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Merge pull request #14 from BerkeleyLab/netcdf-read-write-example
Netcdf read/write example
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‎.github/workflows/CI.yml

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

‎example/netCDF_IO.f90

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

‎fpm.toml

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[dependencies]
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assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.4.0"}
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sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "3.5.0"}
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netcdf-interfaces = {git = "https://github.com/LKedward/netcdf-interfaces.git"}

‎setup.sh

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

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