Merge E3SM/master into Omega/develop

cime_config/config_grids.xml

@@ -3944,7 +3944,8 @@
     <required_gridmap grid1="ocn_grid" grid2="wav_grid">OCN2WAV_SMAPNAME</required_gridmap>
     <required_gridmap grid1="ocn_grid" grid2="wav_grid">WAV2OCN_SMAPNAME</required_gridmap>
     <required_gridmap grid1="ocn_grid" grid2="wav_grid">WAV2OCN_FMAPNAME</required_gridmap>
-    <required_gridmap grid1="ocn_grid" grid2="wav_grid">ICE2WAV_SMAPNAME</required_gridmap> <!-- ??? -->
+    <required_gridmap grid1="ocn_grid" grid2="wav_grid">ICE2WAV_SMAPNAME</required_gridmap> 
+    <required_gridmap grid1="ocn_grid" grid2="wav_grid">WAV2ICE_SMAPNAME</required_gridmap>
     <!-- <required_gridmap grid1="ocn_grid" grid2="rof_grid" not_compset="_POP">ROF2OCN_FMAPNAME</required_gridmap> ?? -->
     <required_gridmap grid1="ocn_grid" grid2="rof_grid">ROF2OCN_LIQ_RMAPNAME</required_gridmap>
     <required_gridmap grid1="ocn_grid" grid2="rof_grid">ROF2OCN_ICE_RMAPNAME</required_gridmap>
@@ -5591,20 +5592,23 @@
       <map name="WAV2OCN_SMAPNAME">cpl/gridmaps/wQU225EC60to30/map_wQU225EC60to30_TO_oEC60to30v3_blin.20210428.nc</map>
       <map name="OCN2WAV_SMAPNAME">cpl/gridmaps/wQU225EC60to30/map_oEC60to30v3_TO_wQU225EC60to30_blin.20210428.nc</map>
       <map name="ICE2WAV_SMAPNAME">cpl/gridmaps/wQU225EC60to30/map_oEC60to30v3_TO_wQU225EC60to30_blin.20210428.nc</map>
+      <map name="WAV2ICE_SMAPNAME">cpl/gridmaps/wQU225EC60to30/map_wQU225EC60to30_TO_oEC60to30v3_blin.20210428.nc</map>
     </gridmap>
 
     <gridmap ocn_grid="EC30to60E2r2" wav_grid="wQU225EC30to60E2r2">
       <map name="WAV2OCN_SMAPNAME">cpl/gridmaps/wQU225EC30to60E2r2/map_wQU225EC30to60E2r2_TO_EC30to60E2r2_blin.20220222.nc</map>
       <map name="WAV2OCN_FMAPNAME">cpl/gridmaps/wQU225EC30to60E2r2/map_wQU225EC30to60E2r2_TO_EC30to60E2r2_aave.20220222.nc</map>
       <map name="OCN2WAV_SMAPNAME">cpl/gridmaps/wQU225EC30to60E2r2/map_EC30to60E2r2_TO_wQU225EC30to60E2r2_blin.20220222.nc</map>
       <map name="ICE2WAV_SMAPNAME">cpl/gridmaps/wQU225EC30to60E2r2/map_EC30to60E2r2_TO_wQU225EC30to60E2r2_blin.20220222.nc</map>
+      <map name="WAV2ICE_SMAPNAME">cpl/gridmaps/wQU225EC30to60E2r2/map_wQU225EC30to60E2r2_TO_EC30to60E2r2_blin.20220222.nc</map>
     </gridmap>
 
     <gridmap ocn_grid="IcoswISC30E3r5" wav_grid="wQU225Icos30E3r5">
       <map name="WAV2OCN_SMAPNAME">cpl/gridmaps/wQU225Icos30E3r5/map_wQU225Icos30E3r5_to_IcoswISC30E3r5_esmfbilin.20240910.nc</map>
       <map name="WAV2OCN_FMAPNAME">cpl/gridmaps/wQU225Icos30E3r5/map_wQU225Icos30E3r5_to_IcoswISC30E3r5_esmfaave.20240910.nc</map>
       <map name="OCN2WAV_SMAPNAME">cpl/gridmaps/wQU225Icos30E3r5/map_IcoswISC30E3r5_to_wQU225Icos30E3r5_esmfbilin.20240910.nc</map>
       <map name="ICE2WAV_SMAPNAME">cpl/gridmaps/wQU225Icos30E3r5/map_IcoswISC30E3r5_to_wQU225Icos30E3r5_esmfbilin.20240910.nc</map>
+      <map name="WAV2ICE_SMAPNAME">cpl/gridmaps/wQU225Icos30E3r5/map_wQU225Icos30E3r5_to_IcoswISC30E3r5_esmfbilin.20240910.nc</map>
     </gridmap>
 
