def generate_codeobj_source(self, writer):
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(
line.format(c_type=c_data_type(v.dtype),
varname=k,
objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = {dyn_array_name}.empty()? 0 : &{dyn_array_name}[0];'
line = line.format(
c_type=c_data_type(v.dtype),
array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(
k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' %
(k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%',
'\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n' + code
writer.write('code_objects/' + codeobj.name + '.cpp', code)
writer.write('code_objects/' + codeobj.name + '.h',
codeobj.code.h_file)
def _add_user_function(self, varname, variable):
impl = variable.implementations[self.codeobj_class]
support_code = []
hash_defines = []
pointers = []
user_functions = [(varname, variable)]
funccode = impl.get_code(self.owner)
if isinstance(funccode, str):
# Rename references to any dependencies if necessary
for dep_name, dep in iteritems(impl.dependencies):
dep_impl = dep.implementations[self.codeobj_class]
dep_impl_name = dep_impl.name
if dep_impl_name is None:
dep_impl_name = dep.pyfunc.__name__
if dep_name != dep_impl_name:
funccode = word_substitute(funccode,
{dep_name: dep_impl_name})
funccode = {'support_code': funccode}
if funccode is not None:
# To make namespace variables available to functions, we
# create global variables and assign to them in the main
# code
func_namespace = impl.get_namespace(self.owner) or {}
for ns_key, ns_value in iteritems(func_namespace):
if hasattr(ns_value, 'dtype'):
if ns_value.shape == ():
raise NotImplementedError((
'Directly replace scalar values in the function '
'instead of providing them via the namespace'))
type_str = c_data_type(ns_value.dtype) + '*'
else: # e.g. a function
type_str = 'py::object'
support_code.append('static {0} _namespace{1};'.format(type_str,
ns_key))
pointers.append('_namespace{0} = {1};'.format(ns_key, ns_key))
support_code.append(deindent(funccode.get('support_code', '')))
hash_defines.append(deindent(funccode.get('hashdefine_code', '')))
dep_hash_defines = []
dep_pointers = []
dep_support_code = []
if impl.dependencies is not None:
for dep_name, dep in iteritems(impl.dependencies):
if dep_name not in self.variables: # do not add a dependency twice
self.variables[dep_name] = dep
dep_impl = dep.implementations[self.codeobj_class]
if dep_name != dep_impl.name:
self.func_name_replacements[dep_name] = dep_impl.name
hd, ps, sc, uf = self._add_user_function(dep_name, dep)
dep_hash_defines.extend(hd)
dep_pointers.extend(ps)
dep_support_code.extend(sc)
user_functions.extend(uf)
return (dep_hash_defines + hash_defines,
dep_pointers + pointers,
dep_support_code + support_code,
user_functions)
def generate_codeobj_source(self, writer):
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(line.format(c_type=c_data_type(v.dtype), varname=k, objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cpp', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
def _add_user_function(self, varname, variable):
impl = variable.implementations[self.codeobj_class]
support_code = []
hash_defines = []
pointers = []
user_functions = [(varname, variable)]
funccode = impl.get_code(self.owner)
if isinstance(funccode, basestring):
funccode = {'support_code': funccode}
if funccode is not None:
# To make namespace variables available to functions, we
# create global variables and assign to them in the main
# code
func_namespace = impl.get_namespace(self.owner) or {}
for ns_key, ns_value in func_namespace.iteritems():
if hasattr(ns_value, 'dtype'):
if ns_value.shape == ():
raise NotImplementedError((
'Directly replace scalar values in the function '
'instead of providing them via the namespace'))
type_str = c_data_type(ns_value.dtype) + '*'
else: # e.g. a function
type_str = 'py::object'
support_code.append('static {0} _namespace{1};'.format(type_str,
ns_key))
pointers.append('_namespace{0} = {1};'.format(ns_key, ns_key))
