Merge pull request #26 from equinor/mesh

Mesh

Author: adamchengtkc

.github/workflows/build_docker.yml

@@ -6,35 +6,31 @@ on:
     paths:
       - 'Dockerfile'
   workflow_dispatch:
-permissions:
-      id-token: write
-      contents: read
-      packages: write
+permissions: {}
 jobs:
   build:
     runs-on: ubuntu-20.04
-
+    permissions:
+          id-token: write
+          contents: read
+          packages: write
     steps:
-    -
-      name: Set up QEMU
-      uses: docker/setup-qemu-action@v1
-    -
-      name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
-      with:
-        driver-opts: |
-          image=moby/buildkit:v0.11.2
-    -
-      name: Login to GitHub Container Registry
-      uses: docker/login-action@v1 
-      with:
-        registry: ghcr.io
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-    -
-      name: Build
-      uses: docker/build-push-action@v2
-      with:
-        push: true
-        platforms: linux/amd64
-        tags: ghcr.io/equinor/warmth:latest
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+        with:
+          driver-opts: |
+            image=moby/buildkit:v0.11.2
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1 
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          platforms: linux/amd64
+          tags: ghcr.io/equinor/warmth:latest

.github/workflows/docs.yml

@@ -8,33 +8,30 @@ on:
     tags:
     - '[0-9]+.[0-9]+.[0-9]'
 
-permissions:
-  id-token: write
-  contents: write
+permissions: {}
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
+      contents: write
     steps:
-    - uses: actions/checkout@v2
-
-        
-    - name: Install dependencies
-      run: |
-        curl -sSL https://install.python-poetry.org | python3
-        poetry install --with dev --no-interaction
-        
-    - name: Build
-      run: |
-        cd docs
-        sudo apt-get install pandoc
-        poetry run make html
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+          curl -sSL https://install.python-poetry.org | python3
+          poetry install --with dev --no-interaction
+          
+      - name: Build
+        run: |
+          cd docs
+          sudo apt-get install pandoc
+          poetry run make html
 
-    - name: Deploy
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs/_build/html
-        destination_dir: ./
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+          destination_dir: ./

.github/workflows/publish.yml

@@ -8,9 +8,7 @@ on:
     tags:
     - '*'
 
-permissions:
-  id-token: write
-  contents: write
+permissions: {}
 
 jobs:
   tests:
@@ -22,13 +20,14 @@ jobs:
     uses: equinor/warmth/.github/workflows/snyk.yml@main
     secrets:
       SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-      GITHUB_TOKEN_WORKFLOW: ${{ secrets.GITHUB_TOKEN }}
 
   deploy:
     needs: [tests, snyk]
     environment: deploy
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
+      contents: write
     steps:
       - uses: actions/checkout@v2
         with:

.github/workflows/snyk.yml

@@ -4,8 +4,6 @@ on:
     secrets:
       SNYK_TOKEN:
         required: true
-      GITHUB_TOKEN_WORKFLOW:
-        required: true
 jobs:
   security:
     runs-on: ubuntu-latest

warmth/build.py

@@ -1,3 +1,4 @@
+import logging
 from pathlib import Path
 import pickle
 from typing import Iterator, List, Literal
@@ -497,7 +498,7 @@ def __init__(self, parameters: Parameters):
         self._ymax = 0
         self.boundary = None
         self.grid: Grid | None = None
-        self.nodes: list[single_node] = []
+        self.nodes: list[list[single_node]] = []
 
     @property
     def single_node_sediments_inputs_template(self):
@@ -901,10 +902,16 @@ def iter_node(self)->Iterator[single_node]:
         Iterator[single_node]
             1D node
         """
+        logging.info("Iterating 1D nodes")
         for row in self.nodes:
             for col in row:
                 if isinstance(col,bool)==False:
                     yield col
+
+    def node_flat(self) -> np.ndarray[single_node]:
+        arr = np.array(self.nodes).flatten()
+        return arr[arr!=False]
+    
     @property
     def indexer_full_sim(self)->list:
         return [i.indexer for i in self.iter_node() if i._full_simulation is True]

warmth/mesh_model.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Tuple
 from pathlib import Path
 import numpy as np
@@ -28,10 +29,10 @@ def tic():
 def toc(msg=""):
     if 'startTime_for_tictoc' in globals():
         delta = time.time() - startTime_for_tictoc
-        logger.debug(msg+": Elapsed time is " + str(delta) + " seconds.")
+        logging.debug(msg+": Elapsed time is " + str(delta) + " seconds.")
         return delta
     else:
-        logger.debug("Toc: start time not set")
+        logging.debug("Toc: start time not set")
 
