Merge pull request #391 from ekluzek/fixfornagonizumi

Some fixes so can run on izumi
ESCOMP · Jul 19, 2023 · 55da196 · 55da196
2 parents f7d7bfc + 030479e
commit 55da196
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Showing 37 changed files with 402 additions and 201 deletions.
diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -56,7 +56,7 @@ def _main_func():
         complib = os.path.join(libroot,"librof.a")
         makefile = os.path.join(casetools, "Makefile")
 
-        cmd = "{} complib -j {} MODEL=mizuRoute COMPLIB={} -f {} {}" \
+        cmd = "{} complib -j {} COMP_NAME=mizuRoute COMPLIB={} -f {} {}" \
               .format(gmake, gmake_j, complib, makefile, get_standard_makefile_args(case))
 
         rc, out, err = run_cmd(cmd)

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -14,14 +14,16 @@ import os, sys
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
     raise SystemExit("ERROR: must set CIMEROOT environment variable")
-sys.path.append(os.path.join(CIMEROOT, "scripts", "Tools"))
+_LIBDIR = os.path.join(CIMEROOT, "CIME", "Tools")
+sys.path.append(_LIBDIR)
 # Path for mizuRoute/route/settings for both a mizuRoute standalone checkout as well as a CESM checkout
 sys.path.append(os.path.join(CIMEROOT, "..", "route", "settings"))
 sys.path.append(os.path.join(CIMEROOT, "..", "components", "mizuRoute", "route", "settings"))
 
 from standard_script_setup import *
 from CIME.case import Case
 from CIME.nmlgen import NamelistGenerator
+from CIME.XML.files import Files
 from CIME.utils import expect, safe_copy
 from CIME.buildnml import create_namelist_infile, parse_input
 from mizuRoute_control import mizuRoute_control
@@ -30,7 +32,7 @@ logger = logging.getLogger(__name__)
 
 # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
 ####################################################################################
-def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile, nmlgen, ctl, data_list_path):
+def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile, nmlgen, ctl):
 ####################################################################################
     """Write out the input configuration file for mizuRoute
 
@@ -124,7 +126,7 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
        varname_downSegId = "Tosegment"
        varname_pfafCode = "pfaf"
     elif (  config['rof_grid'] == "USGS_GFmz" ):
-       fname_ntopOld = "ntopo_USGS-GFmz_Conus_cdf5_c20201008.nc"
+       fname_ntopOld = "ntopo_USGS-GFmz_Conus_cdf5_c20230602.nc"
        varname_area = "Basin_Area"
        varname_length = "Length"
        varname_slope  = "Slope"
@@ -180,7 +182,7 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     #----------------------------------------------------
     # Initialize namelist defaults
     #----------------------------------------------------
-    nmlgen.init_defaults(infile, config)
+    nmlgen.init_defaults(infile, config, skip_default_for_groups="data_files",)
 
     #----------------------------------------------------
     # Check for incompatible options.
@@ -202,6 +204,7 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     ctl.set( "input_dir", rundir+"/" )
     ctl.set( "ancil_dir", ancil_dir )
     ctl.set( "fname_ntopOld", fname_ntopOld )
+    nmlgen.set_value( "fname_ntopold", value=os.path.join( ancil_dir, fname_ntopOld ) )
     ctl.set( "dt_qsim", str(dt_qsim) )
     ctl.set( "dname_sseg", dname_sseg )
     ctl.set( "dname_nhru", dname_nhru )
@@ -239,6 +242,8 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
             fname_state_in = "empty"
 
     ctl.set( "fname_state_in", fname_state_in )
+    if fname_state_in is not "empty":
+        nmlgen.set_value( "fname_state_in", value=os.path.join( ancil_dir, fname_ntopOld ) )
 
     # Read in the user control file for the case and change settings to it
     file_src = "user_nl_mizuroute_control"
@@ -257,17 +262,18 @@ def _create_control_files(case, caseroot, srcroot, confdir, inst_string, infile,
     #----------------------------------------------------
     control_file = os.path.join(confdir, "mizuRoute.control")
     nml_file = os.path.join(confdir, "mizuRoute_in")
-    write_nml_in_file(case, nmlgen, confdir, nml_file)
+    write_nml_in_file(case, nmlgen, confdir, nml_file )
     ctl.write( control_file )
 
