Read4D

xios_examples/read4D/Makefile

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+# Make file for the read demonstartion XIOS programme
+# Targets provided our detailed below...
+#
+# all: (default) Build the read programme
+# clean: Delete all final products and working files
+# run: run the programme
+#
+# Environment Variables expected by this MakeFile:
+#
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
+# XIOS_BINDIR: The directory for XIOS binary files
+
+.PHONY: all, clean, run
+
+all: read
+
+# fortran compilation
+%.o: %.F90
+	$(FC) $(FCFLAGS) -c $<
+
+# fortran linking
+read: read.o
+	$(FC) -o read.exe read.o $(LDFLAGS) \
+		&& ln -fs $(XIOS_BINDIR)/xios_server.exe .
+
+run:
+	mpiexec -n 1 ./read.exe : -n 1 ./xios_server.exe
+
+# cleanup
+clean:
+	rm -f *.exe *.o *.mod *.MOD *.out *.err

xios_examples/read4D/__init__.py

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+

xios_examples/read4D/domain_check.xml

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+<context>
+
+  <calendar type="Gregorian"/>
+
+
+ <grid_definition>
+    <grid id="mlev_grid">
+    <domain id="original_domain" type="rectilinear" >
+      <generate_rectilinear_domain/>
+    </domain>
+      <axis id="mlev" />
+      <axis id="t" />
+    </grid>
+ </grid_definition>
+
+  <file_definition type="one_file">
+    <file id="din" name="sample_smaller" output_freq="1ts" mode="read" enabled=".true.">
+      <field id="specific_humidity" name="specific_humidity" grid_ref="mlev_grid" operation="instant" read_access=".true." />
+    </file>
+  </file_definition>
+
+</context>

xios_examples/read4D/iodef.xml

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+<?xml version="1.0"?>
+<simulation>
+
+<context id="domain_check" src="domain_check.xml"/>
+
+<context id="xios" src="xios.xml"/>
+
+</simulation>

