Merge pull request #89 from vanderhe/hdf5Support1.14.x

Add support for HDF5 1.14.x

Author: vanderhe

.github/workflows/build.yml

@@ -107,17 +107,12 @@ jobs:
         os: [ubuntu-latest]
         mpi: [nompi]
         socket: [nosocket, socket]
-        fc: [ifort]
+        fc: [ifx]
         cc: [icx]
     env:
       FC: ${{ matrix.fc }}
       CC: ${{ matrix.cc }}
       WITH_MPI: false
-      APT_PACKAGES: >-
-        intel-oneapi-compiler-fortran
-        intel-oneapi-compiler-dpcpp-cpp
-        intel-oneapi-mkl
-        intel-oneapi-mkl-devel
       CMAKE_OPTIONS: >-
         -DCMAKE_BUILD_TYPE=RelWithDebInfo
         -DFYPP_FLAGS='-DTRAVIS'
@@ -131,34 +126,28 @@ jobs:
       with:
         python-version: 3.x
 
-    - name: Add Intel repository
-      if: contains(matrix.os, 'ubuntu')
-      run: |
-        wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
-        echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
-        sudo apt-get update
+    - name: Setup Intel compiler
+      uses: rscohn2/setup-oneapi@v0
+      with:
+        components: |
+          [email protected]
+          [email protected]
+          [email protected]
 
-    - name: Install Intel oneAPI compiler
-      if: contains(matrix.os, 'ubuntu')
+    - name: Setup Intel environment
       run: |
-        sudo apt-get update
-        sudo apt-get install ${APT_PACKAGES}
         source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+        printenv >> ${GITHUB_ENV}
+        echo "FC=ifx" >> ${GITHUB_ENV}
+        echo "CC=icx" >> ${GITHUB_ENV}
 
-    - name: Install HDF5 (gcc)
-      if: contains(matrix.os, 'ubuntu')
-      run: |
-        sudo apt-get update
-        sudo apt-get install hdf5-tools libhdf5-dev libhdf5-103
-
-    - name: Install HDF5 (intel)
+    - name: Install HDF5
       if: contains(matrix.os, 'ubuntu')
       run: |
-        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/CMake-hdf5-1.13.2.tar.gz
-        tar xfz CMake-hdf5-1.13.2.tar.gz
-        cd CMake-hdf5-1.13.2/hdf5-1.13.2/
-        CC=icx CXX=icx FC=ifort F9X=ifort ./configure --prefix=${PWD}/hdf5 --enable-fortran --with-default-api-version=v110 --enable-shared
+        wget https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/downloads/hdf5-1.14.4-3.tar.gz
+        tar xfz hdf5-1.14.4-3.tar.gz
+        cd hdf5-1.14.4-3/
+        CC=icx CXX=icx FC=ifx F9X=ifx ./configure --prefix=${PWD}/hdf5 --enable-fortran --enable-shared
         make -j -l2
         make install
         export HDF5_ROOT=${PWD}/hdf5
@@ -169,7 +158,7 @@ jobs:
       if: contains(matrix.mpi, 'nompi')
       run: |
         echo "WITH_MPI=false" >> $GITHUB_ENV
-        echo "FC=ifort" >> $GITHUB_ENV
+        echo "FC=ifx" >> $GITHUB_ENV
 
     - name: Enable socket build
       if: contains(matrix.socket, 'socket')
@@ -198,7 +187,7 @@ jobs:
     - name: Run regression tests
       run: |
         pushd ${BUILD_DIR}
-        ctest -j 2 --output-on-failure
+        ctest -j2 --output-on-failure
         popd
 
     - name: Install project

prog/fortnet/lib_descriptors/acsf.F90

@@ -11,7 +11,6 @@
 module fnet_acsf
 
   use h5lt
-  use hdf5
 
   use dftbp_accuracy, only : dp
   use dftbp_message, only : error
@@ -1780,9 +1779,6 @@ subroutine TAcsf_toFile(this, fname)
     !! auxiliary variables
     integer :: iFunc, iErr, tmp, tExist
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the netstat file
     call h5fopen_f(fname, H5F_ACC_RDWR_F, file_id, iErr)
 
@@ -1905,9 +1901,6 @@ subroutine TAcsf_toFile(this, fname)
     ! close the netstat file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
   end subroutine TAcsf_toFile
 