 ###############################################################################
 def write_nml_in_file(case, nmlgen, confdir, nml_file):
 ###############################################################################
-    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "rof.input_data_list")
+    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "mizuroute.input_data_list")
     if os.path.exists(data_list_path):
         os.remove(data_list_path)
+
     namelist_file = os.path.join(confdir, nml_file)
-    nmlgen.write_output_file(namelist_file, data_list_path )
+    nmlgen.write_output_file(namelist_file, data_list_path=data_list_path, groups=["HSLOPE", "IRF_UH", "KWT"])
 
 ###############################################################################
 def buildnml(case, caseroot, compname):
@@ -294,13 +300,6 @@ def buildnml(case, caseroot, compname):
     ctl = mizuRoute_control()
     ctl.read( sampleFile )
 
-    #----------------------------------------------------
-    # Clear out old data.
-    #----------------------------------------------------
-    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "mizuRoute.input_data_list")
-    if os.path.exists(data_list_path):
-        os.remove(data_list_path)
-
     #----------------------------------------------------
     # Do some checking
     #----------------------------------------------------
@@ -322,12 +321,15 @@ def buildnml(case, caseroot, compname):
     create_namelist_infile(case, user_nl_file, infile)
     control_infile = [infile]
 
+    # NOTE: User definition *replaces* existing definition.
+    files = Files(comp_interface="nuopc")
+
     # Create the namelist generator object - independent of instance
-    definition_files = [srcroot + "/cime_config/namelist_definition_mizuRoute.xml"]
-    nmlgen = NamelistGenerator(case, definition_files)
+    definition_files = [os.path.join( srcroot,  "cime_config/namelist_definition_mizuRoute.xml") ]
+    nmlgen = NamelistGenerator(case, definition_files, files=files)
 
     # create control files
-    _create_control_files(case, caseroot, srcroot, confdir, inst_string, control_infile, nmlgen, ctl, data_list_path)
+    _create_control_files(case, caseroot, srcroot, confdir, inst_string, control_infile, nmlgen, ctl)
 
     # copy control files to rundir
     if os.path.isdir(rundir):
@@ -343,7 +345,7 @@ def buildnml(case, caseroot, compname):
 def _main_func():
 
     caseroot = parse_input(sys.argv)
-    with Case(caseroot) as case:
+    with Case(case_root=caseroot) as case:
         buildnml(case, caseroot, "mizuRoute")
 
 if __name__ == "__main__":

diff --git a/cime_config/config_archive.xml b/cime_config/config_archive.xml
@@ -2,7 +2,8 @@
   <comp_archive_spec compname="mizuroute" compclass="rof">
     <rest_file_extension>r</rest_file_extension>
     <hist_file_extension>h.*\.nc$</hist_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
+    <hist_file_extension>h_gauge.*\.nc$</hist_file_extension>
+    <rest_history_varname>history_file</rest_history_varname>
     <rpointer>
       <rpointer_file>rpointer.rof</rpointer_file>
       <rpointer_content>./$CASE.mizuroute.r.$DATENAME.nc</rpointer_content>

diff --git a/cime_config/namelist_definition_mizuRoute.xml b/cime_config/namelist_definition_mizuRoute.xml
@@ -122,4 +122,27 @@
   </entry>
 
 
+  <!-- =========================== -->
+  <!-- group DATA                  -->
+  <!-- =========================== -->
+ <entry id="fname_ntopold">
+    <type>char</type>
+    <category>datasets</category>
+    <input_pathname>abs</input_pathname>
+    <group>data_files</group>
+    <desc>
+      River network description file
+    </desc>
+  </entry>
+
+ <entry id="fname_state_in">
+    <type>char</type>
+    <category>datasets</category>
+    <input_pathname>abs</input_pathname>
+    <group>data_files</group>
+    <desc>
+      Initial conditions file
+    </desc>
+  </entry>
+
 </entry_id>
diff --git a/cime_config/test/env_case.xml b/cime_config/test/env_case.xml
@@ -13,19 +13,19 @@
     <entry id="CONFIG_ROF_FILE" value="$COMP_ROOT_DIR_ROF/cime_config/config_component.xml">
       <type>char</type>
       <desc>file containing specification of component specific definitions and values(for documentation only - DO NOT EDIT)</desc>
-      <schema version="2.0">$CIMEROOT/config/xml_schemas/entry_id.xsd</schema>
-      <schema version="3.0">$CIMEROOT/config/xml_schemas/entry_id_version3.xsd</schema>
+      <schema version="2.0">$CIMEROOT/CIME/data/config/xml_schemas/entry_id.xsd</schema>
+      <schema version="3.0">$CIMEROOT/CIME/data/config/xml_schemas/entry_id_version3.xsd</schema>
     </entry>
 