 @dataclass
 class rddms_upload_data_initial:
@@ -81,7 +82,7 @@ class UniformNodeGridFixedSizeMeshModel:
     def __init__(self, builder:Builder,parameters:Parameters, sedimentsOnly = False, padding_num_nodes=0):
         self._builder = builder
         self._parameters=parameters
-        self.node1D = [n for n in self._builder.iter_node()]
+        self.node1D = self._builder.node_flat() #[n for n in self._builder.iter_node()]
         self.num_nodes = len(self.node1D)
         self.mesh = None
 
@@ -701,19 +702,17 @@ def updateVertices(self):
     def buildMesh(self,tti:int):
         """Construct a new mesh at the given time index tti, and determine the vertex re-indexing induced by dolfinx
         """        
+        logging.info("Building 3D mesh")
         self.tti = tti
         self.buildVertices(time_index=tti)
-        logger.debug("Built vertices")
         self.constructMesh()
-        logger.debug("Built mesh")
-        self.updateMesh(tti)
-        logger.debug(f"Updated vertices for time {tti}")
-     
+        self.updateMesh(tti)     
 
     def updateMesh(self,tti:int, optimized=False):
         """Construct the mesh positions at the given time index tti, and update the existing mesh with the new values
         """   
         assert self.mesh is not None
+        logging.info(f"Updating 3D mesh for time {tti}")
         self.tti = tti        
         self.buildVertices(time_index=tti, optimized=optimized)
         self.updateVertices()        
@@ -1755,7 +1754,6 @@ def global_except_hook(exctype, value, traceback):
 def run_3d( builder:Builder, parameters:Parameters,  start_time=182, end_time=0, pad_num_nodes=0,
             out_dir = "out-mapA/", sedimentsOnly=False, writeout=True, base_flux=None, 
             callback_fcn_initial=None, callback_fcn_timestep=None):
-    logger.setLevel(10)  # numeric level equals DEBUG
     comm = MPI.COMM_WORLD
     builder=interpolate_all_nodes(builder)
     nums = 4
@@ -1771,13 +1769,11 @@ def run_3d( builder:Builder, parameters:Parameters,  start_time=182, end_time=0,
         for tti in range(start_time, end_time-1,-1): #start from oldest
             rebuild_mesh = (tti==start_time)
             if rebuild_mesh:
-                logger.debug(f"Rebuild/reload mesh at {tti}")          
                 mm2 = UniformNodeGridFixedSizeMeshModel(builder, parameters,sedimentsOnly, padding_num_nodes=pad_num_nodes)
                 mm2.buildMesh(tti)
                 if (base_flux is not None):
                     mm2.baseFluxMagnitude = base_flux
             else:
-                logger.debug(f"Re-generating mesh vertices at {tti}")
                 tic()
                 mm2.updateMesh(tti, optimized=True)
                 toc(msg="update mesh")

warmth/mesh_utils.py

@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+import logging
 from typing import List
 import itertools
 import numpy as np
@@ -117,7 +118,6 @@ def volumeOfTet(points):
 def volumeOfHex(points):
     """ Computes the volume of a hexahedron, given as eight 3D-points
     """ 
-    import numpy as np
     tetsplit1 = [ [1,2,4,8], [1,2,5,8], [4,8,2,3], [2,3,7,8], [2,5,6,8], [2,6,7,8] ]
     vol = 0.0
     for f in tetsplit1:
@@ -173,6 +173,7 @@ def interpolateNode(interpolationNodes: List[single_node], interpolationWeights=
 
 
 def interpolate_all_nodes(builder:Builder)->Builder:
+    logging.info("Interpolating 1D tectonic model results")
     for ni in range(len(builder.nodes)):
         for nj in range(len(builder.nodes[ni])):
             if (builder.nodes[ni][nj] is False) or (not builder.nodes[ni][nj]._full_simulation):

warmth/simulator.py

@@ -127,7 +127,7 @@ def dump_input_data(self, use_mpi=False):
                 from mpi4py.futures import MPIPoolExecutor
                 with MPIPoolExecutor(max_workers=10) as th:
                     futures = [th.submit(self.dump_input_nodes,  i)
-                            for i in self._builder.iter_node() if i is not False]
+                            for i in self._builder.iter_node()]
                     for future in concurrent.futures.as_completed(futures):
                         p.append([parameter_data_path, future.result()])
         else:
@@ -136,7 +136,7 @@ def dump_input_data(self, use_mpi=False):
                 self._builder.grid.dump(self._grid_path)
             with concurrent.futures.ThreadPoolExecutor(max_workers=10) as th:
                 futures = [th.submit(self.dump_input_nodes,  i)
-                        for i in self._builder.iter_node() if i is not False]
+                        for i in self._builder.iter_node()]
                 for future in concurrent.futures.as_completed(futures):
                     p.append([parameter_data_path, future.result()])
         return p