Merge pull request #68 from Matthew-Whitlock/ci_update

Ci update, bugfixes

.github/Dockerfile

@@ -0,0 +1,29 @@
+#Built for testing, not designed for application use.
+
+FROM ubuntu:20.04
+#="open-mpi/ompi" for github.com/open-mpi/ompi
+ARG OPENMPI_REPO="open-mpi/ompi"
+#="tags" or ="heads", for tag or branch name
+ARG OPENMPI_VERS_PREFIX="tags"
+#="v5.0.0rc10" or ="v5.0.x", ie tag name or branch name.
+ARG OPENMPI_VERS="v5.0.0rc10"
+run echo Using https://github.com/${OPENMPI_REPO}/git/refs/${OPENMPI_VERS_PREFIX}/${OPENMPI_VERS}
+
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential python3 m4 autoconf automake libtool flex git zlib1g-dev
+
+#Add files listing latest commit for this branch/tag, which invalidates the clone
+#when a change has been pushed.
+ADD https://api.github.com/repos/${OPENMPI_REPO}/git/refs/${OPENMPI_VERS_PREFIX}/${OPENMPI_VERS} commit_info
+RUN git clone --recursive --branch ${OPENMPI_VERS} --depth 1 https://github.com/${OPENMPI_REPO}.git ompi_src && \
+    mkdir ompi_build ompi_install && cd ompi_src && export AUTOMAKE_JOBS=8 && ./autogen.pl && cd ../ompi_build && ../ompi_src/configure --prefix=/ompi_install --disable-man-pages --with-ft=ulfm && make install -j8 && cd ..
+
+
+#New build stage, tosses out src/build trees from openmpi
+FROM ubuntu:20.04
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential cmake ssh zlib1g-dev
+COPY . ./fenix_src
+COPY --from=0 ompi_install/ /ompi_install/
+ENV PATH="$PATH:/ompi_install/bin"
+RUN mkdir fenix_build fenix_install && cd fenix_build && cmake ../fenix_src -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=/ompi_install/bin/mpicc \
+    -DFENIX_EXAMPLES=ON -DFENIX_TESTS=ON -DCMAKE_INSTALL_PREFIX=../fenix_install -DMPIEXEC_PREFLAGS="--allow-run-as-root;--map-by;:OVERSUBSCRIBE" && make install -j8
+CMD ["sh", "-c", "cd fenix_build && ctest --verbose --timeout 60"]

.github/docker-compose.yml

@@ -0,0 +1,81 @@
+version: "3.9"
+
+x-fenix: &fenix
+  build: &fenix-build
+    context: ./
+    dockerfile: .github/Dockerfile
+    args:
+      OPENMPI_REPO: open-mpi/ompi
+      OPENMPI_VERS_PREFIX: tags
+      OPENMPI_VERS: v5.0.0rc10
+    #Caches should be manually scoped, or they'll conflict.
+    x-bake:
+      cache-from:
+        - type=gha,scope=default
+      cache-to:
+        - type=gha,scope=default,mode=max
+
+services:
+  #fenix_ompi_5rc10:
+  # <<: *fenix
+  # image: "fenix:ompi_5rc10"
+  # build: 
+  #   <<: *fenix-build
+  #   x-bake:
+  #     cache-from:
+  #       - type=gha,scope=ompi_5rc10
+  #     cache-to:
+  #       - type=gha,scope=ompi_5rc10,mode=max
+
+  fenix_ompi_5:
+    <<: *fenix
+    image: "fenix:ompi_5"
+    build:
+      <<: *fenix-build
+      args:
+        - OPENMPI_VERS_PREFIX=heads
+        - OPENMPI_VERS=v5.0.x
+      x-bake:
+        cache-from:
+          - type=gha,scope=ompi_5
+        cache-to:
+          - type=gha,scope=ompi_5,mode=max
+
+  fenix_ompi_main:
+    <<: *fenix
+    image: "fenix:ompi_main"
+    build:
+      <<: *fenix-build
+      args:
+        - OPENMPI_VERS_PREFIX=heads
+        - OPENMPI_VERS=main
+      x-bake:
+        cache-from:
+          - type=gha,scope=ompi_main
+        cache-to:
+          - type=gha,scope=ompi_main,mode=max
+
+  fenix_icldisco_latest:
+    <<: *fenix
+    image: "fenix:icldisco_latest"
+    build:
+      <<: *fenix-build
+      args:
+        - OPENMPI_REPO=icldisco/ompi
+        - OPENMPI_VERS_PREFIX=heads
+        - OPENMPI_VERS=ulfm/latest
+      x-bake:
+        cache-from:
+          - type=gha,scope=icldisco_latest
+        cache-to:
+          - type=gha,scope=icldisco_latest,mode=max
+
+  #fenix_icldisco_experimental:
+  #  <<: *fenix
+  #  image: fenix/icldisco
+  #  build:
+  #    <<: *fenix-build
+  #   args:
+  #     - OPENMPI_REPO=icldisco/ompi
+  #     - OPENMPI_VERS_PREFIX=heads
+  #     - OPENMPI_VERS=ulfm/experimental

