Merge pull request #14 from BerkeleyLab/netcdf-read-write-example

Netcdf read/write example

.github/workflows/CI.yml

@@ -2,35 +2,20 @@ name: CI
 
 on: [push, pull_request]
 
+
 jobs:
   Build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      matrix:
+        os: [macOS-latest]
       fail-fast: true
 
-    env:
-      FC: gfortran
-      GCC_V: 10
-
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
 
-    - name: Install Dependencies
-      run: |
-        sudo apt install -y gfortran-${GCC_V} cmake mpich
-        sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} 100
-        git clone https://github.com/sourceryinstitute/opencoarrays
-        mkdir -p opencoarrays/build
-        cd opencoarrays/build
-        cmake ..
-        sudo make -j $(nproc) install
-        cd -
-        git clone https://github.com/fortran-lang/fpm
-        cd fpm
-        ./install.sh
-
     - name: Build and Test
       run: |
         export PATH="${HOME}/.local/bin:$PATH"
-        fpm test 
+        ./setup.sh

example/netCDF_IO.f90

@@ -0,0 +1,114 @@
+program netCDF_IO
+  use netcdf, only : &
+     nf90_create, nf90_def_dim, nf90_def_var, nf90_enddef, nf90_put_var, nf90_inquire_dimension, & ! functions
+     nf90_close, nf90_open, nf90_inq_varid, nf90_get_var, nf90_inquire_variable, & 
+     nf90_clobber, nf90_noerr, nf90_strerror, nf90_int, nf90_nowrite               ! constants
+  use assert_m, only : assert
+  implicit none
+
+  integer i, j
+  integer, parameter :: ny = 12,  nx = 6
+  integer, parameter :: data_written(*,*) = reshape([((i*j, i=1,nx), j=1,ny)], [ny,nx])
+  integer, allocatable :: data_read(:,:)
+  character(len=*), parameter :: file_name = "netCDF_example.nc"
+
+  call netCDF_write(file_name, data_written)
+  call netCDF_read(file_name, data_read)
+
+  call assert(all(data_written == data_read) , "netCDF_IO: all(data_written == data_read)")
+
+  print *, "-----> netCDF file '" // file_name // "' written and read without error <-----"
+
+contains
+
+  subroutine netCDF_write(file_name_, data_out)
+    character(len=*), intent(in) :: file_name_
+    integer, intent(in) :: data_out(:,:)
+
+    integer ncid, varid, x_dimid, y_dimid
+
+    associate(nf_status => nf90_create(file_name_, nf90_clobber, ncid)) ! create or ovewrite file
+      call assert(nf_status == nf90_noerr, "nf90_create(file_name, nf90_clobber, ncid) succeeds",trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_def_dim(ncid, "x", size(data_out,2), x_dimid)) ! define x dimension & get its ID
+      call assert(nf_status == nf90_noerr,'nf90_def_dim(ncid,"x",size(data_out,2),x_dimid) succeeds',trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_def_dim(ncid, "y", size(data_out,1), y_dimid)) ! define y dimension & get its ID
+      call assert(nf_status==nf90_noerr, 'nf90_def_dim(ncid,"y",size(data_out,2),y_dimid) succeeds', trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_def_var(ncid, "data", nf90_int, [y_dimid, x_dimid], varid))!define integer 'data' variable & get ID
+      call assert(nf_status == nf90_noerr, 'nf90_def_var(ncid,"data",nf90_int,[y_dimid,x_dimid],varid) succeds', &
+        trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_enddef(ncid)) ! exit define mode: tell netCDF we are done defining metadata
+      call assert(nf_status == nf90_noerr, 'nff90_noerr == nf90_enddef(ncid)', trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_put_var(ncid, varid, data_out)) ! write all data to file
+      call assert(nf_status == nf90_noerr, 'nff90_noerr == nf90_put_var(ncid, varid, data_out)', trim(nf90_strerror(nf_status)))
+    end associate
+    associate(nf_status => nf90_close(ncid)) ! close file to free associated netCDF resources and flush buffers
+      call assert(nf_status == nf90_noerr, 'nff90_noerr == nf90_close(ncid)', trim(nf90_strerror(nf_status)))
+    end associate
+
+  end subroutine
+
+  subroutine netCDF_read(file_name_, data_in)
+    character(len=*), intent(in) :: file_name_
+    integer, intent(inout), allocatable :: data_in(:,:)
+    integer ncid, varid, data_in_rank
+
+    associate( nf_status => nf90_open(file_name_, nf90_nowrite, ncid) ) ! open file with read-only acces
+      call assert(nf_status == nf90_noerr, "nf90_open(file_name_, NF90_NOWRITE, ncid) succeeds", trim(nf90_strerror(nf_status)))
+    end associate
+
+    associate( nf_status => nf90_inq_varid(ncid, "data", varid)) ! Get data variable's ID
+      call assert(nf_status == nf90_noerr, 'nf90_inq_varid(ncid, "data", varid) succeeds', trim(nf90_strerror(nf_status)))
+    end associate
+
+    associate(data_in_shape => get_shape(ncid, "data"))
+      allocate(data_in(data_in_shape(1), data_in_shape(2)))
+    end associate
+
+    associate( nf_status => nf90_get_var(ncid, varid, data_in)) ! Read data
+      call assert(nf_status == nf90_noerr, "nf90_get_var(ncid, varid, data_in) succeeds", trim(nf90_strerror(nf_status)))
+    end associate
+
+  end subroutine
+
+  function get_shape(ncid, varname) result(array_shape)
+    implicit none
+    character(len=*), intent(in) :: varname
+    integer, intent(in) :: ncid
+    integer, allocatable :: array_shape(:)
+    character(len=32) varid_string
+
+    integer varid, dimlen, i, var_rank
+    integer, parameter :: max_rank=15
+    integer,dimension(max_rank+1) :: dims, dimIds
+
+    associate(nf_status => nf90_inq_varid(ncid, varname, varid))
+      write(varid_string, *) varid
+      call assert(nf_status == nf90_noerr, "nf90_noerr == nf90_inq_varid(ncid, varname, varid) (" // &
+        trim(nf90_strerror(nf_status)) // "(" // trim(varid_string)// ")")
+    end associate
+    associate(nf_status => nf90_inquire_variable(ncid, varid, ndims = var_rank))
+      call assert(nf_status == nf90_noerr, "nf90_noerr == nf90_inquire_variable(ncid, varid, ndims = var_rank) (" // &
+        trim(nf90_strerror(nf_status)) // "(" // varname // ")")
+    end associate
+    associate(nf_status => nf90_inquire_variable(ncid, varid, dimids = dimIds(:var_rank)))
+      call assert(nf_status == nf90_noerr, "nf90_noerr == nf90_inquire_variable(ncid, varid, dimids = dimIds(:var_rank))", &
+        trim(nf90_strerror(nf_status)) // "(" // varname // ")")
+    end associate
+
+    do i=1,var_rank
+      associate(nf_status => nf90_inquire_dimension(ncid, dimIds(i), len = dimlen))
+        call assert(nf_status == nf90_noerr, "nf90_noerr == nf90_inquire_dimension(ncid, dimIds(i), len = dimlen)", &
+          trim(nf90_strerror(nf_status)) // "(" // varname // ")")
+      end associate
+      dims(i+1)=dimlen
+    end do
+
+    array_shape = dims(2:var_rank+1)
+  end function 
+
+end program netCDF_IO

