Merge branch 'main' into add_MARBL_WW_pelayout

Author: mnlevy1981

.github/workflows/general-ci-tests.yml

@@ -133,11 +133,10 @@ jobs:
       - uses: actions/checkout@v4
 
       # Run black check
-      - uses: psf/black@stable
+      - uses: psf/black@24.1.0
         with:
           options: "--check --verbose"
           src: "./cime_config"
 
-      
 
 

.gitmodules

@@ -2,7 +2,7 @@
   path = MOM6
   url = https://github.com/NCAR/MOM6.git
   fxDONOTUSEurl = https://github.com/NCAR/MOM6.git
-    fxtag = dev/ncar_250128
+    fxtag = dev/ncar_250411
     fxrequired = AlwaysRequired
 
 [submodule "stochastic_physics"]

MOM6

@@ -83,16 +83,19 @@ def gen_auto_mask_table(
         Output directory to write the mask table.
     """
 
-    ds_topog = xr.open_dataset(topo_file_path)
-    ny, nx = ds_topog.mask.shape
-
     ibuf = 2
     jbuf = 2
     num_masked_blocks = 0
 
-    mask = np.zeros((ny + 2 * jbuf, nx + 2 * ibuf))
-
-    mask[jbuf : ny + jbuf, ibuf : nx + ibuf] = ds_topog.mask.data
+    ds_topog = xr.open_dataset(topo_file_path)
+    if "mask" in ds_topog:
+        ny, nx = ds_topog.mask.shape
+        mask = np.zeros((ny + 2 * jbuf, nx + 2 * ibuf))
+        mask[jbuf : ny + jbuf, ibuf : nx + ibuf] = ds_topog.mask.data
+    elif "wet" in ds_topog:
+        ny, nx = ds_topog.wet.shape
+        mask = np.zeros((ny + 2 * jbuf, nx + 2 * ibuf))
+        mask[jbuf : ny + jbuf, ibuf : nx + ibuf] = ds_topog.wet.data
 
     # fill in buffer cells
     if reentrant_x:
@@ -123,37 +126,98 @@ def gen_auto_mask_table(
     # ratio of ocean cells to total number of cells
     glob_ocn_frac = mask[jbuf : ny + jbuf, ibuf : nx + ibuf].sum() / (ny * nx)
 
+    pfrac = 0.01
+    max_feasible_p = 0
+    target_io_pes = args.tiopes
+    found_feasible_layout = False
+
     # Iteratively check for all possible division counts starting from the upper bound of npes/glob_ocn_frac,
-    # which is over-optimistic for realistic domains, but may be satisfied with idealized domains.
-    for p in range(int(np.ceil(npes / glob_ocn_frac)), npes, -1):
-
-        # compute the layout for the current division count, p
-        idiv, jdiv = MOM_define_layout(nx, ny, p)
-
-        # don't bother checking this p if the aspect ratio is extreme
-        r_p = (nx / idiv) / (ny / jdiv)
-        if r_p * r_extreme < 1.0 or r_extreme < r_p:
-            continue
-
-        # Get the number of masked_blocks for this particular division count
-        mask_table = determine_land_blocks(mask, nx, ny, idiv, jdiv, ibuf, jbuf)
-
-        # If we can eliminate enough blocks to reach the target npes, adopt
-        # this p (and the associated layout) and terminate the iteration.
-        num_masked_blocks = len(mask_table)
-        if p - num_masked_blocks <= npes:
-            print("Found the optimum layout for auto-masking. Terminating iteration...")
-            print(f"\t new ndivs: {p}, num_masked_blocks: {p-npes}")
+    # which is over-optimistic for realistic domains, but may be satisfied with idealized domains. The first encountered
+    # feasible division count is stored in max_feasible_p. If the target_io_pes is not achievable with this layout,
+    # the iteration continues until max_feasible_p * (1 - pfrac) is reached or the target_io_pes is satisfiable.
+    # If not, the target_io_pes is decremented and the iteration is re-done from max_feasible_p to max_feasible_p * (1 - pfrac).
+
+    for i in range(target_io_pes, 0, -1):
+
+        if found_feasible_layout:
             break
 