 
@@ -1944,9 +1937,6 @@ subroutine TAcsf_fromFile(this, fname, tReduce, tStandardize, nRadial, nAngular)
     real(dp), allocatable :: tmpRealArray1d(:)
     integer :: iFunc, iErr, tExist, tmpInt(1)
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the netstat file
     call h5fopen_f(fname, H5F_ACC_RDONLY_F, file_id, iErr)
 
@@ -2118,9 +2108,6 @@ subroutine TAcsf_fromFile(this, fname, tReduce, tStandardize, nRadial, nAngular)
     ! close the netstat file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
     nRadial = 0
     nAngular = 0
     allocate(tmpAtomicNumbers(0))

prog/fortnet/lib_fortnet/initprogram.F90

@@ -594,7 +594,7 @@ subroutine readDriverBlock(driver, analysis, driverNode, parent)
 
     type(fnode), pointer :: child, child2, child3, child4,  value1, field
 
-    type(string) :: buffer, buffer2, modifier
+    type(string) :: buffer, buffer2
 
     !! string buffer instance
     type(string) :: strBuffer

prog/fortnet/lib_io/fnetdata.F90

@@ -11,7 +11,6 @@
 module fnet_fnetdata
 
   use h5lt
-  use hdf5
 
   use dftbp_assert
   use dftbp_accuracy, only: dp, mc
@@ -557,9 +556,6 @@ subroutine inquireStructures(fname, tStructures)
     !! auxiliary variable
     integer :: iErr
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the dataset file
     call h5fopen_f(fname, H5F_ACC_RDONLY_F, file_id, iErr)
 
@@ -573,9 +569,6 @@ subroutine inquireStructures(fname, tStructures)
     ! close the dataset file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
   end subroutine inquireStructures
 
 
@@ -606,9 +599,6 @@ subroutine inquireTargets(fname, tGlobalTargets, tAtomicTargets, nGlobalTargets,
     !! auxiliary variables
     integer :: iErr
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the dataset file
     call h5fopen_f(fname, H5F_ACC_RDONLY_F, file_id, iErr)
 
@@ -639,9 +629,6 @@ subroutine inquireTargets(fname, tGlobalTargets, tAtomicTargets, nGlobalTargets,
     ! close the dataset file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
   end subroutine inquireTargets
 
 
@@ -666,9 +653,6 @@ subroutine inquireExtFeatures(fname, tFeatures, nFeatures)
     !! auxiliary variables
     integer :: iErr
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the dataset file
     call h5fopen_f(fname, H5F_ACC_RDONLY_F, file_id, iErr)
 
@@ -687,9 +671,6 @@ subroutine inquireExtFeatures(fname, tFeatures, nFeatures)
     ! close the dataset file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
   end subroutine inquireExtFeatures
 
 
@@ -1033,9 +1014,6 @@ subroutine readHdfDataset(fname, dataset)
     !! auxiliary variables
     integer :: iErr, iDatapoint, tExist
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! open the dataset file
     call h5fopen_f(fname, H5F_ACC_RDONLY_F, file_id, iErr)
 
@@ -1232,9 +1210,6 @@ subroutine readHdfDataset(fname, dataset)
     ! close the dataset file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
     ! perform some basic consistency checks
     call dataset%checkConsistency()
 

prog/fortnet/lib_io/fnetout.F90

@@ -11,7 +11,6 @@
 module fnet_fnetout
 
   use h5lt
-  use hdf5
 
   use dftbp_message, only : error
   use dftbp_accuracy, only: dp
@@ -75,9 +74,6 @@ subroutine writeFnetout(fname, mode, globalTargets, atomicTargets, output, force
       call error('Validation mode only valid in combination with target data.')
     end if
 
-    ! open the hdf5 interface
-    call h5open_f(iErr)
-
     ! create the fnetout file
     call h5fcreate_f(fname, H5F_ACC_TRUNC_F, file_id, iErr)
 
@@ -159,9 +155,6 @@ subroutine writeFnetout(fname, mode, globalTargets, atomicTargets, output, force
     ! close the fnetout file
     call h5fclose_f(file_id, iErr)
 
-    ! close the hdf5 interface
-    call h5close_f(iErr)
-
   end subroutine writeFnetout
 
 end module fnet_fnetout