     <entry id="COMPSET" value="1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MIZUROUTE_CISM2%NOEVOLVE_SWAV_SIAC_SESP">
       <type>char</type>
       <desc>Component set long name (for documentation only - DO NOT EDIT)</desc>
     </entry>
 
-    <entry id="COMP_ROOT_DIR_ROF" value="$SRCROOT">
+    <entry id="COMP_ROOT_DIR_ROF" value="$SRCROOT/components/mizuRoute/">
       <type>char</type>
       <desc>Root directory of the case river runoff model component  </desc>
-      <schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
+       <schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
     </entry>
 
     <entry id="COMP_ROF" value="mizuRoute">
@@ -34,11 +34,20 @@
       <desc>Name of river component</desc>
     </entry>
 
-    <entry id="SRCROOT" value="$ENV{PWD}/../..">
+    <entry id="SRCROOT" value="$ENV{PWD}/../../../..">
       <type>char</type>
       <desc>full pathname of source root directory</desc>
     </entry>
 
+    <entry id="MACH" value="cheyenne">
+      <type>char</type>
+      <desc>Machine name</desc>
+    </entry>
+    <entry id="MACHDIR" value="$SRCROOT/ccs_config/machines">
+      <type>char</type>
+      <desc>Machines directory location</desc>
+    </entry>
+
     <entry id="CASE" value="CASENAME">
       <type>char</type>
       <desc>case name</desc>

diff --git a/cime_config/test/env_run.xml b/cime_config/test/env_run.xml
@@ -11,7 +11,7 @@ Sample env_run.xml file that allows buildnml to be run for testing in this direc
 
 -->
 <group>
-<entry id="DIN_LOC_ROOT"         value="MYDINLOCROOT"  /> 
+<entry id="DIN_LOC_ROOT"         value="/MYDINLOCROOT"  /> 
 
     <entry id="CASESTR" value="test">
     </entry>

diff --git a/cime_config/test/runbuildnml b/cime_config/test/runbuildnml
@@ -1,9 +1,12 @@
 #!/bin/bash
-cd ../../cime >& /dev/null
+# Run the buildnmal for mizuRoute, assing it's under a CTSM or CESM checkout
+cd ../../../../cime >& /dev/null
 if [ $? != 0 ]; then
-   cd ../../../../cime
+   echo "cime directory does not exist where expected"
+   exit -1
 fi
 export CIMEROOT=`pwd`
+echo "CIMEROOT = $CIMEROOT"
 
 cd -
 cp ../user_nl_* .
@@ -22,6 +25,8 @@ if [ $? != 0 ] ; then
 else
    echo "Cat the results...."
    cat Buildconf/mizurouteconf/mizuRoute*
+   echo "input_data_list..."
+   cat Buildconf/mizuroute.input_data_list
 fi
 rm -rf user_* run/* Buildconf/mizurouteconf/* Buildconf/* CaseDocs
 echo "Successfully ran test"
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -48,14 +48,42 @@
       <issue>#390</issue>
     </phase>
   </test>
-  <test name="ERI.nldas2_nldas2_rHDMA_mnldas2.I2000Clm50SpMizGs.cheyenne_intel.mizuroute-default">
+  <test name="ERS_D_Mmpi-serial.5x5_amazon_r05.I2000Clm50SpMizGs.izumi_nag.mizuroute-default"
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#390</issue>
+    </phase>
+  </test>
+  <test name="ERI_Mmpi-serial.5x5_amazon_r05.I2000Clm50SpMizGs.cheyenne_intel.mizuroute-default">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#390</issue>
+    </phase>
+    <phase name="COMPARE_base_hybrid">
+      <status>FAIL</status>
+      <issue>#390</issue>
+    </phase>
+  </test>
+  <test name="ERI_Mmpi-serial.5x5_amazon_r05.I2000Clm50SpMizGs.izumi_gnu.mizuroute-default">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#390</issue>
+    </phase>
     <phase name="COMPARE_base_hybrid">
       <status>FAIL</status>
-      <issue>#388</issue>
+      <issue>#390</issue>
     </phase>
+  </test>
+  <test name="ERS_D_Mmpi-serial_P1x25.5x5_amazon_r05.I2000Clm50SpMizGs.cheyenne_intel.mizuroute-default">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
-      <issue>#388</issue>
+      <issue>#390</issue>
+    </phase>
+  </test>
+  <test name="ERP_D_Mmpi-serial_P1x25.5x5_amazon_r05.I2000Clm50SpMizGs.cheyenne_intel.mizuroute-default">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#390</issue>
     </phase>
   </test>