fpm.toml

@@ -7,3 +7,4 @@ maintainer = "[email protected]"
 [dependencies]
 assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.4.0"}
 sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "3.5.0"}
+netcdf-interfaces = {git = "https://github.com/LKedward/netcdf-interfaces.git"}

setup.sh

@@ -0,0 +1,165 @@
+#!/bin/sh
+
+set -e # exit on error
+
+usage()
+{
+  echo "Inference Engine Setup Script"
+  echo ""
+  echo "USAGE:"
+  echo "./setup.sh [--help|-h] | [-p|--prefix=PREFIX]"
+  echo ""
+  echo " --help             Display this help text"
+  echo " --prefix=PREFIX    Install binary in 'PREFIX/bin'"
+  echo "                    Default prefix='\$HOME/.local/bin'"
+  echo ""
+}
+
+PREFIX="$HOME/.local"
+
+while [ "$1" != "" ]; do
+  PARAM=$(echo "$1" | awk -F= '{print $1}')
+  VALUE=$(echo "$1" | awk -F= '{print $2}')
+  case $PARAM in
+    -h | --help)
+      usage
+      exit
+      ;;
+    -p | --prefix)
+      PREFIX=$VALUE
+      ;;
+    *)
+      echo "ERROR: unknown parameter \"$PARAM\""
+      usage
+      exit 1
+      ;;
+  esac
+  shift
+done
+
+set -u # error on use of undefined variable
+
+if ! command -v brew > /dev/null ; then
+  if ! command -v curl > /dev/null ; then
+    echo "Please install curl and then rerun ./install.sh"
+    exit 1
+  fi
+  /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+  if [ $(uname) = "Linux" ]; then
+    if [ -z "$PATH" ]; then
+      PATH=/home/linuxbrew/.linuxbrew/bin/
+    else
+      PATH=/home/linuxbrew/.linuxbrew/bin/:"$PATH"
+    fi
+  fi
+fi
+
+
+brew tap fortran-lang/fortran # required for building fpm
+brew install fpm cmake netcdf pkg-config coreutils # coreutils supports `realpath` below
+
+PREFIX=`realpath $PREFIX`
+
+mkdir -p build/dependencies
+if [ ! -d ./build/dependencies/netcdf-fortran ]; then
+  git clone https://github.com/Unidata/netcdf-fortran.git build/dependencies/netcdf-fortran
+fi
+mkdir -p build/dependencies/netcdf-fortran/build
+
+CI=${CI:-"false"} # GitHub Actions workflows set CI=true
+
+cd build/dependencies/netcdf-fortran/build
+  GCC_VER="12" # This should be replaced with code extracting the version number from Homebrew
+  export FC=gfortran-${GCC_VER} CC=gcc-${GCC_VER} CXX=g++-${GCC_VER}
+  if [ $CI = true ]; then
+    NETCDFF_PREFIX="/usr/local"
+  else
+    NETCDFF_PREFIX="$PREFIX"
+  fi
+  NETCDF_PREFIX="`brew --prefix netcdf`"
+  cmake .. \
+    -DNETCDF_C_LIBRARY="$NETCDF_PREFIX/lib" \
+    -DNETCDF_C_INCLUDE_DIR="$NETCDF_PREFIX/include" \
+    -DCMAKE_INSTALL_PREFIX="$NETCDFF_PREFIX"
+  make -j4
+  sudo make install
+cd -
+
+GIT_VERSION=`git describe --long --dirty --all --always | sed -e's/heads\///'`
+NETCDF_LIB_PATH="`brew --prefix netcdf`/lib"
+HDF5_LIB_PATH="`brew --prefix hdf5`/lib"
+NETCDFF_LIB_PATH="$NETCDFF_PREFIX/lib"
+
+FPM_FLAG="-cpp -DUSE_ASSERTIONS=.true."
+FPM_FLAG=" $FPM_FLAG -fallow-argument-mismatch -ffree-line-length-none"
