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Ticket Resolution Summary Owner Reporter
#185 duplicate New bounds rectilinear domain crash domain expand ymipsl jderouillat
Description

Since 2440, domain expand crashes with or without the bounds specification for rectilinear domains :

The error without specifications :

In file "domain.cpp", function "void xios::CDomain::checkBounds()",
  line 1664 -> [ id = __domain_undef_id_1 , context = 'atm ] 
  'bounds_lon_1d' dimension is not compatible with 'nvertex'.
  'bounds_lon_1d' dimension is 4 but nvertex is 2.

CDomainAlgorithmExpand::updateRectilinearDomainAttributes calls fillInRectilinearBoundLonLat if bounds_lon/lat_1d is empty. fillInRectilinearBoundLonLat resizes bounds arrays with const int nvertexValue = 4;

With bounds specifications (uncommenting in generic_testcase), the crashs occurs in CDomain::sendLonLat, where bounds_lonvalue is not defined while hasBounds is true.

#3  0x55cf20882f5a in _ZN4xios7CDomain10sendLonLatEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/domain.cpp:2497
#4  0x55cf2087fa66 in _ZN4xios7CDomain14sendAttributesEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/domain.cpp:2270
#5  0x55cf2087a822 in _ZN4xios7CDomain21sendCheckedAttributesEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/domain.cpp:1953
#6  0x55cf209bed67 in _ZN4xios5CGrid14solveDomainRefEb
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/grid.cpp:637
#7  0x55cf209ba593 in _ZN4xios5CGrid18solveDomainAxisRefEb
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/grid.cpp:359
#8  0x55cf208de6a6 in _ZN4xios6CField22solveGridDomainAxisRefEb
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/field.cpp:1689
#9  0x55cf208d0da3 in _ZN4xios6CField32sendGridComponentOfEnabledFieldsEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/field.cpp:964
#10  0x55cf209285c8 in _ZN4xios5CFile32sendGridComponentOfEnabledFieldsEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/file.cpp:861
#11  0x55cf20805b97 in _ZN4xios8CContext37sendGridComponentEnabledFieldsInFilesERKSt6vectorIPNS_5CFileESaIS3_EE
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/context.cpp:759
#12  0x55cf208023db in _ZN4xios8CContext30postProcessingGlobalAttributesEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/context.cpp:632
#13  0x55cf208041cd in _ZN4xios8CContext15closeDefinitionEv
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/node/context.cpp:706
#14  0x55cf20b75c5a in cxios_context_close_definition
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/interface/c/icdata.cpp:124
#15  0x55cf205048cc in __idata_MOD_xios_close_context_definition
	at /home/jderouil/XIOS.Src/XIOS2_trunk/ppsrc/xios/interface/fortran/idata.f90:718
#16  0x55cf204a435d in model
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/test/generic_testcase.f90:625
#17  0x55cf2047f5c6 in generic_testcase
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/test/generic_testcase.f90:103
#18  0x55cf204a5e5f in main
	at /home/jderouil/XIOS.Src/XIOS2_trunk/src/test/generic_testcase.f90:2

bounds_lonvalue should be set using bounds_lon_1d in CDomain::completeLonLatClient

#44 fixed problem with xios_field_is_activate ymipsl jgipsl
Description

Concerning XIOS rev 477

The problem is described in the following exemple in ORCHIDEE :

       IF (xios_field_is_active("RootMoist") .OR. xios_field_is_active("DelSoilMoist") .OR. &
            xios_field_is_active("DelIntercept") .OR. xios_field_is_active("DelSWE") .OR. &
            xios_field_is_active("SoilWet")) THEN

          almaoutput=.TRUE.
          WRITE(numout,*) 'almaoutput has been set to true in xios_orchidee_init'
       END IF

Case 1) Everything is fine when these variables are declared only in field_def_orchidee.xml. almaoutput becomes FALSE. See exemple at curie : /ccc/scratch/cont003/dsm/p86ghatt/LMDZOR/XIOS/RUNDIR/TESTING/RUN_rev1960/prod_mpi_omp/TestAlma

Case 2) If one or several of these variables are set in file_def_orchidee.xml but the file is deactivated, the result is almaoutput=TRUE. This is not ok. See here an extract from file_def_orchidee.xml :

<file id="sechiba2" name="sechiba_out_2_xios" output_level="10" output_freq="1d" enabled=".FALSE.">
  <field field_ref="RootMoist" level="1"/>
  <field field_ref="Areas" level="1"/>

Exemple : /ccc/scratch/cont003/dsm/p86ghatt/LMDZOR/XIOS/RUNDIR/TESTING/RUN_rev1960/prod_mpi_omp/TestAlma2

I think the behaviour of xios_field_is_activate was correct in earlier versions of XIOS.

#45 fixed problem including a file containing a context in iodef.xml ymipsl jgipsl
Description

Following exemple does not work :

iodef.xml :

<?xml version="1.0"?>
<simulation>
  <context id="xios">
    <variable_definition>
      <variable_group id="buffer">
            buffer_size = 80000000
            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">0</variable>
      </variable_group>
    </variable_definition>
  </context>

  <context src=".context_orchidee.xml"/>

</simulation>

context_orchidee.xml :

  <context id="orchidee">
    <field_definition src="./field_def_orchidee.xml"/>
    <file_definition src="./file_def_orchidee.xml"/>

    <domain_definition>
      <domain id="domain_landpoints"/>
    </domain_definition>

    <axis_definition>
      <!-- Vertical axis and extra dimensions in sechiba -->
      <axis id="veget" standard_name="model_level_number" long_name="Vegetation types" unit="1"/>
      <axis id="laiax" standard_name="model_level_number" long_name="Nb LAI" unit="1"/>
      <axis id="solth" standard_name="model_level_number" long_name="Soil levels" unit="m"/>
      <axis id="soiltyp" standard_name="model_level_number" long_name="Soil types" unit="1"/>
      <axis id="nobio" standard_name="model_level_number" long_name="Other surface types" unit="1"/>
      <axis id="albtyp" standard_name="model_level_number" long_name="Albedo types" unit="1"/>
      <axis id="solay" standard_name="model_level_number" long_name="Hydrol soil levels" unit="m"/>
      <!-- Vertical axis and extra dimensions in stomate -->
      <axis id="PFT" standard_name="model_level_number" long_name="Plant functional type" unit="1"/>
      <axis id="P10" standard_name="model_level_number" long_name="Pool 10 years" unit="1"/>
      <axis id="P100" standard_name="model_level_number" long_name="Pool 100 years" unit="1"/>
      <axis id="P11" standard_name="model_level_number" long_name="Pool 10 years + 1" unit="1"/>
      <axis id="P101" standard_name="model_level_number" long_name="Pool 100 years + 1" unit="1"/>
    </axis_definition>
  </context>

The same example works if putting the contents from the file context_orchidee.xml directly into iodef.xml instead of including the file by src.

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