Source code for ANNarchy.generator.Compiler

#     This file is part of ANNarchy.
#     Copyright (C) 2013-2016  Julien Vitay <>,
#     Helge Uelo Dinkelbach <>
#     This program is free software: you can redistribute it and/or modify
#     it under the terms of the GNU General Public License as published by
#     the Free Software Foundation, either version 3 of the License, or
#     (at your option) any later version.
#     ANNarchy is distributed in the hope that it will be useful,
#     but WITHOUT ANY WARRANTY; without even the implied warranty of
#     GNU General Public License for more details.
#     You should have received a copy of the GNU General Public License
#     along with this program.  If not, see <>.
import os, sys, imp
import subprocess
import shutil
import time
import re
import json
import argparse
import numpy as np

# ANNarchy core informations
import ANNarchy
import ANNarchy.core.Global as Global
from .Template.MakefileTemplate import *
from .Sanity import check_structure

# String containing the extra libs which can be added by extensions
# e.g. extra_libs = ['-lopencv_core', '-lopencv_video']
extra_libs = []

def _folder_management(annarchy_dir, profile_enabled, clean, net_id):
    ANNarchy is provided as a python package. For compilation a local folder
    'annarchy' is created in the current working directory.


    * annarchy_dir : subdirectory
    * *profile_enabled*: copy needed data for profile extension

    # Verbose
    if Global.config['verbose']:
        Global._print("Create subdirectory.")

    if clean or profile_enabled:
        shutil.rmtree(annarchy_dir, True)

    # Create the subdirectory
    if not os.path.exists(annarchy_dir):

    # Subdirectory for building networks
    if not os.path.exists(annarchy_dir+'/build/net'+str(net_id)):

    # Create the generate subfolder
    if not os.path.exists(annarchy_dir+'/generate/net'+str(net_id)):

    # Save current ANNarchy version and paradigm
    with open(annarchy_dir+'/release', 'w') as wfile:
        wfile.write(Global.config['paradigm']+', '+ANNarchy.__release__)


def setup_parser():
    ANNarchy scripts can be run by several command line arguments. These are
    checked with the ArgumentParser provided by Python.
    # override the error behavior of OptionParser,
    # normally an unknwon arg would raise an exception
    parser = argparse.ArgumentParser(description='ANNarchy: Artificial Neural Networks architect.')

    group = parser.add_argument_group('General')
    group.add_argument("-c", "--clean", help="Forces recompilation.", action="store_true", default=False, dest="clean")
    group.add_argument("-d", "--debug", help="Compilation with debug symbols and additional checks.", action="store_true", default=False, dest="debug")
    group.add_argument("-v", "--verbose", help="Shows all messages.", action="store_true", default=None, dest="verbose")
    group.add_argument("--prec", help="Set the floating precision used.", action="store", type=str, default=None, dest="precision")

    group = parser.add_argument_group('OpenMP')
    group.add_argument("-j", "--num_threads", help="Number of threads to use.", type=int, action="store", default=None, dest="num_threads")

    group = parser.add_argument_group('CUDA')
    group.add_argument("--gpu", help="Enables CUDA and optionally specifies the GPU id (default: 0).", type=int, action="store", nargs='?', default=-1, const=0, dest="gpu_device")

    group = parser.add_argument_group('Internal')
    group.add_argument("--profile", help="Enables profiling.", action="store_true", default=None, dest="profile")
    group.add_argument("--profile_out", help="Target file for profiling data.", action="store", type=str, default=None, dest="profile_out")

