Add optional MPI for ceptr

Docs/sphinx/Ceptr.rst

@@ -1,7 +1,7 @@
 .. highlight:: rst
 
 .. _sec:ceptr:
-               
+
 CEPTR: Chemistry Evaluation for Pele Through Recasting
 ======================================================
 
@@ -19,10 +19,12 @@ To install CEPTR dependencies::
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry update
 
-
 Usage
 -----
 
+Generating for a single chemistry
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 There are three ways to use CEPTR to generate C++ mechanism files for a given chemistry
 
 1. Using CEPTR directly::
@@ -39,11 +41,23 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch
      $ bash ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/converter.sh -f ./LiDryer/mechanism.yaml
 
 
+Batched generation
+^^^^^^^^^^^^^^^^^^
+
 For non-reduced chemistries, CEPTR can take a file with a list of ``mechanism.yaml`` files to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
 
+.. note::
+
+   If you are generating many mechanisms at once (e.g., a list of mechanism files), then you may want to consider using MPI. `mpi4py` is an optional dependency that can be installed and then used like this::
+
+     $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
+     $ poetry install -E mpi
+     $ poetry run mpirun -np 8 convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
+
+
 For reduced chemistries, CEPTR can take a file with a list of ``qssa.yaml`` and ``qssa_input.toml`` to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
@@ -99,5 +113,3 @@ The full list of options is::
 For a detailed description of these options and a further information on the way QSS mechanism are treated in `CEPTR` the reader may consult :ref:`the QSS section <sec_qss>`.
 
 See Tutorials (:ref:`Generating NC12H26 QSS mechanism with analytical jacobian <sec_tutqss1>` and :ref:`Generating NC12H26 QSS mechanism without analytical jacobian <sec_tutqss2>`) for generating QSS mechanisms from the ``.yaml`` files.
-
-

Support/ceptr/ceptr/ceptr.py

@@ -7,6 +7,24 @@
 import cantera as ct
 
 import ceptr.converter as converter
+import ceptr.optional_mpi as ompi
+
+
+def parse_lst_file(lst):
+    """Parse a file containing a list of mechanism files."""
+    fnames = []
+    with open(lst, "r") as f:
+        for line in f:
+            if not line.startswith("#"):
+                fnames.append(line)
+
+    if ompi.use_mpi():
+        comm = ompi.world_comm()
+        rank = comm.Get_rank()
+        nprocs = comm.Get_size()
+        fnames = fnames[rank::nprocs]
+
+    return fnames
 
 
 def convert(
@@ -35,17 +53,16 @@ def convert_lst(
 ):
     """Convert mechanisms from a file containing a list of directories."""
     lpath = pathlib.Path(lst)
-    with open(lst, "r") as f:
-        for line in f:
-            if not line.startswith("#"):
-                mechname = lpath.parents[0] / line.strip()
-                print(f"""Converting file {mechname}""")
-                convert(
-                    mechname,
-                    jacobian,
-                    qss_format_input,
-                    qss_symbolic_jac,
-                )
+    lines = parse_lst_file(lst)
+    for line in lines:
+        mechname = lpath.parents[0] / line.strip()
+        print(f"""Converting file {mechname}""")
+        convert(
+            mechname,
+            jacobian,
+            qss_format_input,
+            qss_symbolic_jac,
+        )
 
 
 def convert_lst_qss(
@@ -54,19 +71,18 @@ def convert_lst_qss(
 ):
     """Convert QSS mechanisms from a file of directories and format input."""
     lpath = pathlib.Path(lst)
-    with open(lst, "r") as f:
-        for line in f:
-            if not line.startswith("#"):
-                mech_file, format_file, _, _ = line.split()
-                mechname = lpath.parents[0] / mech_file.strip()
-                qss_format_input = lpath.parents[0] / format_file.strip()
-                print(f"""Converting file {mechname}""")
-                convert(
-                    mechname,
-                    jacobian,
-                    qss_format_input,
-                    True,
-                )
+    lines = parse_lst_file(lst)
+    for line in lines:
+        mech_file, format_file, _, _ = line.split()
+        mechname = lpath.parents[0] / mech_file.strip()
+        qss_format_input = lpath.parents[0] / format_file.strip()
+        print(f"""Converting file {mechname}""")
+        convert(
+            mechname,
+            jacobian,
+            qss_format_input,
+            True,
+        )
 
 
 def main():

Support/ceptr/ceptr/optional_mpi.py

@@ -0,0 +1,19 @@
+"""Optional import of mpi4py, only if available in the environment."""
+
+import sys
+
+try:
+    from mpi4py import MPI
+
+except ModuleNotFoundError:
+    pass
+
+
+def use_mpi():
+    """Detect if mpi4py was imported."""
+    return "mpi4py" in sys.modules
+
+
+def world_comm():
+    """Return the world communicator."""
+    return MPI.COMM_WORLD

Support/ceptr/pyproject.toml

@@ -17,6 +17,7 @@ sympy = "^1.12"
 symengine = "^0.9.2"
 pandas = ">=2.0.3"
 toml = ">=0.10.2"
+mpi4py = {version = "^3.1.5", optional = true}
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.4.0"
@@ -30,6 +31,9 @@ flake8-docstrings = "^1.7.0"
 flake8-use-fstring = "^1.4"
 flynt = "^0.77"
 
+[tool.poetry.extras]
+mpi = ["mpi4py"]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"