Added jobbergate-composed subproject to demonstrate stand-alone Jobbe…

…rgate

examples/create-submit-job.py

@@ -19,7 +19,7 @@
 Note: Before running this demo, you will need::
 
 - An Auth token in the same directory named "access.token". You may use the ``cli-login.py`` for this.
-- An application created from the "application-example" directory. It may already exist.
+- An application created from the "simple-application" example directory. It may already exist.
 """
 
 import pathlib
@@ -30,10 +30,10 @@
 def get_application_id(
     base_api_url="https://armada-k8s.staging.omnivector.solutions/jobbergate",
     access_token_file=pathlib.Path("./access.token"),
-    application_identifier="application-example",
+    application_identifier="simple-application",
 ):
     """
-    Get an application id for the application with the identifier "application-example".
+    Get an application id for the application with the identifier "simple-application".
     """
     token = access_token_file.read_text()
     response = httpx.get(
@@ -57,7 +57,7 @@ def create_job_script(
     job_script_name="demo-job-script",
 ):
     """
-    Create a job-script from the "application-example".
+    Create a job-script from the "simple-application".
 
     Application config params and sbatch params are hard-coded but may be easily modified as desired.
     """

examples/motorbike-application/jobbergate.py

@@ -0,0 +1,25 @@
+from jobbergate_cli.subapps.applications.application_base import JobbergateApplicationBase
+from jobbergate_cli.subapps.applications.questions import Text, Integer
+
+class JobbergateApplication(JobbergateApplicationBase):
+    def mainflow(self, *_, **__):
+        questions = []
+
+        questions.append(Text(
+            "partition",
+            message="Choose a partition",
+            default="compute"
+        ))
+        questions.append(Integer(
+            "nodes",
+            message="Choose number of nodes for job",
+            default=2,
+            minval=1,
+        ))
+        questions.append(Integer(
+            "ntasks",
+            message="Choose number of tasks per node for job",
+            default=6,
+            minval=1,
+        ))
+        return questions

examples/motorbike-application/jobbergate.yaml

@@ -0,0 +1,7 @@
+jobbergate_config:
+  default_template: job-script-template.py.j2
+  output_directory: .
+application_config:
+  partition: compute
+  nodes: 2
+  ntasks: 1

examples/motorbike-application/templates/job-script-template.py.j2

@@ -0,0 +1,80 @@
+#!/bin/bash
+#SBATCH --partition {{ data.partition }}
+#SBATCH --nodes={{ data.nodes }}
+#SBATCH --ntasks={{ data.ntasks }}
+#SBATCH -J motorbike
+#SBATCH --output=/nfs/R-%x.%j.out
+#SBATCH --error=/nfs/R-%x.%j.err
+#SBATCH -t 1:00:00
+
+# clone OpenFOAM-10 if it is not available yet
+OPENFOAM_DIR=/nfs/OpenFOAM-10
+if [[ ! -d $OPENFOAM_DIR ]]
+then
+    echo "Cloning OpenFOAM-10"
+    cd /nfs
+    git clone https://github.com/OpenFOAM/OpenFOAM-10.git
+else
+    echo "Skipping clone process...we already have the OpenFOAM-10 source code"
+fi
+
+# create a working folder inside the shared directory
+WORK_DIR=/nfs/$SLURM_JOB_NAME-Job-$SLURM_JOB_ID
+mkdir -p $WORK_DIR
+cd $WORK_DIR
+
+# path to the openfoam singularity image
+export SINGULARITY_IMAGE=/nfs/openfoam10.sif
+
+# download the openfoam v10 singularity image if it is not available yet
+if [[ ! -f $SINGULARITY_IMAGE ]]
+then
+    echo "Fetching the singularity image for OpenFOAM-10"
+    curl -o $SINGULARITY_IMAGE --location "https://omnivector-public-assets.s3.us-west-2.amazonaws.com/singularity/openfoam10.sif"
+else
+    echo "Skipping the image fetch process...we already have the singularity image"
+fi
+
+
+# copy motorBike folder
+cp -r $OPENFOAM_DIR/tutorials/incompressible/simpleFoam/motorBike .
+
+# enter motorBike folder
+cd motorBike
+
+# clear any previous execution
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE ./Allclean
+
+# copy motorBike geometry obj
+cp $OPENFOAM_DIR/tutorials/resources/geometry/motorBike.obj.gz constant/geometry/
+
+# define surface features inside the block mesh
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE surfaceFeatures
+
+# generate the first mesh
+# mesh the environment (block around the model)
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE blockMesh
+
+# decomposition of mesh and initial field data
+# according to the parameters in decomposeParDict located in the system
+# create 6 domains by default
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE decomposePar -copyZero
+
+# mesh the motorcicle
+# overwrite the new mesh files that are generated
+srun singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE snappyHexMesh -overwrite -parallel
+
+# write field and boundary condition info for each patch
+srun singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE patchSummary -parallel
+
+# potential flow solver
+# solves the velocity potential to calculate the volumetric face-flux field
+srun singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE potentialFoam -parallel
+
+# steady-state solver for incompressible turbutent flows
+srun singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE simpleFoam -parallel
+
+# after a case has been run in parallel
+# it can be reconstructed for post-processing
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE reconstructParMesh -constant
+singularity exec --bind $PWD:$HOME $SINGULARITY_IMAGE reconstructPar -latestTime

examples/simple-application/templates/dummy-script.py.j2

@@ -0,0 +1,11 @@
+#!/bin/python3
+
+#SBATCH -J dummy_job
+#SBATCH -t 60
+
+print("Executing dummy job script")
+with open("dummy-ouput.txt", mode="w") as dump_file:
+    print("I am a very, very dumb job script", file=dump_file)
+    print("foo={{ data['foo'] }}", file=dump_file)
+    print("bar={{ data['bar'] }}", file=dump_file)
+    print("baz={{ data['baz'] }}", file=dump_file)

jobbergate-api/Dockerfile-dev

@@ -1,28 +1,19 @@
-FROM tiangolo/uvicorn-gunicorn-fastapi:python3.8-slim
+FROM python:3.8-slim-buster
 
