Experimental/warp x

.flake8

@@ -21,12 +21,22 @@ per-file-ignores =
         # init needs to import the logger.
         libensemble/__init__.py:F401
         libensemble/libensemble/__init__.py:F401
+
         # Need to turn of matching probes (before other imports) on some
         # systems/versions of MPI:
         libensemble/tests/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
         libensemble/libensemble/tests/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
         libensemble/tests/regression_tests/test_uniform_sampling_with_different_resources.py:E402
+
         # Matplotlib needs something set before import
         postproc_scripts/*:E402
+
+        # Ignoring linelength in APOSMM
         libensemble/gen_funcs/*aposmm.py:E501
         examples/gen_funcs/*aposmm.py:E501
+
+        # Need to set something before the APOSMM import
+        libensemble/tests/scaling_tests/warpx/run_libensemble_on_warpx.py:E402
+        libensemble/gen_funcs/persistent_aposmm.py:E402, E501
+        libensemble/tests/regression_tests/test_persistent_aposmm*:E402
+        libensemble/tests/regression_tests/test_aposmm*:E402

docs/conf.py

@@ -30,7 +30,7 @@ class Mock(MagicMock):
     def __getattr__(cls, name):
             return MagicMock()
 
-MOCK_MODULES = ['argparse', 'numpy', 'mpi4py' , 'scipy', 'numpy.lib', 'numpy.lib.recfunctions', 'math', 'petsc4py', 'PETSc', 'nlopt', 'scipy.spatial', 'scipy.spatial.distance']
+MOCK_MODULES = ['argparse', 'numpy', 'mpi4py' , 'dfols', 'scipy', 'numpy.lib', 'numpy.lib.recfunctions', 'math', 'petsc4py', 'PETSc', 'nlopt', 'scipy.spatial', 'scipy.spatial.distance']
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 #from libensemble import *

docs/data_structures/exit_criteria.rst

@@ -21,7 +21,7 @@ Exit criteria for libEnsemble::
 .. seealso::
   From `test_branin_aposmm_nlopt_and_then_scipy.py`_.
 
-  ..  literalinclude:: ../../libensemble/tests/regression_tests/test_sim_dirs.py
+  ..  literalinclude:: ../../libensemble/tests/regression_tests/test_aposmm_sim_dirs.py
       :start-at: exit_criteria
       :end-before: end_exit_criteria_rst_tag
 

docs/examples/gen_funcs.rst

@@ -13,8 +13,36 @@ sampling
   :undoc-members:
 
 APOSMM
-------
-.. automodule:: aposmm
+-----------------
+
+Asynchronously Parallel Optimization Solver for finding Multiple Minima
+(APOSMM) coordinates concurrent local optimization runs in order to identifying
+many local minima.
+
+Configuring APOSMM
+^^^^^^^^^^^^^^^^^^
+
+By default, APOSMM will import several optimizers which require
+external packages and MPI. To import only the optimizers you are using,
+add the following lines in that calling script, before importing APOSMM::
+
+    import libensemble.gen_funcs
+    libensemble.gen_funcs.rc.aposmm_optimizers = <optimizers>
+
+Where ``optimizer`` is a string (or list of strings) from the available options:
+
+``'petsc'``, ``'nlopt'``, ``'dfols'``, ``'scipy'``, ``'external'``
+
+Persistent APOSMM
+^^^^^^^^^^^^^^^^^
+
+.. automodule:: persistent_aposmm
+  :members:
+  :undoc-members:
+
+LocalOptInterfacer
+^^^^^^^^^^^^^^^^^^
+.. automodule:: aposmm_localopt_support
   :members:
   :undoc-members:
 
@@ -24,6 +52,18 @@ uniform_or_localopt
   :members:
   :undoc-members:
 
