Made hybrid vertical coordinate selectable as compset option and defi…

…ned vertical dimension in env_build.xml.
NorESMhub · Aug 21, 2024 · 97ebaec · 97ebaec
1 parent 3c96a7b
commit 97ebaec
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Showing 7 changed files with 63 additions and 54 deletions.
diff --git a/cime_config/buildcpp b/cime_config/buildcpp
@@ -36,20 +36,14 @@ def create_dimmod(case):
     comp_root_dir_ocn = case.get_value("COMP_ROOT_DIR_OCN")
     ocn_grid = case.get_value("OCN_GRID")
     blom_vcoord = case.get_value("BLOM_VCOORD")
+    blom_kdm = case.get_value("BLOM_KDM")
     ntasks_ocn = case.get_value("NTASKS_OCN")
     objroot = case.get_value("OBJROOT")
 
     gridconf_dir = os.path.join(comp_root_dir_ocn, "bld", ocn_grid)
-    kdm_file = os.path.join(gridconf_dir, "kdm." + blom_vcoord)
     blom_dimensions_script = os.path.join(comp_root_dir_ocn, "bld", "blom_dimensions")
 
-    try:
-        with open(kdm_file, "r") as kdm_file_obj:
-            kdm = kdm_file_obj.read().strip()
-    except:
-        expect(False, "Failed to read kdm from file {}".format(kdm_file))
-
-    cmd = "{} -n {} -k {} -d {}".format(blom_dimensions_script, ntasks_ocn, kdm, gridconf_dir)
+    cmd = "{} -n {} -k {} -d {}".format(blom_dimensions_script, ntasks_ocn, blom_kdm, gridconf_dir)
     rc, out, err = run_cmd(cmd, from_dir=blomconf_dir)
     expect(rc == 0, "Command %s failed rc=%d\nout=%s\nerr=%s" % (cmd, rc, out, err))
 
@@ -95,10 +89,10 @@ def buildcpp(case):
     if ocn_grid in ["gx1v5", "gx1v6", "tnx1v1", "tnx1v3", "tnx1v4", "tnx0.25v1", "tnx0.25v3", "tnx0.25v4", "tnx0.125v4"]:
         blom_cppdefs = blom_cppdefs + " -DLEVITUS2X"
 
-    if turbclo or tracers:
+    if turbclo != "null" or tracers:
         blom_cppdefs = blom_cppdefs + " -DTRC"
 
-    if turbclo:
+    if turbclo != "null":
         twoeq = False
         oneeq = False
         for option in turbclo.split():

diff --git a/cime_config/buildlib_2.1 b/cime_config/buildlib_2.1
@@ -53,7 +53,6 @@ def _main_func():
 
             objroot = case.get_value("OBJROOT")
             comp_root_dir_ocn = case.get_value("COMP_ROOT_DIR_OCN")
-            turbclo = case.get_value("BLOM_TURBULENT_CLOSURE")
             tracers = case.get_value("BLOM_TRACER_MODULES")
             driver = case.get_value("COMP_INTERFACE")
 
@@ -65,18 +64,17 @@ def _main_func():
                      os.path.join(comp_root_dir_ocn, "channel"),
                      os.path.join(comp_root_dir_ocn, "single_column"),
                      os.path.join(comp_root_dir_ocn, "pkgs", "CVMix-src", "src", "shared"),
-                     os.path.join(comp_root_dir_ocn, "pkgs", "M4AGO-sinking-scheme", "src"),
-                     os.path.join(comp_root_dir_ocn, "phy")]
-
-            if turbclo != 0 and tracers != 0:
-                paths.append(os.path.join(comp_root_dir_ocn, "trc"))
+                     os.path.join(comp_root_dir_ocn, "phy"),
+                     os.path.join(comp_root_dir_ocn, "trc"),
+                     os.path.join(comp_root_dir_ocn, "idlage")]
 
             if tracers != 0:
                 for module in tracers.split():
                     if module == "iage":
-                        paths.append(os.path.join(comp_root_dir_ocn, "idlage"))
+                        continue
                     elif module == "ecosys":
                         paths.append(os.path.join(comp_root_dir_ocn, "hamocc"))
+                        paths.append(os.path.join(comp_root_dir_ocn, "pkgs", "M4AGO-sinking-scheme", "src"))
                     else:
                         expect(False, "tracer module {} is not recognized".format(module))
 

diff --git a/cime_config/buildlib_2.2 b/cime_config/buildlib_2.2
@@ -54,7 +54,6 @@ def _main_func():
 
             objroot = case.get_value("OBJROOT")
             comp_root_dir_ocn = case.get_value("COMP_ROOT_DIR_OCN")
-            turbclo = case.get_value("BLOM_TURBULENT_CLOSURE")
             tracers = case.get_value("BLOM_TRACER_MODULES")
             driver = case.get_value("COMP_INTERFACE")
 