     <gridmap atm_grid="CFSv2" wav_grid="wQU225EC60to30">

cime_config/machines/cmake_macros/chrysalis_oneapi-ifx.cmake

@@ -1,3 +1,11 @@
 
 string(APPEND CMAKE_EXE_LINKER_FLAGS " -L/gpfs/fs1/soft/chrysalis/spack-latest/opt/spack/linux-rhel8-x86_64/gcc-8.5.0/gcc-11.3.0-jkpmtgq/lib64 -lstdc++")
 
+# Workaround for oneapi ifx v2025.2.0 (and earlier than 2025.3.0):
+# use -mllvm -disable-hir-temp-cleanup to avoid ICE
+# See: https://github.com/argonne-lcf/AuroraBugTracking/issues/64
+if (CMAKE_Fortran_COMPILER_ID STREQUAL "IntelLLVM"
+    AND CMAKE_Fortran_COMPILER_VERSION VERSION_LESS "2025.3.0")
+  string(APPEND CMAKE_Fortran_FLAGS " -mllvm -disable-hir-temp-cleanup")
+endif()
+

components/eam/src/physics/cam/bfb_math.inc

@@ -27,6 +27,7 @@
 #  define bfb_expm1(val) (exp(val) - 1)
 #  define bfb_tanh(val) tanh(val)
 #  define bfb_cos(val) cos(val)
+#  define bfb_sin(val) sin(val)
 #  define bfb_sqrt(val) sqrt(val)
 #  define bfb_erf(val) erf(val)
 #else
@@ -40,6 +41,7 @@
 #  define bfb_expm1(val) scream_expm1(val)
 #  define bfb_tanh(val) scream_tanh(val)
 #  define bfb_cos(val) scream_cos(val)
+#  define bfb_sin(val) scream_sin(val)
 #  define bfb_erf(val) scream_erf(val)
 #endif
 

components/eam/src/physics/cam/zm/zm_conv_mcsp.F90

@@ -1,3 +1,5 @@
+#include "bfb_math.inc"
+
 module zm_conv_mcsp
    !----------------------------------------------------------------------------
    ! Purpose: methods for mesoscale coherent structure parameterization (MCSP)
@@ -29,6 +31,7 @@ module zm_conv_mcsp
    !----------------------------------------------------------------------------
 #ifdef SCREAM_CONFIG_IS_CMAKE
    use zm_eamxx_bridge_params, only: r8
+   use physics_share_f2c, only: scream_sin, scream_cos
 #else
    use shr_kind_mod,     only: r8=>shr_kind_r8
    use cam_abortutils,   only: endrun
@@ -270,10 +273,10 @@ subroutine zm_conv_mcsp_tend( pcols, ncol, pver, pverp, &
                   pdepth_total = state_pint(i,pver+1) - state_pmid(i,jctop(i))
 
                   ! specify the assumed vertical structure
-                  if (do_mcsp_t) mcsp_tend_s(i,k) = -1*zm_param%mcsp_t_coeff * sin(2.0_r8*zm_const%pi*(pdepth_mid_k/pdepth_total))
-                  if (do_mcsp_q) mcsp_tend_q(i,k) = -1*zm_param%mcsp_q_coeff * sin(2.0_r8*zm_const%pi*(pdepth_mid_k/pdepth_total))
-                  if (do_mcsp_u) mcsp_tend_u(i,k) =    zm_param%mcsp_u_coeff * (cos(zm_const%pi*(pdepth_mid_k/pdepth_total)))
-                  if (do_mcsp_v) mcsp_tend_v(i,k) =    zm_param%mcsp_v_coeff * (cos(zm_const%pi*(pdepth_mid_k/pdepth_total)))
+                  if (do_mcsp_t) mcsp_tend_s(i,k) = -1*zm_param%mcsp_t_coeff * bfb_sin(2.0_r8*zm_const%pi*(pdepth_mid_k/pdepth_total))
+                  if (do_mcsp_q) mcsp_tend_q(i,k) = -1*zm_param%mcsp_q_coeff * bfb_sin(2.0_r8*zm_const%pi*(pdepth_mid_k/pdepth_total))
+                  if (do_mcsp_u) mcsp_tend_u(i,k) =    zm_param%mcsp_u_coeff * (bfb_cos(zm_const%pi*(pdepth_mid_k/pdepth_total)))
+                  if (do_mcsp_v) mcsp_tend_v(i,k) =    zm_param%mcsp_v_coeff * (bfb_cos(zm_const%pi*(pdepth_mid_k/pdepth_total)))
 
