feat: Adding launchpad for GEOS in trame

.github/workflows/typing-check.yml

@@ -30,7 +30,7 @@ jobs:
       # working-directory: ./${{ matrix.package-name }}
       run: |
         python -m pip install --upgrade pip
-        python -m pip install mypy ruff types-PyYAML types-pytz
+        python -m pip install mypy ruff types-PyYAML types-paramiko types-pytz
 
     - name: Typing check with mypy
       #  working-directory: ./${{ matrix.package-name }}

.gitignore

@@ -37,6 +37,9 @@ MANIFEST
 *.manifest
 *.spec
 
+#env
+.env
+
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt

geos-trame/README.rst

@@ -21,7 +21,21 @@ Build and install the Vue components
     cd vue-components
     npm i
     npm run build
-    cd -
+    cd ..
+
+then configure the .env
+
+    sh configure.sh
+
+this will generate a `dotenv` environement file defining useful path to trame,
+
+.. code-block:: console
+
+    cat .env
+        TEMPLATE_DIR=/path/to/geosPythonPackages/geos-trame/src/geos/trame/io/jinja_t
+        ASSETS_DIR=/path/to/geosPythonPackages/geos-trame/src/geos/trame/assets
+
+those will have lower precedence than local environement variables if defined
 
 Install the application
 

geos-trame/configure.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+echo "TEMPLATE_DIR=${PWD}/src/geos/trame/app/io/jinja_t/" >> ${PWD}/src/geos/trame/assets/.env
+echo "ASSETS_DIR=${PWD}/src/geos/trame/assets/" >> ${PWD}/src/geos/trame/assets/.env

geos-trame/pyproject.toml

@@ -30,18 +30,19 @@ keywords = [
 ]
 
 dependencies = [
-    "typing-extensions==4.12.2",
     "trame==3.6.5",
-    "trame-vuetify==2.7.1",
+    "trame-vuetify==3.1.0",
     "trame-code==1.0.1",
     "trame-server==3.2.3",
-    "trame-client==3.5.0",
+    "trame-client==3.11.2",
     "trame-simput==2.4.3",
-    "trame-vtk>=2.8.14",
+    "trame-vtk==2.10.0",
     "matplotlib==3.9.4",
     "trame-matplotlib==2.0.3",
     "trame-components==2.4.2",
+    "python-dotenv>=1.2.1",
     "mpld3<0.5.11",
+    "paramiko==4.0.0",
     "xsdata==24.5",
     "xsdata-pydantic[lxml]==24.5",
     "pyvista==0.45.2",
@@ -50,7 +51,7 @@ dependencies = [
     "funcy==2.0",
     "pytz==2025.2",
     "typing_inspect==0.9.0",
-    "typing_extensions>=4.12",
+    "typing_extensions>=4.15.0",
     "PyYAML",
 ]
 
@@ -92,7 +93,7 @@ include-package-data = true
 # include = ['geos-trame*']
 
 [tool.setuptools.package-data]
-"*" = ["*.js", "*.css"]
+"*" = ["*.js", "*.css","assets/*","*.jinja","*.json",".env"]
 
 [tool.pytest.ini_options]
 addopts = [

geos-trame/src/geos/trame/app/core.py

@@ -1,7 +1,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Lionel Untereiner, Jacques Franc
-
+# ignore context collapsing as it is clearer this way
+# ruff: noqa: SIM117
 from trame.ui.vuetify3 import VAppLayout
 from trame.decorators import TrameApp
 from trame.widgets import html, simput
@@ -24,6 +25,9 @@
 from geos.trame.app.ui.viewer.viewer import DeckViewer
 from geos.trame.app.components.alertHandler import AlertHandler
 
+from geos.trame.app.io.simulation import Simulation
+from geos.trame.app.ui.simulation_view import define_simulation_view
+
 import sys
 
