Upgrade base image to Focal

GitHub is sunsetting Bionic.

Signed-off-by: Nicolas Bock <nicolasbock@gmail.com>

.github/workflows/CI.yaml

@@ -23,12 +23,12 @@ env:
 jobs:
   lint:
     name: Lint sources
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
       - name: Check out sources
         uses: actions/checkout@v3
       - name: Prepare container
-        run: ./scripts/prepare-container-bionic.sh
+        run: ./scripts/prepare-container-focal.sh
       - run: bundle install
       - run: bundle exec danger || true
       - run: BML_OPENMP=no EMACS=emacs27 ./build.sh --debug check_indent
@@ -42,12 +42,12 @@ jobs:
 
   docs:
     name: Build docs
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
       - name: Check out sources
         uses: actions/checkout@v3
       - name: Prepare container
-        run: ./scripts/prepare-container-bionic.sh
+        run: ./scripts/prepare-container-focal.sh
       - name: Build docs
         run: ./build.sh --debug docs
 
@@ -90,27 +90,11 @@ jobs:
 
   build:
     name: Build and test the library (${{ matrix.JOBNAME }})
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
         include:
-          - JOBNAME: gcc-4.8 C single real
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-C-single-real.sh
-          - JOBNAME: gcc-4.8 C double real
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-C-double-real.sh
-          - JOBNAME: gcc-4.8 C single complex
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-C-single-complex.sh
-          - JOBNAME: gcc-4.8 C double complex
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-C-double-complex.sh
-          - JOBNAME: gcc-4.8 Fortran single real
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-Fortran-single-real.sh
-          - JOBNAME: gcc-4.8 Fortran double real
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-Fortran-double-real.sh
-          - JOBNAME: gcc-4.8 Fortran single complex
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-Fortran-single-complex.sh
-          - JOBNAME: gcc-4.8 Fortran double complex
-            TEST_SCRIPT: ./scripts/ci-gcc-4.8-Fortran-double-complex.sh
           - JOBNAME: gcc-11 C single real
             TEST_SCRIPT: ./scripts/ci-gcc-11-C-single-real.sh
           - JOBNAME: gcc-11 C double real
@@ -147,21 +131,21 @@ jobs:
             TEST_SCRIPT: ./scripts/ci-MPI-single-complex.sh
           - JOBNAME: MPI double complex
             TEST_SCRIPT: ./scripts/ci-MPI-double-complex.sh
-          - JOBNAME: clang-12 / gfortran-11 C single real
-            TEST_SCRIPT: ./scripts/ci-clang-12-gfortran-11-C-single-real.sh
-          - JOBNAME: clang-12 / gfortran-11 C double real
-            TEST_SCRIPT: ./scripts/ci-clang-12-gfortran-11-C-double-real.sh
-          - JOBNAME: clang-12 / gfortran-11 C single complex
-            TEST_SCRIPT: ./scripts/ci-clang-12-gfortran-11-C-single-complex.sh
-          - JOBNAME: clang-12 / gfortran-11 C double complex
-            TEST_SCRIPT: ./scripts/ci-clang-12-gfortran-11-C-double-complex.sh
+          - JOBNAME: clang-16 / gfortran-11 C single real
+            TEST_SCRIPT: ./scripts/ci-clang-16-gfortran-11-C-single-real.sh
+          - JOBNAME: clang-16 / gfortran-11 C double real
+            TEST_SCRIPT: ./scripts/ci-clang-16-gfortran-11-C-double-real.sh
+          - JOBNAME: clang-16 / gfortran-11 C single complex
+            TEST_SCRIPT: ./scripts/ci-clang-16-gfortran-11-C-single-complex.sh
+          - JOBNAME: clang-16 / gfortran-11 C double complex
+            TEST_SCRIPT: ./scripts/ci-clang-16-gfortran-11-C-double-complex.sh
     steps:
       - name: Check out sources
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Prepare container
-        run: ./scripts/prepare-container-bionic.sh
+        run: ./scripts/prepare-container-focal.sh
       - name: Build and test library
         env:
           BLAS_VENDOR: ${{ matrix.BLAS_VENDOR || env.BLAS_VENDOR }}

build.sh

@@ -34,7 +34,7 @@ compile         - Compile the sources
 install         - Install the compiled sources
 testing         - Run the test suite
 docs            - Generate the API documentation
-indent          - Check the indentation of the sources
+indent          - Indent sources
 check_indent    - Check the indentation of the sources
 tags            - Create tags file for vim and emacs
 dist            - Generate a tar file (this only works with git)
@@ -315,9 +315,9 @@ testing() {
     cd "${TOP_DIR}"
 }
 