                   ! scale the vertical structure by the ZM heating/drying tendencies
                   if (do_mcsp_t) mcsp_tend_s(i,k) = zm_avg_tend_s(i) * mcsp_tend_s(i,k)

components/eamxx/cmake/tpls/CsmShare.cmake

@@ -58,6 +58,7 @@ macro (CreateCsmShareTarget)
     target_compile_definitions(csm_share PUBLIC
       $<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CXX_COMPILER_ID:GNU>>:CPRGNU>
       $<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CXX_COMPILER_ID:Intel>>:CPRINTEL>
+      $<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CXX_COMPILER_ID:IntelLLVM>>:CPRINTEL>
       $<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CXX_COMPILER_ID:Clang>>:CPRCRAY>
       $<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CXX_COMPILER_ID:clang>>:CPRCRAY>
       EAMXX_STANDALONE)

components/eamxx/docs/user/model_configuration.md

@@ -361,7 +361,8 @@ EAMxx allows the user to configure the desired model output via
 with each YAML file associated to a different output stream (i.e., a file).
 In order to add an output stream,
 one needs to run `atmchange output_yaml_files+=/path/to/my/output/yaml`
-(more information on how to use `atmchange` can be found [here](#changing-model-inputs-atmchange)).
+(more information on how to use `atmchange` can be found in the
+[atmchange documentation](#changing-model-inputs-atmchange)).
 During the `buildnml` phase of the case management system, these YAML files
 will be copied into the RUNDIR/data folder.
 During this process, the files will be parsed, and any CIME-related
@@ -432,6 +433,10 @@ in the run directory.
 - `frequency_units`: units of the output frequency.
       - Valid options are `nsteps` (the number of atmosphere time steps),
       `nsecs`, `nmins`, `nhours`, `ndays`, `nmonths`, `nyears`.
+- `transpose`: optional boolean flag to enable transposed output (default: `false`).
+      - When set to `true`, all field dimensions will be reversed in the output file.
+      - For example, a field with layout `(ncol, nlev)` will be written as `(nlev, ncol)`.
+      - This can be useful for post-processing tools that expect a specific dimension ordering.
 
 ## Diagnostic output
 

components/eamxx/scripts/atm_manip.py

@@ -71,6 +71,96 @@ def reset_buffer():
 ###############################################################################
     run_cmd_no_fail(f"./xmlchange {ATMCHANGE_BUFF_XML_NAME}=''")
 
+###############################################################################
+def get_changes_for_node(xml_root, node_name, changes):
+###############################################################################
+    """
+    Return the subset of changes from `changes` that do NOT target the given
+    XML node or any of its descendants.  This is the filtering kernel used by
+    reset_node_changes and can be called directly for testing.
+
+    NOTE: `changes` is a list of already-unescaped change strings
+          (commas are NOT escaped with backslash).
+
+    >>> xml = '''
+    ... <root>
+    ...     <foo type="integer">0</foo>
+    ...     <bar type="integer">10</bar>
+    ...     <sub>
+    ...         <child1 type="integer">1</child1>
+    ...         <child2 type="integer">2</child2>
+    ...     </sub>
+    ... </root>
+    ... '''
+    >>> import xml.etree.ElementTree as ET
+    >>> tree = ET.fromstring(xml)
+    >>> ################ ERROR: node not found #######################
+    >>> get_changes_for_node(tree, 'nonexistent', ['foo=5'])
+    Traceback (most recent call last):
+    SystemExit: ERROR: 'nonexistent' did not match any node in the XML file
+    >>> ################ Reset leaf node (foo), keep bar change #####
+    >>> get_changes_for_node(tree, 'foo', ['foo=5', 'bar=2'])
+    ['bar=2']
+    >>> ################ Reset leaf node (foo), no matching change ##
+    >>> get_changes_for_node(tree, 'foo', ['bar=2', 'sub::child1=99'])
+    ['bar=2', 'sub::child1=99']
+    >>> ################ Reset non-leaf node (sub), removes children
+    >>> get_changes_for_node(tree, 'sub', ['sub::child1=99', 'bar=3'])
+    ['bar=3']
+    >>> ################ Reset child only, keep sibling change #######
+    >>> get_changes_for_node(tree, 'sub::child1', ['sub::child1=99', 'sub::child2=5', 'bar=3'])
+    ['sub::child2=5', 'bar=3']
+    >>> ################ Empty changes list ##########################
+    >>> get_changes_for_node(tree, 'foo', [])
+    []
+    """
+    reset_targets = get_xml_nodes(xml_root, node_name)
+    expect(len(reset_targets) > 0,
+           f"'{node_name}' did not match any node in the XML file")
+
+    if not changes:
+        return []
+
+    parent_map = create_parent_map(xml_root)
+
+    filtered_changes = []
+    for chg in changes:
+        chg_node_name, _, _, _ = parse_change(chg)
+        chg_nodes = get_xml_nodes(xml_root, chg_node_name)
+        # is_anchestor_of(A, B, ...) returns True when A == B too, so
+        # this covers both direct matches and descendant matches.
+        affects_reset = any(
+            is_anchestor_of(reset_target, chg_node, parent_map)
+            for chg_node in chg_nodes
+            for reset_target in reset_targets
+        )
+        if not affects_reset:
+            filtered_changes.append(chg)
+
+    return filtered_changes
+
+###############################################################################
+def reset_node_changes(xml_root, node_name):
+###############################################################################
+    """
+    Remove from the SCREAM_ATMCHANGE_BUFFER all changes that target
+    the given node or any of its descendants.
+    """
+    # Get current buffered changes
+    buff_str = run_cmd_no_fail(f"./xmlquery {ATMCHANGE_BUFF_XML_NAME} --value")
+    changes = []
+    for item in buff_str.split(ATMCHANGE_SEP):
+        if item.strip():
+            changes.append(item.replace(r"\,", ",").strip())
+
+    # Filter changes (also validates node_name exists in xml_root)
+    filtered_changes = get_changes_for_node(xml_root, node_name, changes)
+
+    # Reset buffer and write back the filtered changes
+    run_cmd_no_fail(f"./xmlchange {ATMCHANGE_BUFF_XML_NAME}=''")
+    if filtered_changes:
+        buffer_changes(filtered_changes)
+
 ###############################################################################
 def get_xml_nodes(xml_root, name):
 ###############################################################################