    return parser

[docs]def compile( directory='annarchy', clean=False, populations=None, projections=None, compiler="default", compiler_flags="default", cuda_config={'device': 0}, silent=False, debug_build=False, profile_enabled=False, net_id=0 ): """ This method uses the network architecture to generate optimized C++ code and compile a shared library that will perform the simulation. *Parameters*: * **directory**: name of the subdirectory where the code will be generated and compiled. Must be a relative path. Default: "annarchy/". * **clean**: boolean to specifying if the library should be recompiled entirely or only the changes since last compilation (default: False). * **populations**: list of populations which should be compiled. If set to None, all available populations will be used. * **projections**: list of projection which should be compiled. If set to None, all available projections will be used. * **compiler**: C++ compiler to use. Default: g++ on GNU/Linux, clang++ on OS X. Valid compilers are [g++, clang++]. * **compiler_flags**: platform-specific flags to pass to the compiler. Default: "-march=native -O2". Warning: -O3 often generates slower code and can cause linking problems, so it is not recommended. * **cuda_config**: dictionary defining the CUDA configuration for each population and projection. * **silent**: defines if the "Compiling... OK" should be printed. The ``compiler``, ``compiler_flags`` and part of ``cuda_config`` take their default value from the configuration file ``~/.config/ANNarchy/annarchy.json``. The following arguments are for internal development use only: * **debug_build**: creates a debug version of ANNarchy, which logs the creation of objects and some other data (default: False). * **profile_enabled**: creates a profilable version of ANNarchy, which logs several computation timings (default: False). """ # Check if the network has already been compiled if Global._network[net_id]['compiled']: Global._print("""compile(): the network has already been compiled, doing nothing. If you are re-running a Jupyter notebook, you should call `clear()` right after importing ANNarchy in order to reset everything.""") return # Get the command-line arguments parser = setup_parser() options, unknown = parser.parse_known_args() if len(unknown) > 0: Global._warning('unrecognized arguments:', unknown) # if the parameters set on command-line they overwrite Global.config if options.num_threads != None: Global.config['num_threads'] = options.num_threads # Get CUDA configuration if options.gpu_device >= 0: Global.config['paradigm'] = "cuda" cuda_config['device'] = int(options.gpu_device) # Check that CUDA is enabled try: from .CudaCheck import CudaCheck except: Global._error('CUDA is not installed on your system') # Check that a single backend is chosen if (options.num_threads != None) and (options.gpu_device >= 0): Global._error('CUDA and openMP can not be active at the same time, please check your command line arguments.') # Verbose if options.verbose != None: Global.config['verbose'] = options.verbose # Precision if options.precision != None: Global.config['precision'] = options.precision # Profiling if options.profile != None: profile_enabled = options.profile Global.config['profiling'] = options.profile Global.config['profile_out'] = options.profile_out if profile_enabled != False and options.profile == None: # Profiling enabled due compile() Global.config['profiling'] = True # Debug if not debug_build: debug_build = options.debug # debug build Global.config["debug"] = debug_build # Clean clean = options.clean # enforce rebuild # Populations to compile if populations is None: # Default network populations = Global._network[net_id]['populations'] # Projections to compile if projections is None: # Default network projections = Global._network[net_id]['projections'] # Compiling directory annarchy_dir = os.getcwd() + '/' + directory if not annarchy_dir.endswith('/'): annarchy_dir += '/' Global._network[net_id]['directory'] = annarchy_dir # Turn OMP off for MacOS if (Global._check_paradigm("openmp") and Global.config['num_threads'] > 1 and sys.platform == "darwin"): Global._warning("OpenMP is not supported on Mac OS yet") Global.config['num_threads'] = 1 # Test if the current ANNarchy version is newer than what was used to create the subfolder from pkg_resources import parse_version if os.path.isfile(annarchy_dir+'/release'): with open(annarchy_dir+'/release', 'r') as rfile: prev_release = prev_paradigm = '' # HD (03.08.2016): # in ANNarchy 4.5.7b I added also the paradigm to the release tag. # This if clause can be removed in later releases (TODO) if prev_release.find(',') != -1: prev_paradigm, prev_release = prev_release.split(', ') else: # old release tag clean = True if parse_version(prev_release) < parse_version(ANNarchy.