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Ticket Resolution Summary Owner Reporter
#58 fixed wrong result for "xios_is_valid_context" call rlacroix ymipsl
Description

From Mike Rezny :

The following program does not give the result I was expecting: PROGRAM test1

USE xios USE mod_wait USE mpi IMPLICIT NONE

CHARACTER(len=*),PARAMETER
id = "client"
CHARACTER(len=128)
value
TYPE(xios_time)
dtime
TYPE(xios_context)
ctx_hdl
TYPE(xios_domain)
domain_hdl
TYPE(xios_axis)
axis_hdl
TYPE(xios_grid)
grid_hdl
TYPE(xios_fieldgroup)
fieldgroup_hdl
TYPE(xios_field)
field_hdl
TYPE(xios_file)
file_hdl
INTEGER
comm, rank, size, ierr
LOGICAL
ok CALL MPI_INIT(ierr) CALL init_wait CALL xios_initialize(id, return_comm = comm) CALL MPI_COMM_RANK(comm, rank, ierr) CALL MPI_COMM_SIZE(comm, size, ierr) CALL xios_context_initialize("test", comm) CALL xios_get_handle("test", ctx_hdl) CALL xios_set_current_context(ctx_hdl) CALL xios_get_handle("domain_A", domain_hdl) CALL xios_get_handle("axis_A", axis_hdl) CALL xios_get_handle("grid_A", grid_hdl) PRINT *, 'valid context [test]: ', xios_is_valid_context("test") PRINT *, 'valid domain [domain_A]: ', xios_is_valid_domain("domain_A") PRINT *, 'valid axis [axis_A]: ', xios_is_valid_axis("axis_A") PRINT *, 'valid grid [grid_A]: ', xios_is_valid_grid("grid_A") CALL xios_close_context_definition() CALL xios_context_finalize() CALL xios_finalize() CALL MPI_FINALIZE(ierr)
END PROGRAM test1 The program output is: valid context [test]: F valid domain [domain_A]: T valid axis [axis_A]: T valid grid [grid_A]: T Why is the program returning FALSE for the context ‘test’? I was expecting TRUE. I am sure that I do not understand something. Here is the XML input file: <?xml version="1.0"?> <simulation>

<context id="test" calendar_type="Gregorian" start_date="2012-03-01 15:00:00" >

<domain_definition>

<domain id="domain_A" />

</domain_definition>

<axis_definition>

<axis id="axis_A" />

</axis_definition>

<grid_definition>

<grid id = "grid_A" />

</grid_definition>

<field_definition level="1" enabled=".FALSE." >

<field id="field_A" operation="average" freq_op="3600s"

grid_ref="grid_A" />

</field_definition>

<file_definition

type = "multiple_file" par_access = "collective" output_freq = "6h" output_level = "10" enabled = ".TRUE." > <file id="output" name="output" >

<field field_ref="field_A" />

</file>

</file_definition>

</context>

<context id="xios">

<variable_definition>

<variable_group id="buffer">

buffer_size = 8000000 buffer_server_factor_size = 2

</variable_group>

<variable_group id="parameters" >

<variable id="using_server" type="boolean" >

false

</variable> <variable id="info_level" type="int" >

50

</variable>

</variable_group>

</variable_definition>

</context>

</simulation> kindest regards Mike

#196 fixed XIOS3 not recognising matching dimensions ymipsl acc
Description

I'm having issues trying to create output containing fields with different source grids that map to the same global grid. In particular, this is a global nemo grid collated from MPP domains supplying a mixture of full MPP domain data and MPP domain data from the inner (haloes removed) section only. These grids are defined with the same name attribute:

  <grid id="grid_U_3D" >
    <domain domain_ref="grid_U" />
    <axis axis_ref="depthu" />
  </grid>
  <grid id="grid_U_3D_inner" >
    <domain domain_ref="grid_U_inner" name="grid_U" /> <!-- use name="grid_U" so we don't duplicate x, y, dimensions -->
    <axis axis_ref="depthu" />
  </grid>

but trying to write a file containing a mix of variables such as:

  <field_group id="grid_U"   grid_ref="grid_U_2D">

    <field id="e3u"    long_name="U-cell thickness"             standard_name="cell_thickness"       unit="m"      grid_ref="grid_U_3D_inner"   />
 
