Merge pull request #694 from adi611/adi611-patch-testpsij-1

Draft: Adding new worker which uses PSI/J to run tasks

Author: djarecka

.github/workflows/testpsijlocal.yml

@@ -0,0 +1,45 @@
+name: PSI/J-Local
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.11']
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ github.repository }}
+
+      - name: Setup Python version ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies for PSI/J
+        run: |
+          pip install -e ".[test, psij]"
+
+      - name: Run tests for PSI/J
+        run: |
+          pytest --color=yes -vs --psij=local -n auto pydra/engine --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
+
+      - name: Upload to codecov
+        run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

.github/workflows/testpsijslurm.yml

@@ -0,0 +1,54 @@
+name: PSI/J-SLURM
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: [3.11.5]
+      fail-fast: false
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
+
+    steps:
+    - name: Disable etelemetry
+      run: echo "NO_ET=TRUE" >> $GITHUB_ENV
+    - uses: actions/checkout@v4
+    - name: Pull docker image
+      run: |
+        docker pull $DOCKER_IMAGE
+        # Have image running in the background
+        docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
+    - name: Display previous jobs with sacct
+      run: |
+        echo "Allowing ports/daemons time to start" && sleep 10
+        docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
+        docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
+        if [ $? -ne 0 ]; then
+            echo "Slurm docker image error"
+            exit 1
+        fi
+    - name: Setup Python
+      run: |
+        docker exec slurm bash -c "echo $NO_ET"
+        docker exec slurm bash -c "ls -la && echo list top level dir"
+        docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
+        if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
+            docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
+        fi
+        docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
+        docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test,psij] && python -c 'import pydra; print(pydra.__version__)'"
+    - name: Run pytest
+      run: |
+        docker exec slurm bash -c "pytest --color=yes -vs -n auto --psij=slurm --cov pydra --cov-config /pydra/.coveragerc --cov-report xml:/pydra/cov.xml --doctest-modules /pydra/pydra/ -k 'not test_audit_prov and not test_audit_prov_messdir_1 and not test_audit_prov_messdir_2 and not test_audit_prov_wf and not test_audit_all'"
+    - name: Upload to codecov
+      run: |
+        docker exec slurm bash -c "pip install urllib3==1.26.6"
+        docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
+        docker rm -f slurm

pydra/conftest.py

@@ -7,6 +7,12 @@
 
 def pytest_addoption(parser):
     parser.addoption("--dask", action="store_true", help="run all combinations")
+    parser.addoption(
+        "--psij",
+        action="store",
+        help="run with psij subtype plugin",
+        choices=["local", "slurm"],
+    )
 
 
 def pytest_generate_tests(metafunc):
@@ -21,6 +27,16 @@ def pytest_generate_tests(metafunc):
         except ValueError:
             # Called as --pyargs, so --dask isn't available
             pass
+        try:
+            if metafunc.config.getoption("psij"):
+                Plugins.append("psij-" + metafunc.config.getoption("psij"))
+                if (
+                    bool(shutil.which("sbatch"))
+                    and metafunc.config.getoption("psij") == "slurm"
+                ):
+                    Plugins.remove("slurm")
+        except ValueError:
+            pass
         metafunc.parametrize("plugin_dask_opt", Plugins)
 
     if "plugin" in metafunc.fixturenames:
@@ -35,6 +51,16 @@ def pytest_generate_tests(metafunc):
             Plugins = ["slurm"]
         else:
             Plugins = ["cf"]
+        try:
+            if metafunc.config.getoption("psij"):
+                Plugins.append("psij-" + metafunc.config.getoption("psij"))
+                if (
+                    bool(shutil.which("sbatch"))
+                    and metafunc.config.getoption("psij") == "slurm"
+                ):
+                    Plugins.remove("slurm")
+        except ValueError:
+            pass
         metafunc.parametrize("plugin", Plugins)
 
 

pydra/engine/run_pickled.py

@@ -0,0 +1,31 @@
+import pickle
+import sys
+from pydra.engine.helpers import load_and_run
+
+
+def run_pickled(*file_paths, rerun=False):
+    loaded_objects = []
+
+    for file_path in file_paths:
+        with open(file_path, "rb") as file:
+            loaded_objects.append(pickle.load(file))
+
+    if len(loaded_objects) == 1:
+        result = loaded_objects[0](rerun=rerun)
+    elif len(loaded_objects) == 2:
+        result = load_and_run(loaded_objects[0], loaded_objects[1], rerun=rerun)
+    else:
+        raise ValueError("Unsupported number of loaded objects")
+
+    print(f"Result: {result}")
+
+
+if __name__ == "__main__":
+    rerun = False  # Default value for rerun
+    file_paths = sys.argv[1:]
+
+    if "--rerun" in file_paths:
+        rerun = True
+        file_paths.remove("--rerun")
+
+    run_pickled(*file_paths, rerun=rerun)

pydra/engine/tests/test_workflow.py

@@ -4092,7 +4092,7 @@ def test_wf_lzoutall_st_2a(plugin, tmpdir):
     wf.plugin = plugin
     wf.cache_dir = tmpdir
 