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -94,7 +94,7 @@ def buildnml(case, caseroot, compname):
 
     blom_vcoord = case.get_value("BLOM_VCOORD")
     turbclo = case.get_value("BLOM_TURBULENT_CLOSURE")
-    expect(blom_vcoord != "cntiso_hybrid" or not turbclo,
+    expect(blom_vcoord != "cntiso_hybrid" or turbclo == "null",
            f"BLOM_VCOORD == {blom_vcoord} and BLOM_TURBULENT_CLOSURE == {turbclo} is not a valid combination")
 
     #--------------------------

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -18,7 +18,7 @@
     <valid_values>iage,iage ecosys</valid_values>
     <default_value>iage</default_value>
     <values>
-      <value compset="_BLOM%ECO">iage ecosys</value>
+      <value compset="_BLOM.*%ECO">iage ecosys</value>
     </values>
     <group>build_component_blom</group>
     <file>env_build.xml</file>
@@ -38,6 +38,9 @@
     <type>char</type>
     <valid_values></valid_values>
     <default_value>oneeq advection</default_value>
+    <values>
+      <value compset="_BLOM%HYB">null</value>
+    </values>
     <group>build_component_blom</group>
     <file>env_build.xml</file>
     <desc>Optional turbulent closure.  Valid values one of: twoeq oneeq. Additional values: advection isodif</desc>
@@ -57,11 +60,11 @@
     <valid_values>constant,prognostic,diagnostic</valid_values>
     <default_value>constant</default_value>
     <values>
-      <value compset="_BLOM%ECO"           >constant</value>
-      <value compset="_BLOM%ECO.*_BGC%BPRP">prognostic</value>
-      <value compset="_BLOM%ECO.*_BGC%BDRD">diagnostic</value>
-      <value compset="_DATM%CPLHIST.*_BLOM%ECO">diagnostic</value>
-      <value compset="20TR_DATM%IAF.*_BLOM%ECO">diagnostic</value>
+      <value compset="_BLOM.*%ECO"           >constant</value>
+      <value compset="_BLOM.*%ECO.*_BGC%BPRP">prognostic</value>
+      <value compset="_BLOM.*%ECO.*_BGC%BDRD">diagnostic</value>
+      <value compset="_DATM%CPLHIST.*_BLOM.*%ECO">diagnostic</value>
+      <value compset="20TR_DATM%IAF.*_BLOM.*%ECO">diagnostic</value>
     </values>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
@@ -74,11 +77,26 @@
     <type>char</type>
     <valid_values>isopyc_bulkml,cntiso_hybrid</valid_values>
     <default_value>isopyc_bulkml</default_value>
+    <values>
+      <value compset="_BLOM%HYB">cntiso_hybrid</value>
+    </values>
     <group>build_component_blom</group>
     <file>env_build.xml</file>
     <desc>Vertical coordinate type of BLOM</desc>
   </entry>
 
