Metapackages: pkg_config backend support; HDF5

.github/workflows/meta.yml

@@ -67,6 +67,7 @@ jobs:
           wget
           unzip
           curl
+          hdf5
 
     - name: (Windows) Setup VS Build environment
       if: contains(matrix.os,'windows') && contains(matrix.mpi,'intel')
@@ -93,12 +94,12 @@ jobs:
     - name: (Ubuntu) Install OpenMPI
       if: contains(matrix.os,'ubuntu') && contains(matrix.mpi,'openmpi')
       run: |
-        sudo apt install -y -q openmpi-bin libopenmpi-dev
+        sudo apt install -y -q openmpi-bin libopenmpi-dev hwloc fabric libhdf5-dev libhdf5-fortran-102
 
     - name: (Ubuntu) Install MPICH
       if: contains(matrix.os,'ubuntu') && contains(matrix.mpi,'mpich')
       run: |
-        sudo apt install -y -q mpich
+        sudo apt install -y -q mpich hwloc fabric libhdf5-dev libhdf5-fortran-102
 
     - name: (Ubuntu) Retrieve Intel toolchain
       if: contains(matrix.os,'ubuntu') && contains(matrix.mpi,'intel')
@@ -110,14 +111,27 @@ jobs:
 
     - name: (Ubuntu) Install Intel oneAPI
       if: contains(matrix.os,'ubuntu') && contains(matrix.mpi,'intel')
-      timeout-minutes: 15
-      run: sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-2023.1.0 intel-oneapi-compiler-fortran-2023.1.0 intel-oneapi-mpi-devel ninja-build
+      uses: fortran-lang/[email protected]
+      id: setup-fortran
+      with:
+        compiler: intel 
+        version: 2024.1.0 
 
-    - name: (Ubuntu) Setup Intel oneAPI environment
+    - name: (Ubuntu) finalize oneAPI environment 
       if: contains(matrix.os,'ubuntu') && contains(matrix.mpi,'intel')
       run: |
-        source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+        # Install MPI
+        sudo apt-get install -y -q intel-oneapi-mpi-devel ninja-build cmake
+        source /opt/intel/oneapi/setvars.sh --force
+        printenv >> $GITHUB_ENV        
+        # To run HDF5 with oneAPI, we need to build it from source. Use CMake to generate pkg-config info
+        curl -O -L https://github.com/HDFGroup/hdf5/archive/refs/tags/snapshot-1.14.tar.gz
+        tar zxf snapshot-1.14.tar.gz
+        cd hdf5-snapshot-1.14
+        cmake -B build -DCMAKE_Fortran_COMPILER=ifx -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DHDF5_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/usr
+        cd build
+        make -j
+        sudo make install
 
     - name: (Windows) Put MSYS2_MinGW64 on PATH
       if: contains(matrix.os,'windows') && (!contains(matrix.mpi,'intel'))
@@ -197,6 +211,11 @@ jobs:
       run: |
         brew install openmpi #--cc=gcc-${{ env.GCC_V }} openmpi
 
+    - name: (macOS) Install homebrew HDF5
+      if: contains(matrix.os,'macos')
+      run: | 
+        brew install hdf5 
+
     # Phase 1: Bootstrap fpm with existing version
     - name: Install fpm
       uses: fortran-lang/setup-fpm@v5
@@ -209,8 +228,8 @@ jobs:
         mv $(which fpm) fpm-bootstrap${{ matrix.exe }}
         echo "BOOTSTRAP=$PWD/fpm-bootstrap" >> $GITHUB_ENV
 
-    - name: (macOS) Use gcc/g++ instead of Clang for C/C++
-      if: contains(matrix.os,'macOS')
+    - name: (macOS/Ubuntu) Use gcc/g++ instead of Clang for C/C++ / ifx to build fpm
+      if: contains(matrix.os,'macOS') || contains(matrix.os,'ubuntu')
       shell: bash
       run: |
         echo "FPM_FC=gfortran-${{ env.GCC_V }}" >> $GITHUB_ENV

ci/meta_tests.sh

@@ -42,5 +42,10 @@ pushd metapackage_mpi_c
 "$fpm" run --verbose
 popd
 
+pushd metapackage_hdf5
+"$fpm" build --verbose 
+"$fpm" run --verbose
+popd
+
 # Cleanup
 rm -rf ./*/build

example_packages/metapackage_hdf5/app/main.f90

@@ -0,0 +1,15 @@
+program metapackage_hdf5
+  use hdf5
+  implicit none
+
+  integer :: error
+
+  call h5open_f(error)
+  if (error/=0) stop -1
+
+  call h5close_f(error)
+  if (error/=0) stop -2
+
+  stop 0
+
+end program metapackage_hdf5

