Changeset 224


Ignore:
Timestamp:
05/02/10 23:42:45 (6 years ago)
Author:
mmckerns
Message:

cleanup after core of pyina moves to pathos; remainder moves to mpimystic

Files:
25 deleted
16 edited
8 copied
1 moved

Legend:

Unmodified
Added
Removed

  • mpimystic/Make.mm

    r222 r224  
    11# -*- Makefile -*- 
    22 
    3 PROJECT = pyina 
     3PROJECT = mpimystic 
    44 
    55BUILD_DIRS = \ 
    6     pyinamodule \ 
    7     pyina \ 
    8     tools \ 
    9     applications \ 
     6    mpimystic \ 
    107 
    118OTHER_DIRS = \ 
    … …  
    1310    examples \ 
    1411    examples_other \ 
    15     examples_raw \ 
    16     examples_ezmap \ 
    1712 
    1813RECURSE_DIRS = $(BUILD_DIRS) $(OTHER_DIRS) 

  • mpimystic/examples/Make.mm

    r222 r224  
    11# -*- Makefile -*- 
    22 
    3 PROJECT = pyina 
     3PROJECT = mpimystic 
    44PACKAGE = examples 
    55 

  • mpimystic/examples/ezmap_desolve.py

    r205 r224  
    2323 
    2424from mystic.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
    25 from pyina.differential_evolution_ezmap import ezDESolver as pDESolve 
     25from mpimystic.differential_evolution_ezmap import ezDESolver as pDESolve 
    2626from pyina.launchers import mpirun_launcher 
    2727from pyina.mappers import equalportion_mapper 

  • mpimystic/examples/ezmap_desolve_rosen.py

    r205 r224  
    2323 
    2424from mystic.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
    25 from pyina.differential_evolution_ezmap import ezDESolver as pDESolve 
     25from mpimystic.differential_evolution_ezmap import ezDESolver as pDESolve 
    2626from pyina.launchers import mpirun_launcher 
    2727from pyina.mappers import equalportion_mapper 

  • mpimystic/examples_other/Make.mm

    r222 r224  
    11# -*- Makefile -*- 
    22 
    3 PROJECT = pyina 
     3PROJECT = mpimystic 
    44PACKAGE = examples_other 
    55 
    6 PROJ_TIDY += xx.* 
    7 PROJ_CLEAN += 
     6PROJ_TIDY += *.log *.png *.dat *.out.X *.out.Y *out.V tmp* 
     7PROJ_CLEAN = 
    88 
    9 all: export 
     9#-------------------------------------------------------------------------- 
     10 
     11#all: export 
     12all: clean 
    1013 
    1114release: tidy 
    … …  
    2124#EXPORT_PYTHON_MODULES = \ 
    2225EXPORT_BINS = \ 
    23     hello.py \ 
    24     pypi.py \ 
    25     nodes.py 
    26     test1.py \ 
    27     test2.py \ 
    28     test3.py \ 
    29     test_pmap.py \ 
    30     test_parallelmap.py \ 
    31     logging.py \ 
    32     test_ports.py \ 
    33     test_mogi_bcast.py \ 
    34 #   test_mogi_future.py \ 
     26    parallel_desolve.py \ 
     27    pyre_differential_evolution.py \ 
     28    test_mpimogi.py \ 
     29    test_mpimogi2.py \ 
     30    test_mpimogi3.py \ 
     31#   test_br8_mpi.py \ 
     32#   test_tg3.py \ 
    3533 
    3634 
    … …  
    3937 
    4038 
    41  
    4239# End of file 
    4340 

  • mpimystic/examples_other/parallel_desolve.py

    r222 r224  
    2222""" % { 'file' : __file__, 'launchers' : launchers.getstr({'file':__file__, 'timelimit':'00:05'}) } 
    2323 
    24 from pyina.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
     24from mpimystic.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
    2525from pyina.parallel_map2 import parallel_map 
    2626from mystic.termination import ChangeOverGeneration, VTR 

  • mpimystic/examples_other/pyre_differential_evolution.py

    r222 r224  
    1111This script will demo a Chebyshev8 fit (also see mystic/examples/test_ffit). 
    1212""" 
    13 from pyina.differential_evolution_app import * 
     13from mpimystic.differential_evolution_app import * 
    1414from mystic.termination import ChangeOverGeneration, VTR 
    1515from mystic.tools import VerboseSow 

  • mpimystic/examples_other/test_mpimogi.py

    r222 r224  
    1919""" 
    2020 
    21 from pyina.differential_evolution_app import PyreDifferentialEvolutionSolver2 
     21from mpimystic.differential_evolution_app import PyreDifferentialEvolutionSolver2 
    2222from mystic.termination import ChangeOverGeneration, VTR 
    2323from mystic.tools import VerboseSow 