+  <entry id="BLOM_KDM">
+    <type>integer</type>
+    <valid_values/>
+    <default_value>53</default_value>
+    <values>
+      <value compset="_BLOM%HYB">56</value>
+    </values>
+    <group>build_component_blom</group>
+    <file>env_build.xml</file>
+    <desc>Vertical dimension of BLOM</desc>
+  </entry>
+
   <entry id="BLOM_COUPLING">
     <type>char</type>
     <valid_values>full,partial</valid_values>
@@ -121,19 +139,19 @@
     <valid_values>UNSET,1850,2000,hist,ssp119,ssp126,ssp245,ssp370,ssp434,ssp460,ssp534os,ssp585</valid_values>
     <default_value>1850</default_value>
     <values>
-      <value compset="HIST_CAM60%NORESM.*_BLOM%ECO"    >hist</value>
-      <value compset="20TR_DATM.*_BLOM%ECO"            >hist</value>
-      <value compset="2000_CAM60%NORESM.*_BLOM%ECO"    >2000</value>
-      <value compset="SSP119_CAM60%NORESM.*_BLOM%ECO"  >ssp119</value>
-      <value compset="SSP126_CAM60%NORESM.*_BLOM%ECO"  >ssp126</value>
-      <value compset="SSP245_CAM60%NORESM.*_BLOM%ECO"  >ssp245</value>
-      <value compset="SSP370_CAM60%NORESM.*_BLOM%ECO"  >ssp370</value>
-      <value compset="SSP370LOWNTCF_CAM60%NORESM.*_BLOM%ECO"      >ssp370</value>
-      <value compset="SSP370REFGHGLOWNTCF_CAM60%NORESM.*_BLOM%ECO">ssp370</value>
-      <value compset="SSP434_CAM60%NORESM.*_BLOM%ECO"  >ssp434</value>
-      <value compset="SSP460_CAM60%NORESM.*_BLOM%ECO"  >ssp460</value>
-      <value compset="SSP534_CAM60%NORESM.*_BLOM%ECO"  >ssp534os</value>
-      <value compset="SSP585_CAM60%NORESM.*_BLOM%ECO"  >ssp585</value>
+      <value compset="HIST_CAM60%NORESM.*_BLOM.*%ECO"    >hist</value>
+      <value compset="20TR_DATM.*_BLOM.*%ECO"            >hist</value>
+      <value compset="2000_CAM60%NORESM.*_BLOM.*%ECO"    >2000</value>
+      <value compset="SSP119_CAM60%NORESM.*_BLOM.*%ECO"  >ssp119</value>
+      <value compset="SSP126_CAM60%NORESM.*_BLOM.*%ECO"  >ssp126</value>
+      <value compset="SSP245_CAM60%NORESM.*_BLOM.*%ECO"  >ssp245</value>
+      <value compset="SSP370_CAM60%NORESM.*_BLOM.*%ECO"  >ssp370</value>
+      <value compset="SSP370LOWNTCF_CAM60%NORESM.*_BLOM.*%ECO"      >ssp370</value>
+      <value compset="SSP370REFGHGLOWNTCF_CAM60%NORESM.*_BLOM.*%ECO">ssp370</value>
+      <value compset="SSP434_CAM60%NORESM.*_BLOM.*%ECO"  >ssp434</value>
+      <value compset="SSP460_CAM60%NORESM.*_BLOM.*%ECO"  >ssp460</value>
+      <value compset="SSP534_CAM60%NORESM.*_BLOM.*%ECO"  >ssp534os</value>
+      <value compset="SSP585_CAM60%NORESM.*_BLOM.*%ECO"  >ssp585</value>
      </values>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
@@ -246,8 +264,8 @@
   </entry>
 
   <description>
-    <desc compset="_BLOM"    >BLOM default:</desc>
-    <desc compset="_BLOM%ECO">BLOM/Ecosystem:</desc>
+    <desc compset="_BLOM"      >BLOM default:</desc>
+    <desc compset="_BLOM.*%ECO">BLOM/Ecosystem:</desc>
   </description>
 
   <help>

diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml
@@ -88,7 +88,7 @@
   <!-- GRID: T62_tn14 : start !-->
   <grid name="a%T62.+oi%tnx1v4">
     <mach name="any">
-      <pes pesize="XS" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="XS" compset="_DATM.*_BLOM.*%ECO">
         <comment>Very small pe-layout on 128 pes in total</comment>
         <ntasks>
           <ntasks_atm>4</ntasks_atm>
@@ -164,7 +164,7 @@
 
   <grid name="a%T62.+oi%tnx1v4">
     <mach name="any">
-      <pes pesize="M" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="M" compset="_DATM.*_BLOM.*%ECO">
         <comment>none</comment>
         <ntasks>
           <ntasks_atm>128</ntasks_atm>
@@ -204,7 +204,7 @@
   <!-- GRID: TL319_tn14 : start !-->
   <grid name="a%TL319.+oi%tnx1v4">
     <mach name="any">
-      <pes pesize="XS" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="XS" compset="_DATM.*_BLOM.*%ECO">
         <comment>Very small pe-layout on 128 pes in total</comment>
         <ntasks>
           <ntasks_atm>4</ntasks_atm>
@@ -280,7 +280,7 @@
 