+        if max_feasible_p == 0:  # first iteration
+            p_up = int(np.ceil(npes / glob_ocn_frac))
+        else:
+            p_up = max_feasible_p
+
+        for p in range(p_up, npes, -1):
+
+            # compute the layout for the current division count, p
+            idiv, jdiv = MOM_define_layout(nx, ny, p)
+
+            # don't bother checking this p if the aspect ratio is extreme
+            ar = (nx / idiv) / (ny / jdiv)
+            if ar * r_extreme < 1.0 or r_extreme < ar:
+                continue
+
+            # Get the number of masked_blocks for this particular division count
+            mask_table = determine_land_blocks(mask, nx, ny, idiv, jdiv, ibuf, jbuf)
+
+            # If we can eliminate enough blocks to reach the target npes, adopt
+            # this p (and the associated layout) and terminate the iteration.
+            num_masked_blocks = len(mask_table)
+
+            if p - num_masked_blocks <= npes:
+                print(
+                    f"ndivs: {p}, masked_blocks: {num_masked_blocks}",
+                    "  idiv: ",
+                    idiv,
+                    "jdiv",
+                    jdiv,
+                )
+
+                if max_feasible_p == 0:
+                    print("^^^^^^^^^^^^^^^ first feasible layout ^^^^^^^^^^^^^^^")
+                    max_feasible_p = p
+                if (idiv * jdiv) % i == 0:
+                    idiv_io, jdiv_io = determine_io_layout(idiv, jdiv, i)
+                    # if the io layout ratio is extreme, skip this layout
+                    ar = (idiv / idiv_io) / (jdiv / jdiv_io)
+                    if ar * r_extreme < 1.0 or r_extreme < ar:
+                        continue
+                    print(f"IO layout: {idiv_io} x {jdiv_io}")
+                    print(
+                        "Found the optimum layout for auto-masking. Terminating iteration."
+                    )
+                    found_feasible_layout = True
+                    break
+
+            if p <= max_feasible_p * (1 - pfrac):
+                break
+
     if num_masked_blocks == 0:
         raise RuntimeError(
             "Couldn't auto-eliminate any land blocks. Try to increase the number"
         )
 
     # Call determine_land_blocks once again, this time to retrieve and write out the mask_table.
     mask_table = determine_land_blocks(mask, nx, ny, idiv, jdiv, ibuf, jbuf)
-    write_auto_mask_file(mask_table, idiv, jdiv, npes, output_dir)
+
+
+def determine_io_layout(idiv, jdiv, nio):
+    """Determines the optimal I/O layout given the number of partitions in x and y direction and the number of I/O PEs."""
+    min_ratio_diff = float("inf")
+    best_idiv_io, best_jdiv_io = 1, nio
+
+    for f in range(1, nio + 1):
+        if nio % f == 0:
+            idiv_io, jdiv_io = f, nio // f
+
+            if idiv % idiv_io == 0 and jdiv % jdiv_io == 0:
+                ratio_diff = abs((idiv_io / jdiv_io) - (idiv / jdiv))
+
+                if ratio_diff < min_ratio_diff:
+                    min_ratio_diff = ratio_diff
+                    best_idiv_io, best_jdiv_io = idiv_io, jdiv_io
+
+    return best_idiv_io, best_jdiv_io
 
 
 def write_auto_mask_file(
@@ -209,6 +273,13 @@ def write_auto_mask_file(
         required=True,
         help="Number of MOM6 PEs (NTASKS_OCN)",
     )
+    parser.add_argument(
+        "--tiopes",
+        default=1,
+        type=int,
+        required=False,
+        help="Number of target I/O PEs (NTASKS_IO) (default: 1)",
+    )
     parser.add_argument(
         "-rx",
         default=False,

cime_config/tools/lbe.py

@@ -3650,6 +3650,15 @@ Global:
         datatype: list
         value:
             $OCN_GRID in ["tx2_3v2", "tx0.25v1"]: True
+    TARGET_IO_PES:
+        description: |
+            When AUTO_MASKTABLE is enabled, target number of IO PEs. If the given target
+            number of IO PEs is not achievable, the target number of IO PEs is set to the
+            nearest smaller number of PEs that is achievable.
+        datatype: integer
+        value:
+            $OCN_GRID == "tx2_3v2": = - ( - $NTASKS_OCN // 256) 
+            $OCN_GRID == "tx0.25v1": = - ( - $NTASKS_OCN // 128) 
     GEOM_FILE:
         description: |
             default = ocean_geometry.nc

param_templates/MOM_input.yaml

@@ -47,6 +47,10 @@ diag_manager_nml:
             else: 30
     max_axes:
         values: 90
+    auto_merge_nc:
+        values:
+            $OCN_GRID in ["tx2_3v2", "tx0.25v1"]: .true.
+            else: .false.
 
 mpp_io_nml:
     cf_compliance:

param_templates/input_nml.yaml

@@ -2959,6 +2959,14 @@
             "$OCN_GRID in [\"tx2_3v2\", \"tx0.25v1\"]": true
          }
       },
+      "TARGET_IO_PES": {
+         "description": "When AUTO_MASKTABLE is enabled, target number of IO PEs. If the given target\nnumber of IO PEs is not achievable, the target number of IO PEs is set to the\nnearest smaller number of PEs that is achievable.\n",
+         "datatype": "integer",
+         "value": {
+            "$OCN_GRID == \"tx2_3v2\"": "= - ( - $NTASKS_OCN // 256)",
+            "$OCN_GRID == \"tx0.25v1\"": "= - ( - $NTASKS_OCN // 128)"
+         }
+      },
       "GEOM_FILE": {
          "description": "default = ocean_geometry.nc\nThe file into which to write the ocean geometry.\n",
          "datatype": "string",

param_templates/json/MOM_input.json

@@ -55,6 +55,12 @@
       },
       "max_axes": {
          "values": 90
+      },
+      "auto_merge_nc": {
+         "values": {
+            "$OCN_GRID in [\"tx2_3v2\", \"tx0.25v1\"]": ".true.",
+            "else": ".false."
+         }
       }
    },
    "mpp_io_nml": {