+persistent_deap_nsga2
+---------------------------
+.. automodule:: persistent_deap_nsga2
+  :members:
+  :undoc-members:
+
+persistent_tasmanian
+---------------------------
+.. automodule:: persistent_tasmanian
+  :members:
+  :undoc-members:
+
 persistent_uniform_sampling
 ---------------------------
 .. automodule:: persistent_uniform_sampling

libensemble/executors/mpi_executor.py

@@ -96,17 +96,18 @@ def __init__(self, auto_resources=True,
         mpi_commands = {
             'mpich': ['mpirun', '--env {env}', '-machinefile {machinefile}',
                       '-hosts {hostlist}', '-np {num_procs}',
-                      '--ppn {ranks_per_node}'],
+                      '--ppn {ranks_per_node}', '{extra_args}'],
             'openmpi': ['mpirun', '-x {env}', '-machinefile {machinefile}',
                         '-host {hostlist}', '-np {num_procs}',
-                        '-npernode {ranks_per_node}'],
+                        '-npernode {ranks_per_node}', '{extra_args}'],
             'aprun': ['aprun', '-e {env}',
                       '-L {hostlist}', '-n {num_procs}',
-                      '-N {ranks_per_node}'],
-            'jsrun': ['jsrun', '--np {num_procs}'],  # Need to add more
+                      '-N {ranks_per_node}', '{extra_args}'],
+            'jsrun': ['jsrun', '{extra_args}'],  # Relies on extra_args
             'srun': ['srun', '-w {hostlist}', '-n {num_procs}',
                      '--nodes {num_nodes}',
-                     '--ntasks-per-node {ranks_per_node}']
+                     '--ntasks-per-node {ranks_per_node}',
+                     '{extra_args}']
         }
         self.mpi_launch_type = MPIResources.get_MPI_variant()
         self.mpi_command = mpi_commands[self.mpi_launch_type]
@@ -212,7 +213,8 @@ def _launch_with_retries(self, task, runline, wait_on_run):
     def submit(self, calc_type, num_procs=None, num_nodes=None,
                ranks_per_node=None, machinefile=None, app_args=None,
                stdout=None, stderr=None, stage_inout=None,
-               hyperthreads=False, test=False, wait_on_run=False):
+               hyperthreads=False, test=False, wait_on_run=False,
+               extra_args=None):
         """Creates a new task, and either executes or schedules execution.
 
         The created task object is returned.
@@ -285,6 +287,7 @@ def submit(self, calc_type, num_procs=None, num_nodes=None,
         mpi_specs = self._get_mpi_specs(task, num_procs, num_nodes,
                                         ranks_per_node, machinefile,
                                         hyperthreads)
+        mpi_specs['extra_args'] = extra_args
         runline = launcher.form_command(self.mpi_command, mpi_specs)
         runline.extend(task.app.full_path.split())
         if task.app_args is not None:

libensemble/gen_funcs/__init__.py

@@ -0,0 +1,19 @@
+def rc(**kargs):
+    """Runtime configuration options.
+
+    Parameters
+    ----------
+    aposmm_optimizers : string or list of strings
+        Select the aposmm optimizer/s (to prevent all options being imported).
+
+
+    """
+    for key in kargs:
+        if not hasattr(rc, key):
+            raise TypeError("unexpected argument '{0}'".format(key))
+    for key, value in kargs.items():
+        setattr(rc, key, value)
+
+
+rc.aposmm_optimizers = None
+__import__('sys').modules[__name__ + '.rc'] = rc

libensemble/gen_funcs/aposmm.py

@@ -11,16 +11,32 @@
 import traceback
 import numpy as np
 from scipy.spatial.distance import cdist, pdist, squareform
-from scipy import optimize as scipy_optimize
-
-from mpi4py import MPI
-from petsc4py import PETSc
-
 from numpy.lib.recfunctions import merge_arrays
-
 from math import log, gamma, pi, sqrt
 
-import nlopt
+import libensemble.gen_funcs
+optimizer_list = ['petsc', 'nlopt', 'scipy']
+optimizers = libensemble.gen_funcs.rc.aposmm_optimizers
+
+if optimizers is None:
+    from mpi4py import MPI
+    from petsc4py import PETSc
+    import nlopt
+    from scipy import optimize as scipy_optimize
+else:
+    if not isinstance(optimizers, list):
+        optimizers = [optimizers]
+    unrec = set(optimizers) - set(optimizer_list)
+    if unrec:
+        print('APOSMM Warning: unrecognized optimizers {}'.format(unrec))
+
+    if 'petsc' in optimizers:
+        from mpi4py import MPI
+        from petsc4py import PETSc
+    if 'nlopt' in optimizers:
+        import nlopt
+    if 'scipy' in optimizers:
+        from scipy import optimize as scipy_optimize
 
 
 class APOSMMException(Exception):