__release__): clean = True elif prev_paradigm != Global.config['paradigm']: clean = True else: clean = True # for very old versions # Check if the last compilation was successful if os.path.isfile(annarchy_dir+'/compilation'): with open(annarchy_dir + '/compilation', 'r') as rfile: res = if res.strip() == "0": # the last compilation failed clean = True else: clean = True # Manage the compilation subfolder _folder_management(annarchy_dir, profile_enabled, clean, net_id) # Create a Compiler object compiler = Compiler(annarchy_dir=annarchy_dir, clean=clean, compiler=compiler, compiler_flags=compiler_flags, silent=silent, cuda_config=cuda_config, debug_build=debug_build, profile_enabled=profile_enabled, populations=populations, projections=projections, net_id=net_id) compiler.generate()
def python_environment(): """ Python environment configuration, required by Compiler.generate_makefile. Contains among others the python version, library path and cython version. Warning: changes to this method should be copied to """ # Python version py_version = "%(major)s.%(minor)s" % {'major': sys.version_info[0], 'minor': sys.version_info[1]} py_major = str(sys.version_info[0]) # Python includes and libs # non-standard python installs need to tell the location of # export LD_LIBRARY_PATH=$HOME/anaconda/lib:$LD_LIBRARY_PATH # export DYLD_FALLBACK_LIBRARY_PATH=$HOME/anaconda/lib:$DYLD_FALLBACK_LIBRARY_PATH py_prefix = sys.prefix if py_major == '2': major = '2' test = subprocess.Popen(py_prefix + "/bin/python2-config --includes > /dev/null 2> /dev/null", shell=True) if test.wait() != 0: major = "" else: major = '3' test = subprocess.Popen(py_prefix + "/bin/python3-config --includes > /dev/null 2> /dev/null", shell=True) if test.wait() != 0: major = "" # Test that it exists (virtualenv) cmd = "%(py_prefix)s/bin/python%(major)s-config --includes > /dev/null 2> /dev/null" test = subprocess.Popen(cmd % {'major': major, 'py_prefix': py_prefix}, shell=True) if test.wait() != 0: Global._warning("Can not find python-config in the same directory as python, trying with the default path...") python_config_path = "python%(major)s-config" % {'major': major} else: python_config_path = "%(py_prefix)s/bin/python%(major)s-config" % {'major': major, 'py_prefix': py_prefix} python_include = "`%(pythonconfigpath)s --includes`" % {'pythonconfigpath': python_config_path} python_libpath = "-L%(py_prefix)s/lib" % {'py_prefix': py_prefix} # Identify the -lpython flag test = subprocess.Popen('%(pythonconfigpath)s --ldflags' % {'pythonconfigpath': python_config_path}, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) flagline = str('UTF-8')).strip() errorline = str('UTF-8')) test.wait() if len(errorline) > 0: Global._error("Unable to find python-config. Make sure you have installed the development files of Python (python-dev or -devel) and that either python-config, python2-config or python3-config are in your path.") flags = flagline.split(' ') for flag in flags: if flag.startswith('-lpython'): python_lib = flag break else: python_lib = "-lpython" + py_version # Check cython version test = subprocess.Popen("cython%(major)s -V > /dev/null 2> /dev/null" % {'major': major}, shell=True) if test.wait() != 0: cython = "" else: cython = major return py_version, py_major, python_include, python_lib, python_libpath, cython class Compiler(object): " Main class to generate C++ code efficiently" def __init__(self, annarchy_dir, clean, compiler, compiler_flags, silent, cuda_config, debug_build, profile_enabled, populations, projections, net_id): # Store arguments self.annarchy_dir = annarchy_dir self.clean = clean self.compiler = compiler self.compiler_flags = compiler_flags self.silent = silent self.cuda_config = cuda_config self.debug_build = debug_build self.profile_enabled = profile_enabled self.populations = populations self.projections = projections self.net_id = net_id # Get user-defined config self.user_config = { 'openmp': { 'compiler': 'clang++' if sys.platform == "darwin" else 'g++', 'flags' : "-march=native -O2", } } if os.path.exists(os.path.expanduser('~/.config/ANNarchy/annarchy.json')): with open(os.path.expanduser('~/.config/ANNarchy/annarchy.json'), 'r') as rfile: self.user_config = json.load(rfile) def generate(self): "Method to generate the C++ code." # Check that everything is allright in the structure of the network. check_structure(self.populations, self.projections) # Generate the code self.code_generation() # Generate the Makefile self.generate_makefile() # Copy the files if needed changed = self.copy_files() # Perform compilation if something has changed if changed or not os.path.isfile(self.annarchy_dir + '/ANNarchyCore' + str(self.net_id) + '.so'): self.compilation() Global._network[self.net_id]['compiled'] = True # Create the Python objects _instantiate(self.net_id, cuda_config=self.cuda_config, user_config=self.user_config) def copy_files(self): " Copy the generated files in the build/ folder if needed." changed = False if self.clean: for file in os.listdir(self.annarchy_dir+'/generate/net'+ str(self.net_id)): shutil.copy(self.annarchy_dir+'/generate/net'+ str(self.net_id) + '/' + file, # src self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + file # dest ) changed = True else: # only the ones which have changed import filecmp for file in os.listdir(self.annarchy_dir+'/generate/net'+ str(self.net_id)): if not os.path.isfile(self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + file) or \ not filecmp.cmp(self.annarchy_dir+'/generate/net' + str(self.net_id) + '/' + file, self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + file): shutil.copy(self.annarchy_dir+'/generate//net'+ str(self.net_id) + '/' + file, # src self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' +file # dest ) changed = True # For debugging # print(f, 'has changed') # with open(self.annarchy_dir+'/generate/net'+ str(self.net_id) + '/' + f, 'r') as rfile: # text = # print(text) # Needs to check now if a file existed before in build/net but not in generate anymore for file in os.listdir(self.annarchy_dir+'/build/net'+ str(self.net_id)): if file == 'Makefile': continue basename, extension = os.path.splitext(file) if not extension in ['h', 'hpp', 'cpp', 'cu']: # ex: .o continue if not os.path.isfile(self.annarchy_dir+'/generate/net'+ str(self.net_id) + '/' + file): if file.startswith('ANNarchyCore'): continue os.remove(self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + file) if os.path.isfile(self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + basename + '.o'): os.remove(self.annarchy_dir+'/build/net'+ str(self.net_id) + '/' + basename + '.o') changed = True return changed def compilation(self): """ Create and py extensions if something has changed. """ # STDOUT if not self.silent: msg = 'Compiling' if self.net_id > 0: msg += ' network ' + str(self.net_id) msg += '...' Global._print(msg) if Global.config['show_time']: t0 = time.time() # Switch to the build directory os.chdir(self.annarchy_dir + '/build/net'+ str(self.net_id)) # Start the compilation verbose = "> compile_stdout.log 2> compile_stderr.log" if not Global.config["verbose"] else "" # Start the compilation process make_process = subprocess.Popen("make all -j4" + verbose, shell=True) # Check for errors if make_process.wait() != 0: with open('compile_stderr.log', 'r') as rfile: msg = with open(self.annarchy_dir + '/compilation', 'w') as wfile: wfile.write("0") Global._print(msg) try: os.remove('ANNarchyCore'+str(self.net_id)+'.so') except: pass Global._error('Compilation failed.') else: # Note that the last compilation was successful with open(self.annarchy_dir + '/compilation', 'w') as wfile: wfile.write("1") # Return to the current directory os.chdir('../../..') if not self.silent: Global._print('OK') if Global.config['show_time']: Global._print('Compilation took', time.time() - t0, 'seconds.') def generate_makefile(self): """ Generate the Makefile. The makefile consists of two stages compile the cython wrapper and compile the ANNarchy model files. Both is then linked together to a shared library usable in Python. """ # Compiler if self.compiler == "default": self.compiler = self.user_config['openmp']['compiler'] if self.compiler_flags == "default": self.compiler_flags = self.user_config['openmp']['flags'] # flags are common to all platforms if not self.debug_build: cpu_flags = self.compiler_flags else: cpu_flags = "-O0 -g -D_DEBUG" if self.profile_enabled: cpu_flags += " -g" #extra_libs.append("-lpapi") # OpenMP flag omp_flag = "" if Global.config['paradigm'] == "openmp" and Global.config['num_threads'] > 1 and sys.platform != "darwin": omp_flag = "-fopenmp" # Cuda Library and Compiler # # hdin (22.03.2016): we should verify in the future, if compute_35 remains as best # configuration for Keplar and upwards. cuda_gen = "" gpu_flags = "" gpu_compiler = "nvcc" gpu_ldpath = "" if sys.platform.startswith('linux') and Global.config['paradigm'] == "cuda": from .CudaCheck import CudaCheck cu_version = CudaCheck().version_str() if int(cu_version) < 30: Global._warning("You seem to use a GPU with CC < 3.0 this might lead to problems with newer CUDA SDKs.") else: cuda_gen = "-arch sm_%(ver)s" % {'ver': cu_version} if self.debug_build: gpu_flags = "-g -G -D_DEBUG" # read the config file for the cuda lib path if 'cuda' in self.user_config.keys(): gpu_compiler = self.user_config['cuda']['compiler'] gpu_ldpath = '-L' + self.user_config['cuda']['path'] + '/lib' # Extra libs from extensions such as opencv libs = "" for lib in extra_libs: libs += str(lib) + ' ' # Python environment py_version, py_major, python_include, python_lib, python_libpath, cython_major = python_environment() # Include path to Numpy is not standard on all distributions numpy_include = np.get_include() # The connector module needs to reload some header files, # ANNarchy.