  • mpimystic/examples_other/test_mpimogi2.py

    r222 r224  
    55""" 
    66 
    7 from pyina.differential_evolution_app import PyreDifferentialEvolutionSolver2 
     7from mpimystic.differential_evolution_app import PyreDifferentialEvolutionSolver2 
    88from mystic.termination import ChangeOverGeneration, VTR 
    99from mystic.tools import VerboseSow 

  • mpimystic/examples_other/test_mpimogi3.py

    r222 r224  
    2525""" % { 'launchers' : launchers.getstr({'timelimit' : '00:05','nodes':'6'}) } 
    2626 
    27 from pyina.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
     27from mpimystic.differential_evolution import DifferentialEvolutionSolver2 as DESolve 
    2828from pyina.parallel_map2 import parallel_map 
    2929from mystic.termination import ChangeOverGeneration, VTR 

  • mpimystic/mpimystic/Make.mm

    r207 r224  
    11# -*- Makefile -*- 
    22 
    3 PROJECT = pyina 
    4 PACKAGE = pyina 
     3PROJECT = mpimystic 
     4PACKAGE = mpimystic 
    55 
    66BUILD_DIRS = \ 
    … …  
    2626EXPORT_PYTHON_MODULES = \ 
    2727    __init__.py \ 
    28     mpiconsts.py \ 
    2928    differential_evolution.py \ 
    3029    differential_evolution_app.py \ 
    3130    differential_evolution_ezmap.py \ 
    32     parallel_map.py \ 
    33     parallel_map2.py \ 
    34     ez_map.py \ 
    35     launchers.py \ 
    36     mappers.py \ 
    37     tools.py \ 
    3831 
    3932 

  • mpimystic/mpimystic/README

    r196 r224  
    22of the mystic inversion framework.  The core launcher uses mpi. 
    33 
    4 This package was adapted from the pyina CVS 2008-07-07. 
    5 It requires: 
    6  - numpy 
     4This package was adapted from the pyina CVS 2008-07-07.  Pyina's 
     5"map-reduce" core has been splintered off and now is part of pathos. 
     6The remaining parts are mystic solvers, modified for parallel computing. 
     7This package requires: 
    78 - mystic 
    8  - pyre.mpi (built from svn@danse.us/pyre/branches/mpi-lib) 
    9  - journal (part of pythia-0.8; see http://danse.us/trac/pyre) 
    10  - dill (part of pathos; see http://dev.danse.us/trac/pathos) 
     9 - pyina 
    1110 
    12 pyina/differential_evolution.py is an "incorrect" implementation 
    13 pyina/differential_evolution_ezmap.py hides mpi within "map" and "launcher" 
    14  - ez_map: writes costfunc to temporary sourcefile (.py) 
    15  - ez_map2: writes costfunc to temporary picklefile (.pik) 
     11mpimystic/differential_evolution.py is an "incorrect" implementation 
     12mpimystic/differential_evolution_ezmap.py hides mpi within "map" and "launcher" 
     13 - ez_map: writes cost_function to temporary sourcefile (.py) 
     14 - ez_map2: writes cost_function to temporary picklefile (.pik) 
    1615 
    1716 
    … …  
    2221you _must_ copy some files from mystic/examples. 
    2322 
    24  * Change to the pyina root directory 
     23 * Change to the mpimystic root directory 
    2524     $ cd .. 
    2625 * Copy the files: 
    … …  
    3130 
    3231WARNING: 
    33 To run pyina code, you _must_ have your console configured for MPI. 
     32To run mpimystic code, you _must_ have your console configured for MPI. 
    3433  * Start mpd 
    3534     $ mpd & 

  • mpimystic/mpimystic/__init__.py

    r196 r224  
    1111 
    1212""" 
    13 A Simple Model-Independent Inversion Framework. 
     13mpimystic: a Simple Model-Independent Inversion Framework (MPI version) 
    1414""" 
    1515 
    16 from mpiconsts import mpi 
    17  
    18 # launchers 
    19  
    20 # mappers 
    21 import parallel_map, parallel_map2 
     16from pyina.mpiconsts import mpi 
    2217 
    2318# solvers 
    2419import differential_evolution 
    25 #import differential_evolution_ezmap 
     20import differential_evolution_ezmap 
    2621 
    2722# strategies, termination conditions 
    2823 
    2924# monitors, function wrappers, and other tools 
    30 from tools import * 
    3125 
    3226 

  • mpimystic/mpimystic/differential_evolution.py

    r150 r224  
    5959from pyina._pyina import bcastString, sendString, receiveString 
    6060 
    61 import mpiconsts 
     61from pyina import mpiconsts 
    6262MPI_ANY_SOURCE = mpiconsts.mpi.MPI_ANY_SOURCE 
    6363MPI_ANY_TAG = mpiconsts.mpi.MPI_ANY_TAG 