xios_examples/read4D/read.F90

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+!-----------------------------------------------------------------------------
+! (C) Crown copyright 2020 Met Office. All rights reserved.
+! The file LICENCE, distributed with this code, contains details of the terms
+! under which the code may be used.
+!-----------------------------------------------------------------------------
+!> Read 3D data on a domain + axis grid
+!>
+program resample
+  use xios
+  use mpi
+
+  implicit none
+
+  integer :: comm = -1
+  integer :: rank = -1
+  integer :: npar = 0
+
+  call initialise()
+  call simulate()
+  call finalise()
+contains
+
+  subroutine initialise()
+
+    type(xios_date) :: origin
+    type(xios_date) :: start
+    type(xios_duration) :: tstep
+    integer :: mpi_error
+    integer :: ni_glo
+    integer :: nj_glo
+    integer :: ni
+    integer :: nj
+    integer :: ibegin
+    integer :: jbegin
+    integer :: nk_glo
+    integer :: nk
+    integer :: kbegin
+    integer :: nl_glo
+    integer :: nl
+    integer :: lbegin
+
+    ! Datetime setup, required for XIOS & matched to input
+    origin = xios_date(2024, 11, 15, 0, 0, 0)
+    start = xios_date(2024, 11, 15, 0, 0, 0)
+    tstep = xios_hour * 6
+
+    ! Initialise MPI and XIOS
+    call MPI_INIT(mpi_error)
+
+    call xios_initialize('client', return_comm=comm)
+
+    call MPI_Comm_rank(comm, rank, mpi_error)
+    call MPI_Comm_size(comm, npar, mpi_error)
+
+    call xios_context_initialize('domain_check', comm)
+    call xios_set_time_origin(origin)
+    call xios_set_start_date(start)
+    call xios_set_timestep(tstep)
+    print *, "ready to close context domain_check"
+    call xios_close_context_definition()
+    print *, "context domain_check closed (read?)"
+
+    call xios_get_domain_attr("original_domain", &
+                              ni_glo=ni_glo, nj_glo=nj_glo, &
+                              ni=ni, nj=nj, &
+                              ibegin=ibegin, jbegin=jbegin)
+    print *, 'original_domain: rank,ni_glo,nj_glo,ni,nj,ibegin,jbegin ',rank,ni_glo,nj_glo,ni,nj,ibegin,jbegin
+    call xios_get_axis_attr("mlev", n_glo=nk_glo, n=nk, begin=kbegin)
+    print *, 'mlev: n_glo, n, begin', nk_glo, nk, kbegin
+    call xios_get_axis_attr("t", n_glo=nl_glo, n=nl, begin=lbegin)
+    print *, 't: n_glo, n, begin', nl_glo, nl, lbegin
+
+
+
+  end subroutine initialise
+
+  subroutine finalise()
+
+    integer :: mpi_error
+
+    print *, "! Finalise all XIOS contexts and MPI"
+    call xios_set_current_context('domain_check')
+    call xios_context_finalize()
+    print *, "domain_check context finalised"
+    ! call xios_set_current_context('main')
+    ! call xios_context_finalize()
+    call MPI_Comm_free(comm, mpi_error)
+    call xios_finalize()
+    call MPI_Finalize(mpi_error)
+
+  end subroutine finalise
+
+  subroutine simulate()
+
+    type(xios_date) :: current
+    integer :: ts
+    integer :: lenx
+    integer :: leny
+    integer :: lenz
+    integer :: lent
+
+    ! Allocatable arrays, size is taken from input file
+    double precision, dimension (:,:,:,:), allocatable :: inshdata
+
+    call xios_get_domain_attr("original_domain", ni=lenx, nj=leny)
+    call xios_get_axis_attr("mlev", n=lenz)
+    call xios_get_axis_attr("t", n=lent)
+
+
+    allocate ( inshdata(lent, lenz, leny, lenx) )
+    print *, "ready to load data from specific humidity array variable"
+    ! Load data from the input file
+    call xios_recv_field('specific_humidity', inshdata)
+    print *, "data loaded from specific humidity array variable"
+    deallocate (inshdata)
+
+  end subroutine simulate
+
+end program resample

xios_examples/read4D/readme.md

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+read4D
+------
+
+This example reads in a sample NetCDF file of 4D structured data (data payload is `missing`).
+XIOS simply reads data from that file into memory.
+
+This is designed to be extensible, enabling much larger files to be read,
+across multiple client and server ranks, and performance analyses undertaken