 
@@ -38,10 +42,12 @@ def __init__( self, server: Server, file_name: str ) -> None:
         self.deckEditor: DeckEditor | None = None
         self.timelineEditor: TimelineEditor | None = None
         self.deckInspector: DeckInspector | None = None
+        self.simulationLauncher: Simulation | None = None
         self.server = server
         server.enable_module( module )
 
         self.state.input_file = file_name
+        self.state.user_id = None
 
         # TODO handle hot_reload
 
@@ -67,6 +73,9 @@ def __init__( self, server: Server, file_name: str ) -> None:
         self.region_viewer = RegionViewer()
         self.well_viewer = WellViewer( 5, 5 )
 
+        ######## Simulation runner
+        self.simulation = Simulation( server=server )
+
         # Data loader
         self.data_loader = DataLoader( self.tree, self.region_viewer, self.well_viewer, trame_server=server )
 
@@ -177,24 +186,6 @@ def build_ui( self ) -> None:
                     ):
                         vuetify.VIcon( "mdi-content-save-outline" )
 
-                    with html.Div(
-                            style=
-                            "height: 100%; width: 300px; display: flex; align-items: center; justify-content: space-between;",
-                            v_if=( "tab_idx == 1", ),
-                    ):
-                        vuetify.VBtn(
-                            "Run",
-                            style="z-index: 1;",
-                        )
-                        vuetify.VBtn(
-                            "Kill",
-                            style="z-index: 1;",
-                        )
-                        vuetify.VBtn(
-                            "Clear",
-                            style="z-index: 1;",
-                        )
-
             # input file editor
             with vuetify.VCol( v_show=( "tab_idx == 0", ), classes="flex-grow-1 pa-0 ma-0" ):
                 if self.tree.input_file is not None:
@@ -208,3 +199,16 @@ def build_ui( self ) -> None:
                         "The file " + self.state.input_file + " cannot be parsed.",
                         file=sys.stderr,
                     )
+
+            with vuetify.VCol( v_show=( "tab_idx == 1" ), classes="flex-grow-1 pa-0 ma-0" ):
+                if self.simulation is not None:
+                    define_simulation_view( self.server )
+                else:
+                    self.ctrl.on_add_error(
+                        "Error",
+                        "The execution context " + self.state.exec_context + " is not consistent.",
+                    )
+                    print(
+                        "The execution context " + self.state.exec_context + " is not consistent.",
+                        file=sys.stderr,
+                    )