  • mpimystic/mpimystic/differential_evolution_app.py

    r141 r224  
    4141 
    4242# MPI ######### 
    43 import mpiconsts 
     43from pyina import mpiconsts 
    4444MPI_ANY_SOURCE = mpiconsts.mpi.MPI_ANY_SOURCE 
    4545MPI_ANY_TAG = mpiconsts.mpi.MPI_ANY_TAG 

  • mpimystic/mpimystic/differential_evolution_ezmap.py

    r221 r224  
    130130        #------------------------------------------------------------- 
    131131 
    132        #from ez_map import ez_map             # sourced function 
    133         from ez_map import ez_map2 as ez_map  # pickled function 
     132       #from pyina.ez_map import ez_map             # sourced function 
     133        from pyina.ez_map import ez_map2 as ez_map  # pickled function 
    134134 
    135135        import signal 

  • mpimystic/mystic_files.py

    r222 r224  
    77 
    88target_dir = os.curdir+os.sep+PATH_1+os.sep 
    9 destination_dir = os.curdir+os.sep+"examples_raw"+os.sep 
     9destination_dir = os.curdir+os.sep+"examples_other"+os.sep 
    1010 
    1111def copy(): 

  • mpimystic/setup.py

    r222 r224  
    44# 
    55#                       Patrick Hung & Mike McKerns, Caltech 
    6 #                        (C) 1998-2009  All Rights Reserved 
     6#                        (C) 1998-2010  All Rights Reserved 
    77# 
    88# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
    … …  
    1313import os 
    1414 
    15 mpi_incdir = os.environ['MPI_INCDIR'] 
    16 mpi_libdir = os.environ['MPI_LIBDIR'] 
    17  
    18 if platform[:3] == 'win': 
    19     MPILIBS = [] 
    20     module1 = Extension('_pyina', 
    21                        ['pyinamodule\\dummy.cc', 
    22                         'pyinamodule\_pyina.cc'], 
    23                        include_dirs=['pyinamodule', mpi_incdir], 
    24                        libraries=MPILIBS, 
    25                        library_dirs=[mpi_libdir], 
    26                        ) 
    27 else: #platform = linux or mac 
    28     MPILIBS = [] 
    29     #if platform[:6] == 'darwin': 
    30         #MPILIBS.remove('...') 
    31         #MPILIBS.append('...') 
    32  
    33     module1 = Extension('_pyina', 
    34                        ['pyinamodule/dummy.cc', 
    35                         'pyinamodule/_pyina.cc'], 
    36                        include_dirs=['pyinamodule', mpi_incdir], 
    37                        libraries=MPILIBS, 
    38                        library_dirs=[mpi_libdir], 
    39                        ) 
    40  
    41 setup(name="pyina", 
    42     version="0.2", 
     15setup(name="mpimystic", 
     16    version="0.01", 
    4317    maintainer="Mike McKerns", 
    4418    maintainer_email="mmckerns@caltech.edu", 
    4519    license="BSD", 
    4620    platforms=["any"], 
    47     description="Interactive Parallel-Mapping Inversion Analysis Framework", 
     21    description="MPI version of Parallel-Mapping Inversion Analysis Framework", 
    4822    classifiers=( 
    4923        "Intended Audience :: Developers", 
    … …  
    5226        "Topic :: Physics Programming"), 
    5327 
    54     packages=['pyina','pyina.tools','pyina.applications'], 
    55     package_dir={'pyina':'pyina','pyina.tools':'tools','pyina.applications':'applications'}, 
    56     ext_modules=[module1], 
    57  
     28    packages=['mpimystic'], 
     29    package_dir={'mpimystic':'mpimystic'}, 
    5830    scripts=[]) 
    5931 

  • mpimystic/tests/Make.mm

    r88 r224  
    22# 
    33 
    4 PROJECT = pyina 
     4PROJECT = mpimystic 
    55PACKAGE = tests 
    66 
    … …  
    1010PROJ_CPPTESTS =  
    1111PROJ_TESTS = $(PROJ_PYTESTS) # $(PROJ_CPPTESTS) 
    12 PROJ_LIBRARIES = -L$(BLD_LIBDIR) # -lpyina 
     12PROJ_LIBRARIES = -L$(BLD_LIBDIR) # -lmpimystic 
    1313 
    1414#-------------------------------------------------------------------------- 

  • mystic/mystic/README

    r133 r224  
    33Storn and Price differential evolution solver in python. 
    44 
    5 The parallel framework implementation is being developed in the pyina branch. 
     5If 'pyina' is installed, the global optimizers can launched in parallel 
     6mode using MPI. Pyina is part of the pathos package, available here: 
     7  http://dev.danse.us/trac/pathos 
     8 
    69 
    710# end of file 

  • mystic/mystic/__init__.py

    r144 r224  
    44# 
    55#                       Patrick Hung & Mike McKerns, Caltech 
    6 #                        (C) 1997-2008  All Rights Reserved 
     6#                        (C) 1997-2010  All Rights Reserved 
    77# 
    88# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
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