   <grid name="a%TL319.+oi%tnx1v4">
     <mach name="any">
-      <pes pesize="M" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="M" compset="_DATM.*_BLOM.*%ECO">
         <comment>none</comment>
         <ntasks>
           <ntasks_atm>128</ntasks_atm>
@@ -437,7 +437,7 @@
 
   <grid name="a%TL319.+oi%tnx0.5v1">
     <mach name="any">
-      <pes pesize="M" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="M" compset="_DATM.*_BLOM.*%ECO">
         <comment>none</comment>
         <ntasks>
           <ntasks_atm>256</ntasks_atm>
@@ -591,7 +591,7 @@
 
   <grid name="a%T62.+oi%tnx0.25v4">
     <mach name="any">
-      <pes pesize="any" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="any" compset="_DATM.*_BLOM.*%ECO">
         <comment>none</comment>
         <ntasks>
           <ntasks_atm>16</ntasks_atm>
@@ -674,7 +674,7 @@
   <!-- GRID: T62_tn21 !-->
   <grid name="a%T62.+oi%tnx2v1">
     <mach name="any">
-      <pes pesize="XS" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="XS" compset="_DATM.*_BLOM.*%ECO">
         <comment>Very small and efficent pe-layout on 128 pes in total</comment>
         <ntasks>
           <ntasks_atm>1</ntasks_atm>
@@ -712,7 +712,7 @@
 
   <grid name="a%T62.+oi%tnx2v1">
     <mach name="any">
-      <pes pesize="S" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="S" compset="_DATM.*_BLOM.*%ECO">
         <comment>Small pe-layout with 219 pes in total</comment>
         <ntasks>
           <ntasks_atm>1</ntasks_atm>
@@ -788,7 +788,7 @@
 
   <grid name="a%T62.+oi%tnx2v1">
     <mach name="any">
-      <pes pesize="M" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="M" compset="_DATM.*_BLOM.*%ECO">
         <comment>Medium sized pe-layout with 384 pes in total</comment>
         <ntasks>
           <ntasks_atm>18</ntasks_atm>
@@ -826,7 +826,7 @@
 
   <grid name="a%T62.+oi%tnx2v1">
     <mach name="any">
-      <pes pesize="L" compset="_DATM.*_BLOM%ECO">
+      <pes pesize="L" compset="_DATM.*_BLOM.*%ECO">
         <comment>Large pe-layout with 512 pes in total</comment>
         <ntasks>
           <ntasks_atm>1</ntasks_atm>

diff --git a/cime_config/namelist_definition_blom.xml b/cime_config/namelist_definition_blom.xml
@@ -338,7 +338,7 @@
     <values>
       <value>5.e-5</value>
       <value ocn_grid="tnx1v4" ocn_ncpl="24">.75e-4</value>
-      <value ocn_grid="tnx0.5v1" >.75e-4</value>
+      <value ocn_grid="tnx0.5v1"  >.75e-4</value>
       <value ocn_grid="tnx0.25v4" >.75e-4</value>
       <value ocn_grid="tnx0.125v4">.75e-4</value>
     </values>
@@ -3997,8 +3997,8 @@
     <group>config_bgc</group>
     <values>
       <value>.false.</value>
-      <value compset="HIST_CAM60%NORESM.*_BLOM%ECO">.true.</value>
-      <value compset="20TR_DATM.*_BLOM%ECO">.true.</value>
+      <value compset="HIST_CAM60%NORESM.*_BLOM.*%ECO">.true.</value>
+      <value compset="20TR_DATM.*_BLOM.*%ECO">.true.</value>
     </values>
     <desc>activates HAMOCC CFC code</desc>
   </entry>
@@ -4010,7 +4010,7 @@
     <values>
       <value>.false.</value>
       <value compset="HIST_CAM60%NORESM.*">.true.</value>
-      <value compset="20TR_DATM.*_BLOM%ECO">.true.</value>
+      <value compset="20TR_DATM.*_BLOM.*%ECO">.true.</value>
     </values>
     <desc>activates HAMOCC natural tracer code</desc>
   </entry>