.github/workflows/ci_checks.yaml

@@ -0,0 +1,31 @@
+name: Build & Test
+
+on:
+  push:
+  pull_request_target:
+    types:
+      - opened
+      - synchronized
+      - edited
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: docker/setup-buildx-action@v2
+      - name: Build
+        uses: docker/bake-action@master
+        with:
+          files: |
+            .github/docker-compose.yml
+          load: true
+      - name: Test open-mpi v5.0.x
+        if: success() || failure()
+        run: docker run fenix:ompi_5
+      - name: Test open-mpi main
+        if: success() || failure()
+        run: docker run fenix:ompi_main
+      - name: Test icldisco latest
+        if: success() || failure()
+        run: docker run fenix:icldisco_latest

.gitignore

@@ -39,6 +39,8 @@ examples/05_subset_create/subset_create
 examples/06_subset_createv/subset_createv
 test/request_tracking/fenix_request_tracking_test
 test/request_tracking/fenix_request_tracking_test_nofenix
+build/
+install/
 
 # Other
 *~

CMakeLists.txt

@@ -8,108 +8,66 @@
 #  directory.
 #
 
-cmake_minimum_required(VERSION 3.0.2)
+cmake_minimum_required(VERSION 3.10.2)
 
 project(Fenix C)
 # The version number.
 set(FENIX_VERSION_MAJOR 1)
 set(FENIX_VERSION_MINOR 0)
 
-option(BUILD_EXAMPLES  "Builds example programs from the examples directory"   OFF)
-option(BUILD_TESTING   "Builds tests and test modes of files"                  ON)
+option(BUILD_EXAMPLES    "Builds example programs from the examples directory" OFF)
+option(BUILD_TESTING     "Builds tests and test modes of files" ON)
 
 
-# Set empty string for shared linking (we use static library only at this moment)
-set(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)
+#Solves an issue with some system environments putting their MPI headers before
+#the headers CMake includes. Forces non-system MPI headers when incorrect headers
+#detected in include path.
+option(FENIX_SYSTEM_INC_FIX    "Attempts to force overriding any system MPI headers" ON)
+option(FENIX_PROPAGATE_INC_FIX "Attempt overriding system MPI headers in linking projects" ON)
 
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+find_package(MPI REQUIRED)
 
-#set(CMAKE_BUILD_TYPE Release)
-set(CMAKE_BUILD_TYPE Debug)
-#set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -O0 -ggdb")
+if(${FENIX_SYSTEM_INC_FIX})
+  include(cmake/systemMPIOverride.cmake)
+endif()
 
-#ENABLE_TESTING
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR})
-#include(testref/TestAgainstReference)
 
-configure_file(
-    ${CMAKE_CURRENT_SOURCE_DIR}/include/fenix-config.h.in
-    ${CMAKE_CURRENT_BINARY_DIR}/include/fenix-config.h @ONLY
-)
+add_subdirectory(src)
 
 
-#Check for MPICC definition, if not try to find MPI
-if(NOT "a$ENV{MPICC}" STREQUAL "a")
-    #set(CMAKE_C_COMPILER ${MPI_C_COMPILER} CACHE STRING "The compiler CMake should use - often set to mpicc" FORCE)
-    set(MPI_C_COMPILER $ENV{MPICC})
-    set(CMAKE_C_COMPILER ${MPI_C_COMPILER})
-
-    message("[fenix] MPICC has been passed: $ENV{MPICC}")
-else()
-    message("[fenix] MPICC was not passed, searching for MPI")
-    find_package(MPI REQUIRED)
-    if(${MPI_C_FOUND})
-        message("[fenix] Found MPICC: ${MPI_C_COMPILER}")
-    else()
-        message( FATAL_ERROR "[fenix] MPI not found :( Aborting!")
-    endif()
+include(CTest)
+list(APPEND MPIEXEC_PREFLAGS "--with-ft;mpi")
+
+if(BUILD_EXAMPLES)
+    add_subdirectory(examples)
 endif()
 