-    with Submitter(plugin="cf") as sub:
+    with Submitter(plugin=plugin) as sub:
         sub(wf)
 
     assert wf.output_dir.exists()

pydra/engine/workers.py

@@ -892,10 +892,158 @@ def close(self):
         pass
 
 
+class PsijWorker(Worker):
+    """A worker to execute tasks using PSI/J."""
+
+    def __init__(self, subtype, **kwargs):
+        """
+        Initialize PsijWorker.
+
+        Parameters
+        ----------
+        subtype : str
+            Scheduler for PSI/J.
+        """
+        try:
+            import psij
+        except ImportError:
+            logger.critical("Please install psij.")
+            raise
+        logger.debug("Initialize PsijWorker")
+        self.psij = psij
+
+        # Check if the provided subtype is valid
+        valid_subtypes = ["local", "slurm"]
+        if subtype not in valid_subtypes:
+            raise ValueError(
+                f"Invalid 'subtype' provided. Available options: {', '.join(valid_subtypes)}"
+            )
+
+        self.subtype = subtype
+
+    def run_el(self, interface, rerun=False, **kwargs):
+        """Run a task."""
+        return self.exec_psij(interface, rerun=rerun)
+
+    def make_spec(self, cmd=None, arg=None):
+        """
+        Create a PSI/J job specification.
+
+        Parameters
+        ----------
+        cmd : str, optional
+            Executable command. Defaults to None.
+        arg : list, optional
+            List of arguments. Defaults to None.
+
+        Returns
+        -------
+        psij.JobSpec
+            PSI/J job specification.
+        """
+        spec = self.psij.JobSpec()
+        spec.executable = cmd
+        spec.arguments = arg
+
+        return spec
+
+    def make_job(self, spec, attributes):
+        """
+        Create a PSI/J job.
+
+        Parameters
+        ----------
+        spec : psij.JobSpec
+            PSI/J job specification.
+        attributes : any
+            Job attributes.
+
+        Returns
+        -------
+        psij.Job
+            PSI/J job.
+        """
+        job = self.psij.Job()
+        job.spec = spec
+        return job
+
+    async def exec_psij(self, runnable, rerun=False):
+        """
+        Run a task (coroutine wrapper).
+
+        Raises
+        ------
+        Exception
+            If stderr is not empty.
+
+        Returns
+        -------
+        None
+        """
+        import pickle
+        from pathlib import Path
+
+        jex = self.psij.JobExecutor.get_instance(self.subtype)
+        absolute_path = Path(__file__).parent
+
+        if isinstance(runnable, TaskBase):
+            cache_dir = runnable.cache_dir
+            file_path = cache_dir / "runnable_function.pkl"
+            with open(file_path, "wb") as file:
+                pickle.dump(runnable._run, file)
+            func_path = absolute_path / "run_pickled.py"
+            spec = self.make_spec("python", [func_path, file_path])
+        else:  # it could be tuple that includes pickle files with tasks and inputs
+            cache_dir = runnable[-1].cache_dir
+            file_path_1 = cache_dir / "taskmain.pkl"
+            file_path_2 = cache_dir / "ind.pkl"
+            ind, task_main_pkl, task_orig = runnable
+            with open(file_path_1, "wb") as file:
+                pickle.dump(task_main_pkl, file)
+            with open(file_path_2, "wb") as file:
+                pickle.dump(ind, file)
+            func_path = absolute_path / "run_pickled.py"
+            spec = self.make_spec(
+                "python",
+                [
+                    func_path,
+                    file_path_1,
+                    file_path_2,
+                ],
+            )
+
+        if rerun:
+            spec.arguments.append("--rerun")
+
+        spec.stdout_path = cache_dir / "demo.stdout"
+        spec.stderr_path = cache_dir / "demo.stderr"
+
+        job = self.make_job(spec, None)
+        jex.submit(job)
+        job.wait()
+
+        if spec.stderr_path.stat().st_size > 0:
+            with open(spec.stderr_path, "r") as stderr_file:
+                stderr_contents = stderr_file.read()
+            raise Exception(
+                f"stderr_path '{spec.stderr_path}' is not empty. Contents:\n{stderr_contents}"
+            )
+
+        return
+
+    def close(self):
+        """Finalize the internal pool of tasks."""
+        pass
+
+
 WORKERS = {
     "serial": SerialWorker,
     "cf": ConcurrentFuturesWorker,
     "slurm": SlurmWorker,
     "dask": DaskWorker,
     "sge": SGEWorker,
+    **{
+        "psij-" + subtype: lambda subtype=subtype: PsijWorker(subtype=subtype)
+        for subtype in ["local", "slurm"]
+    },
 }

pyproject.toml

@@ -48,6 +48,9 @@ classifiers = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
+psij = [
+    "psij-python",
+]
 dask = [
     "dask",
     "distributed",