Merge pull request #188 from yardasol/mpi-arguments

Overhaul parallel runs

README.md

@@ -8,10 +8,9 @@ reactors.
 How to run SaltProc:
 
 cd /path/to/saltproc
-python saltproc -n 4 -d 1 -i examples/tap/tap_main.json
+python saltproc -s 2 -i examples/tap/tap_main.json
 ```
--n          number of cluster nodes to use in Serpent
--d          number of threads to use in Serpent
+-s          number of threads to use for shared-memory paralleism (optional)
 -i          path and name of SaltProc main input file
 ```
 

doc/fileformatspec/depcode_input.rst

@@ -340,6 +340,9 @@ OpenMC-specific properties
   :description:
     Path to fission Q values
 
+  :type:
+    ``string``, ``null``
+
   :default:
     ``null``
 
@@ -383,6 +386,9 @@ OpenMC-specific properties
   :description:
     Arguments for the fission yield helper
 
+  :type:
+    ``object``, ``null``
+
   :default:
     ``null``. See :ref:`openmc_constant_fission_yield_opts_properties`
     and :ref:`openmc_cutoff_fission_yield_opts_properties` for object
@@ -409,6 +415,9 @@ OpenMC-specific properties
 ``reaction_rate_opts``
 ~~~~~~~~~~~~~~~~~~~~~~
 
+  :type:
+    ``object``, ``null``
+
   :default:
     ``null``. See :ref:`openmc_flux_reaction_rate_opts_properties` for
     object properties when ``reaction_rate_mode`` is ``flux``.
@@ -433,6 +442,9 @@ OpenMC-specific properties
   :description:
     Depth of serach while reducing depletion chain
 
+  :type:
+    ``integer``, ``null``
+
   :default:
     ``null``
 

doc/fileformatspec/saltproc_input.rst

@@ -69,6 +69,27 @@ Required properties are as follows: ``proc_input_file``, ``dot_input_file``, ``o
     ``number``
 
 
+.. _mpi_args_property:
+
+``mpi_args``
+---------------------
+
+  :description:
+    Arguments for running simulations on supercomputers using ``mpiexec``
+    or similar programs
+
+  :type:
+    ``array``, ``null``
+
+  :items:
+
+    :type:
+      ``string``, ``integer``
+
+  :default:
+    ``null``
+
+
 .. _depcode_property:
 
 ``depcode``

doc/releasenotes/v0.5.0.rst

@@ -97,6 +97,9 @@ Python API Changes
 
 - Input file format changes:
 
+  - Removed the ``-n`` command line argument in favor of the new ``mpi_args`` input parameter
+  - Chaged the ``-d`` command line argument to ``-s``/``--threads``.
+  - (new)  → ``mpi_args``
   - Added default values for certain input parameters
   - Added depletion settings for OpenMC
   - ``num_depsteps`` → ``n_depletion_steps``
@@ -195,6 +198,11 @@ Python API Changes
     - (new) → ``timestep_units``
     - (new) → ``timestep_type``
 
+  - ``Simulation``
+
+    -  ``core_number`` →  (removed)
+    -  ``node_number`` →  (removed)
+
   - ``Sparger``
 
     - ``calc_rem_efficiency()`` → ``calculate_removal_efficiency``

saltproc/_schema_default.py

@@ -13,8 +13,9 @@ def set_defaults(validator, properties, instance, schema):
         ):
             yield error
 
+
     return validators.extend(
-        validator_class, {"properties" : set_defaults},
+        validator_class, {"properties" : set_defaults}
     )
 
 

saltproc/abc.py

@@ -101,15 +101,17 @@ def read_depleted_materials(self, read_at_end=False):
         """
 
     @abstractmethod
-    def run_depletion_step(self, cores, nodes):
+    def run_depletion_step(self, mpi_args, threads):
         """Runs a depletion step as a subprocess with the given parameters.
 
         Parameters
         ----------
-        cores : int
-            Number of cores to use for depletion code run.
-        nodes : int
-            Number of nodes to use for depletion code run.
+        mpi_args : list of str
+            Arguments for running simulations on supercomputers using
+            ``mpiexec`` or similar programs.
+        threads : int
+            Threads to use for shared-memory parallelism
+
         """
 
     @abstractmethod

saltproc/app.py

@@ -1,11 +1,12 @@
 from pathlib import Path
 from copy import deepcopy
+
 from collections import OrderedDict
 
 import argparse
 import numpy as np
-import json
-import jsonschema
+import traceback
+import json, jsonschema
 import gc
 import networkx as nx
 import pydotplus
@@ -28,14 +29,14 @@
 
 def run():
     """ Inititializes main run"""
-    nodes, cores, saltproc_input = parse_arguments()
-    input_path, process_file, dot_file, object_input = \
+    threads, saltproc_input = parse_arguments()
+    input_path, process_file, dot_file, mpi_args, object_input = \
         read_main_input(saltproc_input)
     _print_simulation_input_info(object_input[1], object_input[0])
     # Intializing objects
