Gate mpi4py import on MPI launcher environment (fixes #744)

src/shapepipe/run.py

@@ -6,6 +6,7 @@
 
 """
 
+import os
 import sys
 from datetime import datetime
 from importlib.metadata import requires
@@ -22,12 +23,27 @@
 from shapepipe.pipeline.job_handler import JobHandler
 from shapepipe.pipeline.mpi_run import split_mpi_jobs, submit_mpi_jobs
 
-try:
-    from mpi4py import MPI
-except ImportError:  # pragma: no cover
-    import_mpi = False
+# Importing mpi4py initializes MPI immediately, which aborts the whole
+# process when no MPI launcher is available — e.g. inside an
+# ``srun``-launched shell on a SLURM cluster, where Open MPI detects the
+# SLURM step environment, expects a PMI server that srun never started,
+# and calls MPI_Abort before even ``shapepipe_run -h`` can print (#744).
+# Only import (and hence initialize) MPI when a launcher environment is
+# actually present: ``mpirun``/``orterun`` set OMPI_COMM_WORLD_SIZE,
+# ``srun --mpi=pmi2`` sets PMI_RANK and ``srun --mpi=pmix`` sets
+# PMIX_RANK. A bare ``shapepipe_run`` (login node, compute-node shell,
+# container) runs in SMP mode without ever touching MPI.
+_MPI_LAUNCHER_VARS = ("OMPI_COMM_WORLD_SIZE", "PMI_RANK", "PMIX_RANK")
+
+if any(var in os.environ for var in _MPI_LAUNCHER_VARS):
+    try:
+        from mpi4py import MPI
+    except ImportError:  # pragma: no cover
+        import_mpi = False
+    else:
+        import_mpi = True
 else:
-    import_mpi = True
+    import_mpi = False
 
 
 class ShapePipe:
@@ -178,7 +194,7 @@ def _check_dependencies(self):
         module_dep = self._get_module_depends("depends") + __installs__
         module_exe = self._get_module_depends("executes")
 
-        module_dep += ["mpi4py"] if import_mpi else module_dep
+        module_dep += ["mpi4py"] if import_mpi else []
 
         exe_to_module = {
             exe: module

src/shapepipe/tests/test_run.py

@@ -0,0 +1,54 @@
+"""UNIT TESTS FOR RUN.
+
+This module contains unit tests for the shapepipe.run module, in
+particular the MPI-launcher gating of the mpi4py import (#744): a bare
+``shapepipe_run`` must never initialize MPI, otherwise the whole process
+aborts inside an ``srun``-launched shell whose Open MPI lacks SLURM PMI
+support.
+
+:Author: Claude (on behalf of Cail Daley) <cail.daley@cea.fr>
+
+"""
+
+import os
+import subprocess
+import sys
+
+import pytest
+
+SNIPPET = "import shapepipe.run as r; print(r.import_mpi)"
+
+# Env vars that either mark an MPI launcher (the gate) or make Open MPI
+# believe it was direct-launched by srun (the failure mode under test).
+_SCRUBBED_PREFIXES = ("OMPI_", "PMI_", "PMIX_", "SLURM_")
+
+
+def _import_mpi_flag(extra_env):
+    """Report shapepipe.run.import_mpi in a subprocess with a clean env."""
+    env = {
+        key: value
+        for key, value in os.environ.items()
+        if not key.startswith(_SCRUBBED_PREFIXES)
+    }
+    env.update(extra_env)
+    result = subprocess.run(
+        [sys.executable, "-c", SNIPPET],
+        env=env,
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 0, (
+        f"subprocess failed (exit {result.returncode}): {result.stderr}"
+    )
+    return result.stdout.strip()
+
+
+def test_bare_launch_skips_mpi():
+    """A bare launch (no MPI launcher env) must not import/init MPI."""
+    assert _import_mpi_flag({}) == "False"
+
+
+def test_mpirun_launch_imports_mpi():
+    """An mpirun-style env (OMPI_COMM_WORLD_SIZE) must import MPI."""
+    pytest.importorskip("mpi4py")
+    assert _import_mpi_flag({"OMPI_COMM_WORLD_SIZE": "1"}) == "True"