xios_examples/read4D/sample_smaller.cdl

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+netcdf sample_smaller {
+dimensions:
+	time = 2 ;
+	model_level_number = 4 ;
+	latitude = 95 ;
+	longitude = 127 ;
+	bnds = 2 ;
+variables:
+	float specific_humidity(time, model_level_number, latitude, longitude) ;
+		specific_humidity:standard_name = "specific_humidity" ;
+		specific_humidity:units = "kg kg-1" ;
+		specific_humidity:grid_mapping = "latitude_longitude" ;
+		specific_humidity:coordinates = "forecast_period forecast_reference_time level_height sigma surface_altitude" ;
+	int latitude_longitude ;
+		latitude_longitude:grid_mapping_name = "latitude_longitude" ;
+		latitude_longitude:longitude_of_prime_meridian = 0. ;
+		latitude_longitude:earth_radius = 6371229. ;
+	double time(time) ;
+		time:axis = "T" ;
+		time:units = "hours since 1970-01-01 00:00:00" ;
+		time:standard_name = "time" ;
+		time:calendar = "standard" ;
+	int model_level_number(model_level_number) ;
+		model_level_number:axis = "Z" ;
+		model_level_number:units = "1" ;
+		model_level_number:standard_name = "model_level_number" ;
+		model_level_number:positive = "up" ;
+	float latitude(latitude) ;
+		latitude:axis = "Y" ;
+		latitude:units = "degrees_north" ;
+		latitude:standard_name = "latitude" ;
+	float longitude(longitude) ;
+		longitude:axis = "X" ;
+		longitude:units = "degrees_east" ;
+		longitude:standard_name = "longitude" ;
+	double forecast_period ;
+		forecast_period:units = "hours" ;
+		forecast_period:standard_name = "forecast_period" ;
+	double forecast_reference_time(time) ;
+		forecast_reference_time:units = "hours since 1970-01-01 00:00:00" ;
+		forecast_reference_time:standard_name = "forecast_reference_time" ;
+		forecast_reference_time:calendar = "standard" ;
+	float level_height(model_level_number) ;
+		level_height:bounds = "level_height_bnds" ;
+		level_height:units = "m" ;
+		level_height:long_name = "level_height" ;
+		level_height:positive = "up" ;
+		level_height:standard_name = "atmosphere_hybrid_height_coordinate" ;
+		level_height:axis = "Z" ;
+		level_height:formula_terms = "a: level_height b: sigma orog: surface_altitude" ;
+	float level_height_bnds(model_level_number, bnds) ;
+	float sigma(model_level_number) ;
+		sigma:bounds = "sigma_bnds" ;
+		sigma:units = "1" ;
+		sigma:long_name = "sigma" ;
+	float sigma_bnds(model_level_number, bnds) ;
+	float surface_altitude(latitude, longitude) ;
+		surface_altitude:units = "m" ;
+		surface_altitude:standard_name = "surface_altitude" ;
+
+// global attributes:
+		:Conventions = "CF-1.7" ;
+data:
+
+ time = 481008, 481014 ;
+
+ model_level_number = 0, 1, 2, 3 ;
+
+ latitude = -89.95312, -89.85938, -89.76562, -89.67188, -89.57812, -89.48438, 
+    -89.39062, -89.29688, -89.20312, -89.10938, -89.01562, -88.92188, 
+    -88.82812, -88.73438, -88.64062, -88.54688, -88.45312, -88.35938, 
+    -88.26562, -88.17188, -88.07812, -87.98438, -87.89062, -87.79688, 
+    -87.70312, -87.60938, -87.51562, -87.42188, -87.32812, -87.23438, 
+    -87.14062, -87.04688, -86.95312, -86.85938, -86.76562, -86.67188, 
+    -86.57812, -86.48438, -86.39062, -86.29688, -86.20312, -86.10938, 
+    -86.01562, -85.92188, -85.82812, -85.73438, -85.64062, -85.54688, 
+    -85.45312, -85.35938, -85.26562, -85.17188, -85.07812, -84.98438, 
+    -84.89062, -84.79688, -84.70312, -84.60938, -84.51562, -84.42188, 
+    -84.32812, -84.23438, -84.14062, -84.04688, -83.95312, -83.85938, 
+    -83.76562, -83.67188, -83.57812, -83.48438, -83.39062, -83.29688, 
+    -83.20312, -83.10938, -83.01562, -82.92188, -82.82812, -82.73438, 
+    -82.64062, -82.54688, -82.45312, -82.35938, -82.26562, -82.17188, 
+    -82.07812, -81.98438, -81.89062, -81.79688, -81.70312, -81.60938, 
+    -81.51562, -81.42188, -81.32812, -81.23438, -81.14062 ;
+
+ longitude = 0.0703125, 0.2109375, 0.3515625, 0.4921875, 0.6328125, 
+    0.7734375, 0.9140625, 1.054688, 1.195312, 1.335938, 1.476562, 1.617188, 
+    1.757812, 1.898438, 2.039062, 2.179688, 2.320312, 2.460938, 2.601562, 
+    2.742188, 2.882812, 3.023438, 3.164062, 3.304688, 3.445312, 3.585938, 
+    3.726562, 3.867188, 4.007812, 4.148438, 4.289062, 4.429688, 4.570312, 
+    4.710938, 4.851562, 4.992188, 5.132812, 5.273438, 5.414062, 5.554688, 
+    5.695312, 5.835938, 5.976562, 6.117188, 6.257812, 6.398438, 6.539062, 
+    6.679688, 6.820312, 6.960938, 7.101562, 7.242188, 7.382812, 7.523438, 
+    7.664062, 7.804688, 7.945312, 8.085938, 8.226562, 8.367188, 8.507812, 
+    8.648438, 8.789062, 8.929688, 9.070312, 9.210938, 9.351562, 9.492188, 
+    9.632812, 9.773438, 9.914062, 10.05469, 10.19531, 10.33594, 10.47656, 
+    10.61719, 10.75781, 10.89844, 11.03906, 11.17969, 11.32031, 11.46094, 
+    11.60156, 11.74219, 11.88281, 12.02344, 12.16406, 12.30469, 12.44531, 
+    12.58594, 12.72656, 12.86719, 13.00781, 13.14844, 13.28906, 13.42969, 
+    13.57031, 13.71094, 13.85156, 13.99219, 14.13281, 14.27344, 14.41406, 
+    14.55469, 14.69531, 14.83594, 14.97656, 15.11719, 15.25781, 15.39844, 
+    15.53906, 15.67969, 15.82031, 15.96094, 16.10156, 16.24219, 16.38281, 
+    16.52344, 16.66406, 16.80469, 16.94531, 17.08594, 17.22656, 17.36719, 
+    17.50781, 17.64844, 17.78906 ;
+}