example_packages/metapackage_hdf5/fpm.toml

@@ -0,0 +1,2 @@
+name = "metapackage_hdf5"
+dependencies.hdf5="*"

src/fpm/manifest/meta.f90

@@ -48,6 +48,9 @@ module fpm_manifest_metapackages
 
         !> fortran-lang minpack
         type(metapackage_request_t) :: minpack
+
+        !> HDF5
+        type(metapackage_request_t) :: hdf5
 
     end type metapackage_config_t
 
@@ -196,6 +199,9 @@ subroutine new_meta_config(self, table, meta_allowed, error)
 
         call new_meta_request(self%mpi, "mpi", table, meta_allowed, error)
         if (allocated(error)) return
+
+        call new_meta_request(self%hdf5, "hdf5", table, meta_allowed, error)
+        if (allocated(error)) return
 
     end subroutine new_meta_config
 
@@ -208,7 +214,7 @@ logical function is_meta_package(key)
         select case (key)
 
             !> Supported metapackages
-            case ("openmp","stdlib","mpi","minpack")
+            case ("openmp","stdlib","mpi","minpack","hdf5")
                 is_meta_package = .true.
 
             case default

src/fpm/manifest/profiles.f90

@@ -749,25 +749,25 @@ function get_default_profiles(error) result(default_profiles)
                 & 'ifort', &
                 & OS_ALL, &
                 & flags = ' -fp-model precise -pc64 -align all -error-limit 1 -reentrancy&
-                          & threaded -nogen-interfaces -assume byterecl -standard-semantics', &
+                          & threaded -nogen-interfaces -assume byterecl', &
                 & is_built_in=.true.), &
               & new_profile('release', &
                 & 'ifort', &
                 & OS_WINDOWS, &
                 & flags = ' /fp:precise /align:all /error-limit:1 /reentrancy:threaded&
-                          & /nogen-interfaces /assume:byterecl /standard-semantics', &
+                          & /nogen-interfaces /assume:byterecl', &
                 & is_built_in=.true.), &
               & new_profile('release', &
                 & 'ifx', &
                 & OS_ALL, &
                 & flags = ' -fp-model=precise -pc64 -align all -error-limit 1 -reentrancy&
-                          & threaded -nogen-interfaces -assume byterecl -standard-semantics', &
+                          & threaded -nogen-interfaces -assume byterecl', &
                 & is_built_in=.true.), &
               & new_profile('release', &
                 & 'ifx', &
                 & OS_WINDOWS, &
                 & flags = ' /fp:precise /align:all /error-limit:1 /reentrancy:threaded&
-                          & /nogen-interfaces /assume:byterecl /standard-semantics', &
+                          & /nogen-interfaces /assume:byterecl', &
                 & is_built_in=.true.), &
               & new_profile('release', &
                 &'nagfor', &
@@ -805,28 +805,28 @@ function get_default_profiles(error) result(default_profiles)
               & new_profile('debug', &
                 & 'ifort', &
                 & OS_ALL, &
-                & flags = ' -warn all -check all -error-limit 1 -O0 -g -assume byterecl -standard-semantics -traceback', &
+                & flags = ' -warn all -check all -error-limit 1 -O0 -g -assume byterecl -traceback', &
                 & is_built_in=.true.), &
               & new_profile('debug', &
                 & 'ifort', &
                 & OS_WINDOWS, &
                 & flags = ' /warn:all /check:all /error-limit:1&
-                          & /Od /Z7 /assume:byterecl /standard-semantics /traceback', &
+                          & /Od /Z7 /assume:byterecl /traceback', &
                 & is_built_in=.true.), &
               & new_profile('debug', &
                 & 'ifx', &
                 & OS_ALL, &
-                & flags = ' -warn all -check all -error-limit 1 -O0 -g -assume byterecl -standard-semantics -traceback', &
+                & flags = ' -warn all -check all -error-limit 1 -O0 -g -assume byterecl -traceback', &
                 & is_built_in=.true.), &
               & new_profile('debug', &
                 & 'ifx', &
                 & OS_WINDOWS, &
-                & flags = ' /warn:all /check:all /error-limit:1 /Od /Z7 /assume:byterecl /standard-semantics', &
+                & flags = ' /warn:all /check:all /error-limit:1 /Od /Z7 /assume:byterecl', &
                 & is_built_in=.true.), &
               & new_profile('debug', &
                 & 'ifx', &
                 & OS_WINDOWS, &
-                & flags = ' /warn:all /check:all /error-limit:1 /Od /Z7 /assume:byterecl /standard-semantics', &
+                & flags = ' /warn:all /check:all /error-limit:1 /Od /Z7 /assume:byterecl', &
                 & is_built_in=.true.), &
               & new_profile('debug', &
                 & 'lfortran', &