components/eamxx/scripts/atmchange

@@ -14,7 +14,7 @@ sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 
 from eamxx_buildnml_impl import check_value, is_array_type
 from eamxx_buildnml import create_raw_xml_file
-from atm_manip import atm_config_chg_impl, buffer_changes, reset_buffer, get_xml_nodes, parse_change
+from atm_manip import atm_config_chg_impl, buffer_changes, reset_buffer, reset_node_changes, get_xml_nodes, parse_change
 from utils import run_cmd_no_fail, expect, GoodFormatter
 
 # Add path to cime
@@ -47,9 +47,17 @@ def atm_config_chg(changes, reset=False, buffer_only=False):
         expect(not reset, "Makes no sense for buffer_only and reset to both be on")
 
     if reset:
-        reset_buffer()
-        print("All buffered atmchanges have been removed.")
         hack_xml = run_cmd_no_fail("./xmlquery SCREAM_HACK_XML --value")
+        if reset is True:
+            reset_buffer()
+            print("All buffered atmchanges have been removed.")
+        else:
+            with open("namelist_scream.xml", "r") as fd:
+                tree = ET.parse(fd)
+                root = tree.getroot()
+            reset_node_changes(root, reset)
+            print(f"Buffered atmchanges for '{reset}' have been removed.")
+
         if hack_xml == "TRUE":
             print("SCREAM_HACK_XML is on. Removing namelist_scream.xml to force regen")
             os.remove("namelist_scream.xml")
@@ -118,8 +126,10 @@ OR
     parser.add_argument(
         "-r", "--reset",
         default=False,
-        action="store_true",
-        help="Forget all previous atmchanges",
+        nargs="?",
+        const=True,
+        metavar="NODE",
+        help="Forget all previous atmchanges (if NODE is given, only forget changes targeting that XML node)",
     )
 
     parser.add_argument(

components/eamxx/scripts/compare-nc-files

@@ -51,6 +51,10 @@ OR
     parser.add_argument("-c","--compare",nargs='+', default=[],
                         help="Compare variables from src file against variables from tgt file")
 
+    # Allow the test to continue if variables are transposes of each other.
+    parser.add_argument("-a","--allow_transpose",action="store_true", default=False,
+                        help="Whether to allow comparison between variables that are transposed")
+
     return parser.parse_args(args[1:])
 
 ###############################################################################
@@ -62,7 +66,8 @@ def _main_func(description):
     print (f" **** Comparing nc files **** \n"
            f"  src file: {pncf._src_file}\n"
            f"  tgt file: {pncf._tgt_file}\n"
-           f"  comparisons: {cmp_str}")
+           f"  comparisons: {cmp_str}"
+           f"  allow transpose: {pncf._allow_transpose}")
     success = pncf.run()
 
     print("Comparisons result: {}".format("SUCCESS" if success else "FAIL"))