+FPM_FLAG=" $FPM_FLAG -DVERSION=\\\'$GIT_VERSION\\\'"
+FPM_FLAG=" $FPM_FLAG -L$NETCDF_LIB_PATH -L$HDF5_LIB_PATH -L$NETCDFF_LIB_PATH"
+FPM_FC="$FC"
+FPM_CC="$CC"
+
+if [ $CI = true ]; then
+  PKG_CONFIG_PATH=`realpath ./build/pkgconfig`
+  echo "---------------"
+  echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH"
+  echo "---------------"
+else
+  PKG_CONFIG_PATH=`realpath "$PREFIX"/lib/pkgconfig`
+fi
+
+if [ ! -d $PKG_CONFIG_PATH ]; then
+  mkdir -p $PKG_CONFIG_PATH 
+fi
+
+INFERENCE_ENGINE_PC="$PKG_CONFIG_PATH/inference-engine.pc"
+echo "INFERENCE_ENGINE_FPM_CXX=\"$CXX\""       >  $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_CC=\"$FPM_CC\""     >> $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_FC=\"$FPM_FC\""     >> $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_FLAG=\"$FPM_FLAG\"" >> $INFERENCE_ENGINE_PC
+echo "Name: inference-engine"                  >> $INFERENCE_ENGINE_PC
+echo "Description: Inference Engine"           >> $INFERENCE_ENGINE_PC
+echo "URL: https://github.com/berkeleylab/inference-engine" >> $INFERENCE_ENGINE_PC
+echo "Version: 0.1.0"                                       >> $INFERENCE_ENGINE_PC
+if [ $CI = true ]; then
+  echo "---------------"
+  echo "cat $INFERENCE_ENGINE_PC"
+  cat $INFERENCE_ENGINE_PC
+  echo "---------------"
+fi
+
+export PKG_CONFIG_PATH
+RUN_FPM_SH="`realpath ./build/run-fpm.sh`"
+echo "#!/bin/sh"                                                    >  $RUN_FPM_SH
+echo "#-- DO NOT EDIT -- created by inference-engine/install.sh"    >> $RUN_FPM_SH
+echo "export PKG_CONFIG_PATH"                                       >> $RUN_FPM_SH
+echo "`brew --prefix fpm`/bin/fpm \$@ --verbose \\"                 >> $RUN_FPM_SH
+echo "--profile debug \\"                                           >> $RUN_FPM_SH
+echo "--c-compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_CC`\" \\" >> $RUN_FPM_SH
+echo "--compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FC`\" \\"   >> $RUN_FPM_SH
+echo "--flag \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FLAG`\""        >> $RUN_FPM_SH
+chmod u+x $RUN_FPM_SH
+if [ $CI = true ]; then
+  echo "---------------"
+  echo "cat $RUN_FPM_SH"
+  cat $RUN_FPM_SH
+  echo "---------------"
+fi
+
+if command -v fpm > /dev/null 2>&1; then
+  brew tap fortran-lang/fortran
+  brew install fpm
+fi
+
+echo "$RUN_FPM_SH test"
+$RUN_FPM_SH test
+
+echo ""
+echo "______________ Inference-Engine has been installed! ______________" 
+echo ""
+echo "To use use or test with Inference-Engine with the Fortran Package"
+echo "Manager (fpm) and using the required compiler/linker flags, pass"
+echo "a fpm command to the build/run-fpm.sh script.  For example, to"
+echo "run one of the provided example programs with a path of the form"
+echo "example/<name>.f90, enter a command of the following form at " 
+echo "a shell command prompt:"
+echo ""
+echo "./build/run-fpm.sh run --example <name>"