geos-trame/src/geos/trame/app/io/hpc_tools.py

@@ -0,0 +1,97 @@
+from geos.trame.app.io.ssh_tools import SimulationConstant
+
+
+class SuggestDecomposition:
+
+    def __init__( self, selected_cluster: SimulationConstant, n_unknowns: int, job_type: str = 'cpu' ) -> None:
+        """Initialize the decomposition hinter for HPC."""
+        self.selected_cluster: SimulationConstant = selected_cluster
+        self.n_unknowns: int = n_unknowns
+        self.job_type: str = job_type  #TODO should be an enum
+        self.sd: list[ dict ] = []
+
+    @staticmethod
+    def compute( n_unknowns: int,
+                 memory_per_unknown_bytes: int,
+                 node_memory_gb: int,
+                 cores_per_node: int,
+                 min_unknowns_per_rank: int = 10000,
+                 strong_scaling: bool = True ) -> list[ dict ]:
+        """Suggests node/rank distribution for a cluster computation.
+
+        Parameters:
+        - n_unknowns: total number of unknowns
+        - memory_per_unknown_bytes: estimated memory per unknown
+        - node_memory_gb: available memory per node
+        - cores_per_node: cores available per node
+        - min_unknowns_per_rank: minimum for efficiency
+        - strong_scaling: True if problem size is fixed
+
+        Note:
+            - 10,000-100,000 unknowns per rank is often a sweet spot for many PDE solvers
+            - Use power-of-2 decompositions when possible (helps with communication patterns)
+            - For 3D problems, try to maintain cubic subdomains (minimizes surface-to-volume ratio, reducing communication)
+            - Don't oversubscribe: avoid using more ranks than provide parallel efficiency
+
+        """
+        # Memory constraint
+        node_memory_bytes = node_memory_gb * 1e9
+        max_unknowns_per_node = int( 0.8 * node_memory_bytes / memory_per_unknown_bytes )
+
+        # Compute minimum nodes needed
+        min_nodes = max( 1, ( n_unknowns + max_unknowns_per_node - 1 ) // max_unknowns_per_node )
+
+        # Determine ranks per node
+        unknowns_per_node = n_unknowns // min_nodes
+        unknowns_per_rank = max( min_unknowns_per_rank, unknowns_per_node // cores_per_node )
+
+        # Calculate total ranks needed
+        n_ranks = max( 1, n_unknowns // unknowns_per_rank )
+
+        # Distribute across nodes
+        ranks_per_node = min( cores_per_node, ( n_ranks + min_nodes - 1 ) // min_nodes )
+        n_nodes = ( n_ranks + ranks_per_node - 1 ) // ranks_per_node
+
+        return [
+            {
+                'id':1,
+                'nodes': n_nodes,
+                'ranks_per_node': ranks_per_node,
+                'total_ranks': n_nodes * ranks_per_node,
+                'unknowns_per_rank': n_unknowns // ( n_nodes * ranks_per_node )
+            },
+            {
+                'id':2,
+                'nodes': n_nodes * 2,
+                'ranks_per_node': ranks_per_node // 2,
+                'total_ranks': n_nodes * ranks_per_node,
+                'unknowns_per_rank': n_unknowns // ( n_nodes * ranks_per_node )
+            },
+        ]
+
+    def get_sd( self ) -> list[ dict ]:
+        """Get the suggested decomposition popoulated."""
+        if self.job_type == 'cpu' and self.selected_cluster:  #make it an enum
+            self.sd = SuggestDecomposition.compute( self.n_unknowns, 64, self.selected_cluster.mem_per_node,
+                                                    self.selected_cluster.cores_per_node )
+            self.sd = [{**item,'label': f"{self.selected_cluster.name} : {item['nodes']} x {item['ranks_per_node']}"} for item in self.sd ]
+        else:
+            self.sd = [
+                {
+                    'id': -1,
+                    'label':'No: 0x0',
+                    'nodes': 0,
+                    'ranks_per_node': 0,
+                    'total_ranks': 0,
+                    'unknowns_per_rank': 0
+                },
+            ]
+        # elif job_type == 'gpu':
+        # selected_cluster['n_nodes']*selected_cluster['gpu']['per_node']
+
+        return self.sd
+
+    # def to_list( self ) -> list[ str ]:
+    #     """Pretty printer to list of string for display in UI."""
+    #     sd = self.get_sd()
+    #     return [ f"{self.selected_cluster.name} : {sd_item['nodes']} x {sd_item['ranks_per_node']}" for sd_item in sd ]

geos-trame/src/geos/trame/app/io/jinja_t/local_copyback.jinja

@@ -0,0 +1,15 @@
+#!/bin/sh
+#SBATCH --job-name="{{ job_name }}"
+#SBATCH --ntasks={{ ntasks }}
+#SBATCH --partition={{ partition }}
+#SBATCH --comment={{ comment_gr }}
+#SBACTH --account={{ account }}
+#SBATCH --nodes={{ nodes }}
+#SBATCH --time={{ time | default('00:10:00') }}
+#SBATCH --mem={{ mem }}
+#SBATCH --output=job_GEOS_%j.out
+#SBATCH --error=job_GEOS_%j.err
+#SBATCH --dependency=afterok:{{ dep_job_id }}
+
+srun tar cfz {{ dep_job_id }}.tgz Outputs_{{ dep_job_id }}/ log_{{ dep_job_id }}.out 
+srun mkdir -p {{ target_dl_path }} && mv -v {{ dep_job_id }}.tgz {{ target_dl_path }}