xios_examples/read4D/test_read4D.py

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+import copy
+import glob
+import netCDF4
+import numpy as np
+import os
+import subprocess
+import unittest
+
+import xios_examples.shared_testing as xshared
+
+this_path = os.path.realpath(__file__)
+this_dir = os.path.dirname(this_path)
+
+class TestRead4D(xshared._TestCase):
+    test_dir = this_dir
+    transient_inputs = ['sample_smaller.nc']
+    transient_outputs = []
+    executable = './read.exe'
+
+    @unittest.skipIf(os.environ.get('MVER', '') == 'XIOS/trunk@2252',
+                     "skipping for ")
+    def test_read_4d(self):
+        inputfile = self.transient_inputs[0]
+        infile = inputfile.replace('.nc', '.cdl')
+
+        subprocess.run(['ncgen', '-k', 'nc4', '-o', inputfile,
+                        infile], cwd=self.test_dir, check=True)
+        self.run_mpi_xios()
+
+    @classmethod
+    def setUpClass(cls):
+        if os.environ.get('MVER', '').startswith('XIOS3/trunk'):
+            with open(os.path.join(cls.test_dir, 'read.F90'), 'r') as ioin:
+                iodef_in = ioin.read()
+            # patch in XIOS3 domain access source code syntax
+            in2 = 'xios_get_domain_attr("original_domain"'
+            in3 = ('xios_get_domain_attr("specific_humidity::"')
+            iodef_out = iodef_in.replace(in2, in3)
+            with open(os.path.join(cls.test_dir, 'read.F90'), 'w') as ioout:
+                ioout.write(iodef_out)
+        super().setUpClass()

xios_examples/read4D/xios.xml

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+<context>
+  <variable_definition>
+    <variable_group id="buffer">
+      <variable id="optimal_buffer_size" type="string">
+	performance
+      </variable>
+      <variable id="buffer_size_factor" type="double">
+	1.0
+      </variable>
+    </variable_group>
+
+    <variable_group id="parameters" >
+       <variable id="using_server" type="bool">true</variable>
+       <variable id="info_level" type="int">
+	100
+      </variable>
+      <variable id="print_file" type="bool">
+	true
+      </variable>
+    </variable_group>
+  </variable_definition>
+</context>