     depcode = _create_depcode_object(object_input[0])
     simulation = _create_simulation_object(
-        object_input[1], depcode, cores, nodes)
+        object_input[1], depcode)
     msr = _create_reactor_object(object_input[2])
 
     # Check: Restarting previous simulation or starting new?
@@ -47,7 +48,7 @@ def run():
         simulation.sim_depcode.write_runtime_input(msr,
                                                    step_idx,
                                                    simulation.restart_flag)
-        depcode.run_depletion_step(cores, nodes)
+        depcode.run_depletion_step(mpi_args, threads)
         if step_idx == 0 and simulation.restart_flag is False:  # First step
             # Read general simulation data which never changes
             simulation.store_run_init_info()
@@ -111,31 +112,24 @@ def parse_arguments():
 
     Returns
     -------
-    n: int
-        Number of nodes for use in depletion code simulation.
-    d: int
-        Number of cores for use in depletion code simulation.
-    i: str
+    s : int
+        Number of threads to use for shared-memory parallelism.
+    i : str
         Path and name of main SaltProc input file (json format).
 
     """
     parser = argparse.ArgumentParser()
-    parser.add_argument('-n',      # Number of nodes to use
-                        type=int,
-                        default=1,
-                        help='number of cluster nodes to use in \
-                        depletion code simulation')
-    parser.add_argument('-d',      # Number of cores to use
+    parser.add_argument('-s', '--threads',
                         type=int,
-                        default=1,
-                        help='number of threads to use in \
-                        depletion code simulation')
+                        default=None,
+                        help='Number of threads to use for shared-memory \
+                        parallelism.')
     parser.add_argument('-i',      # main input file
                         type=str,
                         default=None,
-                        help='path and name of SaltProc main input file')
+                        help='Path and name of SaltProc main input file')
     args = parser.parse_args()
-    return int(args.n), int(args.d), str(args.i)
+    return args.threads, args.i
 
 
 def read_main_input(main_inp_file):
@@ -154,6 +148,9 @@ def read_main_input(main_inp_file):
         Path to the `.json` file describing the fuel reprocessing components.
     dot_file : str
         Path to the `.dot` describing the fuel reprocessing paths.
+    mpi_args : list of str
+        Arguments for running simulations on supercomputers using mpiexec or
+        similar programs.
     object_inputs : 3-tuple of dict
         tuple containing the inputs for constructing the
         :class:`~saltproc.Depcode`, :class:`~saltproc.Simulation`, and
@@ -169,8 +166,13 @@ def read_main_input(main_inp_file):
             try:
                 DefaultFillingValidator(schema).validate(input_parameters)
             except jsonschema.exceptions.ValidationError:
-                print("Your input file is improperly structured.\
-                      Please see saltproc/tests/test.json for an example.")
+                print("Your input file is improperly structured: \n")
+                traceback.print_exc()
+            except jsonschema.exceptions.SchemaError:
+                traceback.print_exc()
+            except:
+                print("Something went wrong during schema validation.")
+                traceback.print_exc()
 
         # Global input path
         input_path = (Path.cwd() / Path(f.name).parents[0])
@@ -183,6 +185,7 @@ def read_main_input(main_inp_file):
             input_parameters['dot_input_file']).resolve())
         output_path = input_parameters['output_path']
         n_depletion_steps = input_parameters['n_depletion_steps']
+        mpi_args = input_parameters['mpi_args']
 
         # Global output path
         output_path = (input_path / output_path)
@@ -231,7 +234,7 @@ def read_main_input(main_inp_file):
         reactor_input = _process_main_input_reactor_params(
             reactor_input, n_depletion_steps, depcode_input['codename'])
 
-        return input_path, process_file, dot_file, (
+        return input_path, process_file, dot_file, mpi_args, (
             depcode_input, simulation_input, reactor_input)
 
 def _print_simulation_input_info(simulation_input, depcode_input):
@@ -258,13 +261,11 @@ def _create_depcode_object(depcode_input):