-check_indent() {
+indent() {
     cd "${TOP_DIR}"
-    "${TOP_DIR}/scripts/indent.sh" 2>&1 | tee -a "${LOG_FILE}"
+    "${TOP_DIR}/scripts/indent.sh" "$@" 2>&1 | tee -a "${LOG_FILE}"
     check_pipe_error
 }
 
@@ -399,10 +399,10 @@ if [[ $# -gt 0 ]]; then
                 docs
                 ;;
             "indent")
-                check_indent
+                indent
                 ;;
             "check_indent")
-                check_indent
+                indent check
                 ;;
             "tags")
                 tags

scripts/ci-MPI-double-complex.sh

@@ -14,6 +14,7 @@ export BML_MPI=${BML_MPI:-yes}
 export TESTING_EXTRA_ARGS=${TESTING_EXTRA_ARGS:-"-R MPI-C-.*-double_complex"}
 export BML_SCALAPACK=${BML_SCALAPACK:-yes}
 export SCALAPACK_LIBRARIES=${SCALAPACK_LIBRARIES:=scalapack-openmpi.so}
+export BML_MPIEXEC_PREFLAGS=--oversubscribe
 
 [[ -f ${basedir}/scripts/ci-defaults.sh ]] && . ${basedir}/scripts/ci-defaults.sh
 

scripts/ci-MPI-double-real.sh

@@ -14,6 +14,7 @@ export BML_MPI=${BML_MPI:-yes}
 export TESTING_EXTRA_ARGS=${TESTING_EXTRA_ARGS:-"-R MPI-C-.*-double_real"}
 export BML_SCALAPACK=${BML_SCALAPACK:-yes}
 export SCALAPACK_LIBRARIES=${SCALAPACK_LIBRARIES:=scalapack-openmpi.so}
+export BML_MPIEXEC_PREFLAGS=--oversubscribe
 
 [[ -f ${basedir}/scripts/ci-defaults.sh ]] && . ${basedir}/scripts/ci-defaults.sh
 

scripts/ci-MPI-single-complex.sh

@@ -14,6 +14,7 @@ export BML_MPI=${BML_MPI:-yes}
 export TESTING_EXTRA_ARGS=${TESTING_EXTRA_ARGS:-"-R MPI-C-.*-single_complex"}
 export BML_SCALAPACK=${BML_SCALAPACK:-yes}
 export SCALAPACK_LIBRARIES=${SCALAPACK_LIBRARIES:=scalapack-openmpi.so}
+export BML_MPIEXEC_PREFLAGS=--oversubscribe
 
 [[ -f ${basedir}/scripts/ci-defaults.sh ]] && . ${basedir}/scripts/ci-defaults.sh
 

scripts/ci-MPI-single-real.sh

@@ -14,6 +14,7 @@ export BML_MPI=${BML_MPI:-yes}
 export TESTING_EXTRA_ARGS=${TESTING_EXTRA_ARGS:-"-R MPI-C-.*-single_real"}
 export BML_SCALAPACK=${BML_SCALAPACK:-yes}
 export SCALAPACK_LIBRARIES=${SCALAPACK_LIBRARIES:=scalapack-openmpi.so}
+export BML_MPIEXEC_PREFLAGS=--oversubscribe
 
 [[ -f ${basedir}/scripts/ci-defaults.sh ]] && . ${basedir}/scripts/ci-defaults.sh
 

scripts/ci-clang-12-gfortran-11-C-double-complex.sh → scripts/ci-clang-16-gfortran-11-C-double-complex.sh

@@ -4,8 +4,8 @@ set -e -u -x
 
 basedir=$(readlink --canonicalize $(dirname $0)/..)
 
