLOB TEST_SOURCES ${CMAKE_SOURCE_DIR}/test/unit/separate_binary/*.cc)
   # file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/empty_header.h "")

diff --git a/cmake/CheckCompiler.cmake b/cmake/CheckCompiler.cmake
@@ -25,15 +25,15 @@ else()
     IF(${DETECTED_OS} MATCHES "centos.*")
         if (NOT DEFINED ENV{CXX})
             UNSET(CMAKE_CXX_COMPILER CACHE)
-            SET(CMAKE_CXX_COMPILER "/opt/rh/devtoolset-8/root/usr/bin/g++")
-            link_directories(/opt/rh/devtoolset-8/root/usr/lib)
-            link_directories(/opt/rh/devtoolset-8/root/usr/lib/dyninst)
-            link_directories(/opt/rh/devtoolset-8/root/usr/lib64)
-            link_directories(/opt/rh/devtoolset-8/root/usr/lib64/dyninst)
+            SET(CMAKE_CXX_COMPILER "/opt/rh/devtoolset-10/root/usr/bin/g++")
+            link_directories(/opt/rh/devtoolset-10/root/usr/lib)
+            link_directories(/opt/rh/devtoolset-10/root/usr/lib/dyninst)
+            link_directories(/opt/rh/devtoolset-10/root/usr/lib64)
+            link_directories(/opt/rh/devtoolset-10/root/usr/lib64/dyninst)
         endif()
         if (NOT DEFINED ENV{CC})
             UNSET(CMAKE_C_COMPILER CACHE)
-            SET(CMAKE_C_COMPILER "/opt/rh/devtoolset-8/root/usr/bin/gcc")
+            SET(CMAKE_C_COMPILER "/opt/rh/devtoolset-10/root/usr/bin/gcc")
         endif()
         enable_language(CXX)
     endif()
@@ -47,7 +47,7 @@ else()
     IF(${DETECTED_OS} MATCHES "centos.*")
         if (NOT DEFINED ENV{CC})
             UNSET(CMAKE_C_COMPILER CACHE)
-            SET(CMAKE_C_COMPILER "/opt/rh/devtoolset-8/root/usr/bin/gcc")
+            SET(CMAKE_C_COMPILER "/opt/rh/devtoolset-10/root/usr/bin/gcc")
         endif()
     endif()
     enable_language(C)

diff --git a/cmake/SetCompilerFlags.cmake b/cmake/SetCompilerFlags.cmake
@@ -14,15 +14,15 @@
 
 # This file sets all compiler flags
 
-# check if compiler supports C++14
+# check if compiler supports C++17
 include(CheckCXXCompilerFlag)
-check_cxx_compiler_flag("-std=c++14" COMPILER_SUPPORTS_CXX14)
-if(NOT COMPILER_SUPPORTS_CXX14)
-  message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} has no C++14 support. Please use a different C++ compiler.")
+check_cxx_compiler_flag("-std=c++17" COMPILER_SUPPORTS_CXX17)
+if(NOT COMPILER_SUPPORTS_CXX17)
+  message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} has no C++17 support. Please use a different C++ compiler.")
 endif()
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-# turn off compiler specific extensions e.g. gnu++14
+# turn off compiler specific extensions e.g. gnu++17
 set(CMAKE_CXX_EXTENSIONS OFF)
 
 # general flags

diff --git a/cmake/env/thisbdm.fish b/cmake/env/thisbdm.fish
@@ -426,7 +426,7 @@ function source_thisbdm
         if test "$os_id" = 'centos'
             set -gx MESA_GL_VERSION_OVERRIDE "3.3"
             if test -z "$CXX"; and test -z "$CC"
-                . scl_source enable devtoolset-8; or return 1
+                . scl_source enable devtoolset-10; or return 1
             end
 
             . /etc/profile.d/modules.sh; or return 1

diff --git a/cmake/env/thisbdm.sh b/cmake/env/thisbdm.sh
@@ -554,7 +554,7 @@ _source_thisbdm()
     if [ "$os_id" = 'centos' ]; then
         export MESA_GL_VERSION_OVERRIDE=3.3
         if [ -z "${CXX}" ] && [ -z "${CC}" ] ; then
-            . scl_source enable devtoolset-8 || return 1
+            . scl_source enable devtoolset-10 || return 1
         fi
         . /etc/profile.d/modules.sh || return 1
         module load mpi || return 1