-#Helper function for linking with MPI only if needed
-function(linkMPI TOLINK)
-    #We only want to try to find MPI outrselves if it wasn't provided in MPICC by user
-    if("a$ENV{MPICC}" STREQUAL "a")
-           #find_package(MPI REQUIRED)
-           target_link_libraries(${TOLINK} MPI::MPI_C)
-    endif()    
-endfunction(linkMPI)
+if(BUILD_TESTING)
+    add_subdirectory(test)
+endif()
+
+
+
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/include/fenix-config.h.in
+    ${CMAKE_CURRENT_BINARY_DIR}/include/fenix-config.h @ONLY
+)
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/systemMPIOverride.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/systemMPIOverride.cmake COPYONLY
+)
 
-add_subdirectory(src)
 
 include(CMakePackageConfigHelpers)
-configure_package_config_file(fenixConfig.cmake.in
-                              ${CMAKE_CURRENT_BINARY_DIR}/fenixConfig.cmake
+configure_package_config_file(cmake/fenixConfig.cmake.in
+                              ${CMAKE_CURRENT_BINARY_DIR}/cmake/fenixConfig.cmake
                               INSTALL_DESTINATION cmake)
-write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/fenixConfigVersion.cmake
+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/cmake/fenixConfigVersion.cmake
                                  VERSION "${FENIX_VERSION_MAJOR}.${FENIX_VERSION_MINOR}"
                                  COMPATIBILITY SameMajorVersion)
 install(
     FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/fenixConfig.cmake
-    ${CMAKE_CURRENT_BINARY_DIR}/fenixConfigVersion.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/fenixConfig.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/systemMPIOverride.cmake
     DESTINATION cmake
 )
-
-
-include(CTest)
-
-if(BUILD_EXAMPLES)
-    add_subdirectory(examples/01_hello_world/fenix)
-    add_subdirectory(examples/01_hello_world/mpi)
-    add_subdirectory(examples/02_send_recv/fenix)
-    add_subdirectory(examples/02_send_recv/mpi)
-    add_subdirectory(examples/03_reduce/fenix)
-    #add_subdirectory(examples/03_reduce/mpi)
-    add_subdirectory(examples/04_Isend_Irecv/fenix)
-    add_subdirectory(examples/04_Isend_Irecv/mpi)
-    add_subdirectory(examples/05_subset_create)
-    add_subdirectory(examples/06_subset_createv)
-
-elseif(BUILD_TESTING)
-    #Some examples are useful tests as well.
-    add_subdirectory(examples/01_hello_world/fenix)
-    add_subdirectory(examples/02_send_recv/fenix)
-    add_subdirectory(examples/03_reduce/fenix)
-    add_subdirectory(examples/05_subset_create)
-    add_subdirectory(examples/06_subset_createv)
-endif()
-
-if(BUILD_TESTING)
-    add_subdirectory(test/subset_internal)
-    add_subdirectory(test/subset_merging)
-    add_subdirectory(test/request_tracking)
-    add_subdirectory(test/request_cancelled)
-    add_subdirectory(test/no_jump)
-    add_subdirectory(test/issend)
-endif()

README.md

@@ -17,17 +17,16 @@
 These instructions assume you are in your home directory.
 
 1. Checkout Fenix sources
-   * For example: ` git clone <address of this repo> `
+   * For example: ` git clone <address of this repo> && cd Fenix`
 2. Create a build directory.
-   * For example: ` mkdir -p ~/build/fenix/ && cd ~/build/fenix/ `
 3. Specify the MPI C compiler to use. [Open MPI 5+](https://github.com/open-mpi/ompi/tree/v5.0.x) is the required version.
-   * To manually indicate which compiler `cmake` should use, set the `MPICC` variable to point to it.
-      * For example: ` export MPICC=~/install/mpi-ulfm/bin/mpicc `
-   * If the `MPICC` environment variable is not there, `cmake` will try to guess where the MPI implementation is. To help, make sure you include the installation directory of MPI in your `PATH`.
-      * For example: ` export PATH=~/install/mpi-ulfm/bin:$PATH `
-4. Run ` cmake <Fenix source directory> ` and ` make `
-   * For example: ` cmake ~/Fenix && make `
-5. For best compatibility with other cmake projects, run ` make install ` and add the install directory to your CMAKE\_PREFIX\_PATH
+   * Check out the CMake documentation for the best information on how to do this, but in general:
+      * Set the CC environment variable to the correct `mpicc`,
+      * Invoke cmake with `-DCMAKE_C_COMPILER=mpicc`,
+      * Add the mpi install directory to CMAKE_PREFIX_PATH.
+   * If you experience segmentation faults during simple MPI function calls, this is often caused by accidentally building against multiple versions of MPI. See the FENIX_SYSTEM_INC_FIX CMake option for a potential fix.
+4. Run ` cmake ../ -DCMAKE_INSTALL_PREFIX=... && make install`
+5. Optionally, add the install prefix to your CMAKE\_PREFIX\_PATHS environment variable, to enable `find_package(fenix)` in your other projects.
 
 
 <pre>