geos-trame/src/geos/trame/app/io/jinja_t/local_slurm.jinja

@@ -0,0 +1,27 @@
+#!/bin/sh
+#SBATCH --job-name="{{ job_name }}"
+#SBATCH --ntasks={{ ntasks }}
+#SBATCH --partition={{ partition }}
+#SBATCH --comment={{ comment_gr }}
+#SBACTH --account={{ account }}
+#SBATCH --nodes={{ nodes }}
+#SBATCH --time={{ time | default('00:10:00') }}
+#SBATCH --mem={{ mem }}
+#SBATCH --output=job_GEOS_%j.out
+#SBATCH --error=job_GEOS_%j.err
+
+ulimit -s unlimited
+ulimit -c unlimited
+
+module purge
+module use {{ geos_module }}
+module load {{ geos_load_list }}
+
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMP_NUM_THREADS=1
+export EXEC={{ geos_path }}
+
+srun --hint=nomultithread \
+    -n {{ ntasks }} ${EXEC} \
+    -o Outputs_${SLURM_JOBID} \
+    -i {{ input_file | default('geosDeck.xml') }} | tee Outputs_${SLURM_JOBID}/log_${SLURM_JOBID}.out

geos-trame/src/geos/trame/app/io/jinja_t/p4_copyback.jinja

@@ -0,0 +1,15 @@
+#!/bin/sh
+#SBATCH --job-name="{{ job_name }}"
+#SBATCH --ntasks={{ ntasks }}
+#SBATCH --partition={{ partition }} 
+#SBATCH --comment={{ comment_gr }}
+#SBACTH --account={{ account }}
+#SBATCH --nodes={{ nodes }}
+#SBATCH --time={{ time | default('00:10:00') }}
+#SBATCH --mem={{ mem }}
+#SBATCH --output=job_GEOS_%j.out
+#SBATCH --err=job_GEOS_%j.err
+#SBATCH --dependency=afterok:{{ dep_job_id }}
+
+srun tar cfz {{ dep_job_id }}.tgz Outputs_{{ dep_job_id }}/ log_{{ dep_job_id }}.out 
+srun mkdir -p {{ target_dl_path }} && mv -v {{ dep_job_id }}.tgz {{ target_dl_path }}

geos-trame/src/geos/trame/app/io/jinja_t/p4_slurm.jinja

@@ -0,0 +1,27 @@
+#!/bin/sh
+#SBATCH --job-name="{{ job_name }}"
+#SBATCH --ntasks={{ ntasks }}
+#SBATCH --partition={{ partition }}
+#SBATCH --comment={{ comment_gr }}
+#SBACTH --account={{ account }}
+#SBATCH --nodes={{ nodes }}
+#SBATCH --time={{ time | default('00:10:00') }}
+#SBATCH --mem={{ mem }}
+#SBATCH --output=job_GEOS_%j.out
+#SBATCH --error=job_GEOS_%j.err
+
+ulimit -s unlimited
+ulimit -c unlimited
+
+module purge
+module use {{ geos_module }}
+module load {{ geos_load_list }}
+
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMP_NUM_THREADS=1
+export EXEC={{ geos_path }}
+
+srun --mpi=pmix_v3 --hint=nomultithread \
+    -n {{ ntasks }} ${EXEC} \
+    -o Outputs_${SLURM_JOBID} \
+    -i {{ input_file | default('geosDeck.xml') }} | tee log_${SLURM_JOBID}.out

geos-trame/src/geos/trame/app/io/jinja_t/pine_copyback.jinja

@@ -0,0 +1,15 @@
+#!/bin/sh
+#SBATCH --job-name="{{ job_name }}"
+#SBATCH --ntasks={{ ntasks }}
+#SBATCH --partition={{ partition }}
+#SBATCH --comment={{ comment_gr }}
+#SBACTH --account={{ account }}
+#SBATCH --nodes={{ nodes }}
+#SBATCH --time={{ time | default('00:10:00') }}
+#SBATCH --mem={{ mem }}
+#SBATCH --output=job_GEOS_%j.out
+#SBATCH --error=job_GEOS_%j.err
+#SBATCH --dependency=afterok:{{ dep_job_id }}
+
+srun tar cfz {{ dep_job_id }}.tgz Outputs_{{ dep_job_id }}/ log_{{ dep_job_id }}.out 
+srun mkdir -p {{ target_dl_path }} && mv -v {{ dep_job_id }}.tgz {{ target_dl_path }}