__path__ provides the installation directory path_to_cython_ext = ANNarchy.__path__[0]+'/core/cython_ext/' # Gather all Makefile flags makefile_flags = { 'compiler': self.compiler, 'cpu_flags': cpu_flags, 'cuda_gen': cuda_gen, 'gpu_compiler': gpu_compiler, 'gpu_flags': gpu_flags, 'gpu_ldpath': gpu_ldpath, 'openmp': omp_flag, 'extra_libs': libs, 'py_version': py_version, 'py_major': py_major, 'cy_major': cython_major, 'python_include': python_include, 'python_lib': python_lib, 'python_libpath': python_libpath, 'numpy_include': numpy_include, 'net_id': self.net_id, 'cython_ext': path_to_cython_ext } # Create Makefiles depending on the target platform and parallel framework if sys.platform.startswith('linux'): # Linux systems if Global.config['paradigm'] == "cuda": makefile_template = linux_cuda_template else: makefile_template = linux_omp_template elif sys.platform == "darwin": # mac os makefile_template = osx_seq_template else: # Windows: to test.... Global._warning("Compilation on windows is not supported yet.") # Write the Makefile to the disk with open(self.annarchy_dir + '/generate/net'+ str(self.net_id) + '/Makefile', 'w') as wfile: wfile.write(makefile_template % makefile_flags) def code_generation(self): """ Code generation dependent on paradigm """ from .CodeGenerator import CodeGenerator generator = CodeGenerator(self.annarchy_dir, self.populations, self.projections, self.net_id, self.cuda_config) generator.generate() def _instantiate(net_id, import_id=-1, cuda_config=None, user_config=None): """ After every is compiled, actually create the Cython objects and bind them to the Python ones.""" # parallel_run(number=x) defines multiple networks (net_id) but only network0 is compiled if import_id < 0: import_id = net_id # subdirectory where the library lies annarchy_dir = Global._network[import_id]['directory'] if Global.config['verbose']: Global._print('Building network ...') # Import the Cython library try: cython_module = imp.load_dynamic( 'ANNarchyCore' + str(import_id), # Name of the network annarchy_dir + '/ANNarchyCore' + str(import_id) + '.so' # Path to the library ) except Exception as e: Global._print(e) Global._error('Something went wrong when importing the network. Force recompilation with --clean.') Global._network[net_id]['instance'] = cython_module # Set the CUDA device if Global._check_paradigm("cuda"): device = 0 if cuda_config: device = int(cuda_config['device']) elif 'cuda' in user_config['cuda']: device = int(user_config['cuda']['device']) if Global.config['verbose']: Global._print('Setting GPU device', device) cython_module.set_device(device) # Bind the py extensions to the corresponding python objects for pop in Global._network[net_id]['populations']: if Global.config['verbose']: Global._print('Creating population', if Global.config['show_time']: t0 = time.time() # Instantiate the population pop._instantiate(cython_module) if Global.config['show_time']: Global._print('Creating',, 'took', (time.time()-t0)*1000, 'milliseconds') # Instantiate projections for proj in Global._network[net_id]['projections']: if Global.config['verbose']: Global._print('Creating projection from',, 'to',, 'with target="',, '"') if Global.config['show_time']: t0 = time.time() # Create the projection proj._instantiate(cython_module) if Global.config['show_time']: Global._print('Creating the projection took', (time.time()-t0)*1000, 'milliseconds') # Finish to initialize the network cython_module.pyx_create(Global.config['dt'], Global.config['seed']) # Set the user-defined constants for obj in Global._objects['constants']: getattr(cython_module, '_set_' # Transfer initial values for pop in Global._network[net_id]['populations']: if Global.config['verbose']: Global._print('Initializing population', pop._init_attributes() for proj in Global._network[net_id]['projections']: if Global.config['verbose']: Global._print('Initializing projection from',, 'to',, 'with target="',, '"') proj._init_attributes() # The rng dist must be initialized after the pops and projs are created! if Global._check_paradigm("openmp"): cython_module.pyx_init_rng_dist() # Sets the desired number of threads if Global.config['num_threads'] > 1 and Global._check_paradigm("openmp"): cython_module.set_number_threads(Global.config['num_threads']) if Global.config['verbose']: Global._print('Running simulation with', Global.config['num_threads'], 'threads.') # Start the monitors for monitor in Global._network[net_id]['monitors']: monitor._init_monitoring()