     return depcode
 
 
-def _create_simulation_object(simulation_input, depcode, cores, nodes):
+def _create_simulation_object(simulation_input, depcode):
     """Helper function for `run()` """
     simulation = Simulation(
         sim_name='Super test',
         sim_depcode=depcode,
-        core_number=cores,
-        node_number=nodes,
         restart_flag=simulation_input['restart_flag'],
         adjust_geo=simulation_input['adjust_geo'],
         db_path=simulation_input['db_name'])

saltproc/input_schema.json

@@ -24,6 +24,12 @@
             "description": "Number of steps for constant power and depletion interval case",
             "type": "number"
         },
+        "mpi_args": {
+            "description": "Arguments for running simulations on supercomputers using ``mpiexec`` or similar programs.",
+            "type": ["array", "null"],
+            "items": { "type": ["string", "integer"]},
+            "default": null
+        },
         "depcode": {
             "description": "Depcode class input parameters",
             "type": "object",
@@ -192,6 +198,7 @@
                                                 "default": "fission-q"},
                                             "fission_q": {
                                                 "description": "Path to fission Q values",
+                                                "type": ["string", "null"],
                                                 "default": null},
                                             "dilute_initial": {
                                                 "description": "Initial atom density to add for nuclides that are zero in initial condition.",
@@ -205,20 +212,23 @@
                                                 "default": "constant"},
                                             "fission_yield_opts": {
                                                 "description": "Arguments for the fission yield helper",
+                                                "type": ["object", "null"],
                                                 "default": null},
                                             "reaction_rate_mode": {
                                                 "description": "Indicate how one-group reaction rates should be calculated",
                                                 "type": "string",
                                                 "enum": ["direct", "flux"],
                                                 "default": "direct"},
                                             "reaction_rate_opts": {
+                                                "type": ["object", "null"],
                                                 "default": null},
                                             "reduce_chain": {
                                                 "description": "Whether or not to reduce the depletion chain.",
                                                 "type": "boolean",
                                                 "default": false},
                                             "reduce_chain_level": {
                                                 "description": "Depth of serach while reducing depletion chain",
+                                                "type": ["integer", "null"],
                                                 "default": null}
                                         },
                                         "default": {}
@@ -252,6 +262,7 @@
         "simulation": {
             "description": "Simulation class input parameters",
             "type": "object",
+            "default": {},
             "properties": {
                 "sim_name": {
                     "description": "Name of simulation",
@@ -270,12 +281,12 @@
                     "type": "boolean",
                     "default": false}
             },
-            "default": {},
             "required": ["sim_name"]
         },
         "reactor": {
             "description": "Reactor class input parameters",
             "type": "object",
+            "default": {},
             "properties": {
                 "volume": {
                     "description": "reactor core volume [cm^3]",
@@ -308,7 +319,6 @@
                     "enum": ["s", "sec", "min", "minute", "h", "hr", "hour", "d", "day", "a", "yr", "year", "MWd/kg", "mwd/kg", "MWD/KG", "MWD/kg", "MWd/KG"]
                     }
             },
-            "default": {},
             "required": ["volume", "mass_flowrate", "power_levels", "depletion_timesteps", "timestep_units"]
         }
     },