-export CC=${CC:-clang-12}
-export CXX=${CXX:-clang++-12}
+export CC=${CC:-clang-16}
+export CXX=${CXX:-clang++-16}
 export FC=${FC:-gfortran-11}
 export BUILD_SHARED_LIBS=${BUILD_SHARED_LIBS:-no}
 export BML_OPENMP=${BML_OPENMP:-no}

scripts/ci-clang-12-gfortran-11-C-double-real.sh → scripts/ci-clang-16-gfortran-11-C-double-real.sh

@@ -4,8 +4,8 @@ set -e -u -x
 
 basedir=$(readlink --canonicalize $(dirname $0)/..)
 
-export CC=${CC:-clang-12}
-export CXX=${CXX:-clang++-12}
+export CC=${CC:-clang-16}
+export CXX=${CXX:-clang++-16}
 export FC=${FC:-gfortran-11}
 export BUILD_SHARED_LIBS=${BUILD_SHARED_LIBS:-no}
 export BML_OPENMP=${BML_OPENMP:-no}

scripts/ci-clang-12-gfortran-11-C-single-complex.sh → scripts/ci-clang-16-gfortran-11-C-single-complex.sh

@@ -4,8 +4,8 @@ set -e -u -x
 
 basedir=$(readlink --canonicalize $(dirname $0)/..)
 
-export CC=${CC:-clang-12}
-export CXX=${CXX:-clang++-12}
+export CC=${CC:-clang-16}
+export CXX=${CXX:-clang++-16}
 export FC=${FC:-gfortran-11}
 export BUILD_SHARED_LIBS=${BUILD_SHARED_LIBS:-no}
 export BML_OPENMP=${BML_OPENMP:-no}

scripts/ci-clang-12-gfortran-11-C-single-real.sh → scripts/ci-clang-16-gfortran-11-C-single-real.sh

@@ -4,8 +4,8 @@ set -e -u -x
 
 basedir=$(readlink --canonicalize $(dirname $0)/..)
 
-export CC=${CC:-clang-12}
-export CXX=${CXX:-clang++-12}
+export CC=${CC:-clang-16}
+export CXX=${CXX:-clang++-16}
 export FC=${FC:-gfortran-11}
 export BUILD_SHARED_LIBS=${BUILD_SHARED_LIBS:-no}
 export BML_OPENMP=${BML_OPENMP:-no}

scripts/indent.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 : ${EMACS:=$(command -v emacs)}
-: ${INDENT_ARGS:="-gnu -nut -i4 -bli0 -cli4 -ppi0 -cbi0 -npcs -bfda"}
+: ${INDENT_ARGS:="-gnu -nut -i4 -bli0 -cli4 -ppi0 -cbi0 -npcs -bfda -par"}
 
 declare -a SH_FILES
 declare -a C_FILES
@@ -15,6 +15,14 @@ EOF
     exit 1
 fi
 
+check_only=0
+
+if (( $# > 0 )); then
+    if [[ $1 == 'check' ]]; then
+        check_only=1
+        shift
+    fi
+fi
 if (( $# > 0 )); then
     while (( $# > 0 )); do
         case "${1##*.}" in
@@ -81,9 +89,16 @@ if (( ${#FAILED_FILES[@]} > 0 )); then
         if [[ ${file} =~ .sh$ ]]; then
             echo "bashate ${file}"
             bashate "${file}"
+            if (( check_only == 0 )); then
+                mv "${file}" "${file}.backup"
+                bashat "${file}.backup" > "${file}"
+            fi
         else
             echo "diff -Naur ${file} ${file}.indented"
             diff -Naur "${file}" "${file}".indented
+            if (( check_only == 0 )); then
+                mv "${file}.indented" "${file}"
+            fi
         fi
     done
     echo