-RUN apt-get -y update
-RUN apt-get install -y --fix-missing build-essential cmake libpq-dev curl
+RUN apt update && apt install -y curl libpq-dev gcc
 
-RUN pip install 'poetry==1.1.7'
+RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=/opt/poetry python && \
+    cd /usr/local/bin && \
+    ln -s /opt/poetry/bin/poetry && \
+    poetry config virtualenvs.create false
 
-ENV MODULE_NAME="jobbergate_api.main"
-
-COPY ./pyproject.toml /app/
-COPY ./poetry.lock /app/
-COPY ./dev_tools/entrypoint.sh /app/
-RUN chmod +x /app/entrypoint.sh
-
-ARG AWS_ACCESS_KEY_ID
-ENV AWS_ACCESS_KEY_ID=$AWS_ACCESS_KEY_ID
-
-ARG AWS_SECRET_ACCESS_KEY
-ENV AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY
-
-RUN poetry config virtualenvs.create false --local
-RUN poetry install
+COPY ./pyproject.toml ./poetry.lock* ./README* ./LICENSE* /app/
+WORKDIR /app
+RUN poetry install --no-root
 
 VOLUME /app/jobbergate_api
 VOLUME /app/dev_tools
 VOLUME /app/alembic
 
-ENTRYPOINT /app/entrypoint.sh
+ENTRYPOINT /app/dev_tools/entrypoint.sh
+#CMD ["uvicorn", "jobbergate_api.main:app", "--host", "0.0.0.0", "--port", "80"]

jobbergate-api/dev_tools/db.py

@@ -7,6 +7,8 @@
 
 import docker_gadgets
 import typer
+from alembic.config import Config
+from alembic.command import upgrade as sqla_upgrade, revision as sqla_migrate
 from loguru import logger
 
 from jobbergate_api.config import settings
@@ -75,16 +77,8 @@ def migrate(
     Create alembic migrations for a local database.
     """
     logger.debug(f"Creating migration with message: {message}")
-    commands = [
-        "alembic",
-        "--config=alembic/alembic.ini",
-        "revision",
-        f"--message={message}",
-    ]
-    if not blank:
-        commands.append("--autogenerate")
-
-    subprocess.run(commands)
+    config = Config(file_="alembic/alembic.ini")
+    sqla_migrate(config, message=message, autogenerate=not blank)
 
 
 @app.command()
@@ -93,11 +87,6 @@ def upgrade(target: str = typer.Option("head", help="The migration to which the
     Apply alembic migrations to a local database.
     """
     logger.debug("Upgrading database...")
-    commands = [
-        "alembic",
-        "--config=alembic/alembic.ini",
-        "upgrade",
-        target,
-    ]
-
-    subprocess.run(commands)
+
+    config = Config(file_="alembic/alembic.ini")
+    sqla_upgrade(config, target)

jobbergate-api/dev_tools/dev_server.py

@@ -47,6 +47,7 @@ def dev_server(
     Start a development server locally.
     """
     try:
+        logger.info("Waiting for the database")
         _wait_for_db(db_wait_count, db_wait_interval)
     except Exception:
         logger.error("Database is not available")

jobbergate-api/dev_tools/entrypoint.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
+set -e
+cd /app
 poetry run dev-tools db upgrade
-poetry run dev-tools dev-server --port=8000
-
-tail -f /dev/null
+poetry run dev-tools dev-server --port=80

jobbergate-api/dev_tools/show_env.py

@@ -1,6 +1,7 @@
 """
 Provide command for showing the current environment.
 """
+import json
 
 import typer
 
@@ -10,11 +11,11 @@
 
 
 @app.command()
-def show_env(json: bool = typer.Option(False, help="Dump as JSON")):
+def show_env(use_json: bool = typer.Option(False, "--json", help="Dump as JSON")):
     """
     Print out the current environment settings.
     """
-    if json:
+    if use_json:
         output = json.dumps(settings.dict())
     else:
         output = "\n  ".join(

jobbergate-api/jobbergate_api/config.py

@@ -39,7 +39,7 @@ class Settings(BaseSettings):
 
     DEPLOY_ENV: str = "LOCAL"
 
-    LOG_LEVEL: LogLevelEnum = LogLevelEnum.INFO
+    LOG_LEVEL: LogLevelEnum = LogLevelEnum.DEBUG
 
     # Database settings  # Default to values from docker-compose.yml
     DATABASE_HOST: str = "localhost"
@@ -61,6 +61,7 @@ class Settings(BaseSettings):
 
     # Security Settings. For details, see https://github.com/omnivector-solutions/armasec
     ARMASEC_DOMAIN: str
+    ARMASEC_USE_HTTPS: bool = Field(True)
     ARMASEC_AUDIENCE: Optional[HttpUrl]
     ARMASEC_DEBUG: bool = Field(False)
     ARMASEC_ADMIN_DOMAIN: Optional[str]