    <field id="uoce"   long_name="ocean current along i-axis"   standard_name="sea_water_x_velocity" unit="m/s"    grid_ref="grid_U_3D"   />
.
.
        <file id="file12" name_suffix="_grid_U" mode="write" gatherer="ugatherer" writer="uwriter" using_server2="true" description="ocean U grid variables" >
          <field field_ref="e3u" />
          <field field_ref="uoce"         name="uo".   />
.
.

results in:

cat xios_server_09.err
In file "nc4_data_output.cpp", function "void xios::CNc4DataOutput::writeDomain_(xios::CDomain *)",  line 476 -> On writing the domain : Opool__ugatherer_0__nemo__domain_undef_id_1
In the context : Opool__uwriter_0__nemo
Error when calling function nc_def_dim(ncid, dimName.c_str(), dimLen, &dimId)
NetCDF: String match to name in use
Unable to create dimension with name: x and with length 180

180 is the correct size for the global grid but the two level servers in play (ugatherer and uwriter) do not seem to recognise that the dimensions have already been defined. The contents of the incomplete output file are:

ncdump -h O2L3P_LONG_5d_00010101_00010303_grid_U.nc
netcdf O2L3P_LONG_5d_00010101_00010303_grid_U {
dimensions:
	axis_nbounds = 2 ;
	x = 180 ;
	y = 148 ;
	depthu = 31 ;
variables:
	float nav_lat(y, x) ;
		nav_lat:standard_name = "latitude" ;
		nav_lat:long_name = "Latitude" ;
		nav_lat:units = "degrees_north" ;
	float nav_lon(y, x) ;
		nav_lon:standard_name = "longitude" ;
		nav_lon:long_name = "Longitude" ;
		nav_lon:units = "degrees_east" ;
	float depthu(depthu) ;
		depthu:name = "depthu" ;
		depthu:long_name = "Vertical U levels" ;
		depthu:units = "m" ;
		depthu:positive = "down" ;
		depthu:bounds = "depthu_bounds" ;
	float depthu_bounds(depthu, axis_nbounds) ;
		depthu_bounds:units = "m" ;

// global attributes:
		:name = "O2L3P_LONG_5d_00010101_00010303_grid_U" ;
		:description = "ocean U grid variables" ;
		:title = "ocean U grid variables" ;
		:Conventions = "CF-1.6" ;

This is using rev 2634 of XIOS3 with the following services:

 <context id="xios" >
    <variable_definition>
      <variable_group id="buffer">
        <variable id="min_buffer_size" type="int">400000</variable>
        <variable id="optimal_buffer_size" type="string">performance</variable>
      </variable_group>

      <variable_group id="parameters" >
        <variable id="using_server" type="bool">true</variable>
        <variable id="info_level" type="int">0</variable>
        <variable id="print_file" type="bool">false</variable>
        <variable id="using_server2" type="bool">false</variable>
        <variable id="transport_protocol" type="string" >p2p</variable>
        <variable id="using_oasis"      type="bool">false</variable>
      </variable_group>
    </variable_definition>
    <pool_definition>
     <pool name="Opool" nprocs="12">
      <service name="tgatherer" nprocs="2" type="gatherer"/>
      <service name="igatherer" nprocs="2" type="gatherer"/>
      <service name="ugatherer" nprocs="2" type="gatherer"/>
      <service name="pgatherer" nprocs="2" type="gatherer"/>
      <service name="twriter" nprocs="1" type="writer"/>
      <service name="uwriter" nprocs="1" type="writer"/>
      <service name="iwriter" nprocs="1" type="writer"/>
      <service name="pwriter" nprocs="1" type="writer"/>
     </pool>
    </pool_definition>
  </context>

Is there a trick to making this work correctly? Or any tips to where to look for errors in my setup?

#113 fixed XIOS attribute to specify netcdf attribute "cell_methods" ymipsl aclsce
Description

For CMIP6 workflow, the user needs to specify by hand, the netcdf attribute "cell_methods", especially when the requested cell_methods attribute is not associated to a XIOS filter. For example : "area: mean where land time: mean". Examples of cell_methids required by CMIP Data Request are here : http://clipc-services.ceda.ac.uk/dreq/index/cellMethods.html

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