scripts/prepare-container-focal.sh

@@ -24,28 +24,43 @@ deb http://apt.llvm.org/focal/ llvm-toolchain-focal-11 main
 # 12
 deb http://apt.llvm.org/focal/ llvm-toolchain-focal-12 main
 # deb-src http://apt.llvm.org/focal/ llvm-toolchain-focal-12 main
+# 13
+deb http://apt.llvm.org/focal/ llvm-toolchain-focal-13 main
+# deb-src http://apt.llvm.org/focal/ llvm-toolchain-focal-13 main
+# 14
+deb http://apt.llvm.org/focal/ llvm-toolchain-focal-14 main
+# deb-src http://apt.llvm.org/focal/ llvm-toolchain-focal-14 main
+# 15
+deb http://apt.llvm.org/focal/ llvm-toolchain-focal-15 main
+# deb-src http://apt.llvm.org/focal/ llvm-toolchain-focal-15 main
+# 16
+deb http://apt.llvm.org/focal/ llvm-toolchain-focal-16 main
+# deb-src http://apt.llvm.org/focal/ llvm-toolchain-focal-16 main
 EOF
-${SUDO} cat > /etc/apt/trusted.gpg.d/llvm.gpg < <(wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | gpg --dearmor)
+wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | ${SUDO} tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
 
-cat <<EOF | ${SUDO} tee /etc/apt/sources.list.d/toolchain.list
-deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu focal main
-# deb-src http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu focal main
+if ! apt-cache policy | grep --quiet toolchain; then
+    cat <<EOF | ${SUDO} tee /etc/apt/sources.list.d/toolchain.list
+    deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu focal main
+    # deb-src http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu focal main
 EOF
-gpg --keyserver keyserver.ubuntu.com \
-    --recv-keys 60C317803A41BA51845E371A1E9377A2BA9EF27F
-${SUDO} cat > /etc/apt/trusted.gpg.d/toolchain.gpg < <(gpg --export 60C317803A41BA51845E371A1E9377A2BA9EF27F)
+    gpg --keyserver keyserver.ubuntu.com \
+        --recv-keys 60C317803A41BA51845E371A1E9377A2BA9EF27F
+    gpg --armor --export 60C317803A41BA51845E371A1E9377A2BA9EF27F | ${SUDO} tee /etc/apt/trusted.gpg.d/toolchain.asc
+fi
 
 cat <<EOF | ${SUDO} tee /etc/apt/sources.list.d/emacs.list
 deb http://ppa.launchpad.net/kelleyk/emacs/ubuntu focal main
 # deb-src http://ppa.launchpad.net/kelleyk/emacs/ubuntu focal main
 EOF
 gpg --keyserver keyserver.ubuntu.com \
     --recv-keys 873503A090750CDAEB0754D93FF0E01EEAAFC9CD
-${SUDO} cat > /etc/apt/trusted.gpg.d/emacs.gpg < <(gpg --export 873503A090750CDAEB0754D93FF0E01EEAAFC9CD)
+gpg --armor --export 873503A090750CDAEB0754D93FF0E01EEAAFC9CD | ${SUDO} tee /etc/apt/trusted.gpg.d/emacs.asc
 
 apt-key list
 
 for i in $(seq 5); do
+    echo "Attempt ${i} to update apt"
     ${SUDO} apt-get update && break
 done
 
@@ -61,15 +76,12 @@ ${SUDO} apt-get install --assume-yes --no-install-recommends \
     bundler \
     cmake cmake-data \
     emacs27 \
-    clang-12 llvm-12-dev libomp-12-dev \
-    gcc-9 g++-9 gfortran-9 \
-    gcc-10 g++-10 gfortran-10 \
-    gcc-11 g++-11 gfortran-11 \
     git-core \
     indent \
     less \
     libblas-dev liblapack-dev \
     libscalapack-openmpi-dev \
+    libopenblas-dev \
     mpi-default-dev \
     openmpi-bin \
     openssh-client \
@@ -79,4 +91,16 @@ ${SUDO} apt-get install --assume-yes --no-install-recommends \
     valgrind \
     vim
 
+${SUDO} apt-get remove --purge 'libomp*' || echo "no previous clang installation found"
+
+dpkg -l 'libomp*'
+
+${SUDO} apt-get install --assume-yes --no-install-recommends \
+    clang-16 llvm-16-dev libomp-16-dev
+
+${SUDO} apt-get install --assume-yes --no-install-recommends \
+    gcc-9 g++-9 gfortran-9 \
+    gcc-10 g++-10 gfortran-10 \
+    gcc-11 g++-11 gfortran-11
+
 ${SUDO} pip install --system bashate