src/fpm_compiler.F90

@@ -309,8 +309,7 @@ subroutine get_release_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_pthread//&
             flag_intel_nogen//&
-            flag_intel_byterecl//&
-            flag_intel_standard_compliance
+            flag_intel_byterecl
 
     case(id_intel_classic_mac)
         flags = &
@@ -320,8 +319,7 @@ subroutine get_release_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_pthread//&
             flag_intel_nogen//&
-            flag_intel_byterecl//&
-            flag_intel_standard_compliance
+            flag_intel_byterecl
 
     case(id_intel_classic_windows)
         flags = &
@@ -331,8 +329,7 @@ subroutine get_release_compile_flags(id, flags)
             flag_intel_limit_win//&
             flag_intel_pthread_win//&
             flag_intel_nogen_win//&
-            flag_intel_byterecl_win//&
-            flag_intel_standard_compliance_win
+            flag_intel_byterecl_win
 
     case(id_intel_llvm_nix)
         flags = &
@@ -342,8 +339,7 @@ subroutine get_release_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_pthread//&
             flag_intel_nogen//&
-            flag_intel_byterecl//&
-            flag_intel_standard_compliance
+            flag_intel_byterecl
 
     case(id_intel_llvm_windows)
         flags = &
@@ -353,8 +349,7 @@ subroutine get_release_compile_flags(id, flags)
             flag_intel_limit_win//&
             flag_intel_pthread_win//&
             flag_intel_nogen_win//&
-            flag_intel_byterecl_win//&
-            flag_intel_standard_compliance_win
+            flag_intel_byterecl_win
 
     case(id_nag)
         flags = &
@@ -418,7 +413,6 @@ subroutine get_debug_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_debug//&
             flag_intel_byterecl//&
-            flag_intel_standard_compliance//&
             flag_intel_backtrace
 
     case(id_intel_classic_mac)
@@ -428,7 +422,6 @@ subroutine get_debug_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_debug//&
             flag_intel_byterecl//&
-            flag_intel_standard_compliance//&
             flag_intel_backtrace
     case(id_intel_classic_windows)
         flags = &
@@ -437,7 +430,6 @@ subroutine get_debug_compile_flags(id, flags)
             flag_intel_limit_win//&
             flag_intel_debug_win//&
             flag_intel_byterecl_win//&
-            flag_intel_standard_compliance_win//&
             flag_intel_backtrace_win
     case(id_intel_llvm_nix)
         flags = &
@@ -446,16 +438,14 @@ subroutine get_debug_compile_flags(id, flags)
             flag_intel_limit//&
             flag_intel_debug//&
             flag_intel_byterecl//&
-            flag_intel_standard_compliance//&
             flag_intel_backtrace
     case(id_intel_llvm_windows)
         flags = &
             flag_intel_warn_win//&
             flag_intel_check_win//&
             flag_intel_limit_win//&
             flag_intel_debug_win//&
-            flag_intel_byterecl_win//&
-            flag_intel_standard_compliance_win
+            flag_intel_byterecl_win
     case(id_nag)
         flags = &
             flag_nag_debug//&

src/fpm_environment.c

@@ -0,0 +1,38 @@
+#include <stdlib.h>
+#include <stdio.h>
+
+/// @brief Set environment variable using the C standard library
+/// @param envname: points to a string containing the name of an environment variable to be added or altered.
+/// @param envval: points to the value the environment variable is set to
+/// @param overwrite: flag to determine whether an old value should be overwritten
+/// @return success flag, 0 on successful execution
+int c_setenv(const char *envname, const char *envval, int overwrite) {
+#ifndef _WIN32
+   return setenv(envname, envval, overwrite);
+#else
+   int errcode = 0;
+   if(!overwrite) {
+       size_t envsize = 0;
+       errcode = getenv_s(&envsize, NULL, 0, envname);
+       if (errcode || envsize) return errcode;
+   }
+   return _putenv_s(envname, envval);
+#endif
+}
+
+/// @brief Delete environment variable using the C standard library
+/// @param envname: points to a string containing the name of an environment variable.
+/// @return success flag, 0 on successful execution
+int c_unsetenv(const char *envname) {
+#ifndef _WIN32
+   return unsetenv(envname);
+#else
+   char* str = malloc(64*sizeof(char));
+   *str = '\0';
+   int errcode = _putenv_s(envname,str);
+   // Windows returns a non-0 code when setting empty variable
+   if (errcode==-1) errcode=0;
+   free(str);
+   return errcode;
+#endif
+}