support_code.append(deindent(funccode.get('support_code', '')))
hash_defines.append(deindent(funccode.get('hashdefine_code', '')))
dep_hash_defines = []
dep_pointers = []
dep_support_code = []
if impl.dependencies is not None:
for dep_name, dep in impl.dependencies.iteritems():
self.variables[dep_name] = dep
hd, ps, sc, uf = self._add_user_function(dep_name, dep)
dep_hash_defines.extend(hd)
dep_pointers.extend(ps)
dep_support_code.extend(sc)
user_functions.extend(uf)
return (dep_hash_defines + hash_defines,
dep_pointers + pointers,
dep_support_code + support_code,
user_functions)
def write_static_arrays(self, directory):
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(directory, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
self.static_array_specs = static_array_specs
def generate_codeobj_source(self, writer):
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = (
"{c_type}* const {array_name} = {dyn_array_name}.empty()? 0 : &{dyn_array_name}[0];"
)
line = line.format(
c_type=c_data_type(v.dtype), array_name=array_name, dyn_array_name=dyn_array_name
)
lines.append(line)
line = "const int _num{k} = {dyn_array_name}.size();"
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append("const int _num%s = %s;" % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = self.freeze(codeobj.code.cpp_file, ns)
code = code.replace("%CONSTANTS%", "\n".join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n' + code
writer.write("code_objects/" + codeobj.name + ".cpp", code)
writer.write("code_objects/" + codeobj.name + ".h", codeobj.code.h_file)
def write_static_arrays(self, directory):
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
logger.debug("static arrays: " +
str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(directory, 'static_arrays', name))
static_array_specs.append(
(name, c_data_type(arr.dtype), arr.size, name))
self.static_array_specs = static_array_specs
def generate_codeobj_source(self, writer):
#check how many random numbers are needed per step
for code_object in self.code_objects.itervalues():
num_occurences_rand = code_object.code.cu_file.count("_rand(")
num_occurences_randn = code_object.code.cu_file.count("_randn(")
if num_occurences_rand > 0:
if code_object.template_name != "synapses_create":
#first one is alway the definition, so subtract 1
code_object.rand_calls = num_occurences_rand - 1
for i in range(0, code_object.rand_calls):
if code_object.owner.N != 0:
code_object.code.cu_file = code_object.code.cu_file.replace("_rand(_vectorisation_idx)", "_rand(_vectorisation_idx + " + str(i) + " * " + str(code_object.owner.N) + ")", 1)
else:
code_object.code.cu_file = code_object.code.cu_file.replace("_rand(_vectorisation_idx)", "_rand(_vectorisation_idx + " + str(i) + " * _N)", 1)
else:
code_object.code.cu_file = code_object.code.cu_file.replace("_rand(_vectorisation_idx)", "(rand()/(float)RAND_MAX)")
if num_occurences_randn > 0 and code_object.template_name != "synapses_create":
#first one is alway the definition, so subtract 1
code_object.randn_calls = num_occurences_randn - 1
for i in range(0, code_object.randn_calls):
if code_object.owner.N != 0:
code_object.code.cu_file = code_object.code.cu_file.replace("_randn(_vectorisation_idx)", "_randn(_vectorisation_idx + " + str(i) + " * " + str(code_object.owner.N) + ")", 1)
else:
code_object.code.cu_file = code_object.code.cu_file.replace("_randn(_vectorisation_idx)", "_randn(_vectorisation_idx + " + str(i) + " * _N)", 1)
code_object_defs = defaultdict(list)
host_parameters = defaultdict(list)
device_parameters = defaultdict(list)
kernel_variables = defaultdict(list)
# Generate data for non-constant values
for codeobj in self.code_objects.itervalues():
code_object_defs_lines = []
host_parameters_lines = []
device_parameters_lines = []
kernel_variables_lines = []
additional_code = []
number_elements = ""
if hasattr(codeobj, 'owner') and hasattr(codeobj.owner, '_N') and codeobj.owner._N != 0:
number_elements = str(codeobj.owner._N)
else:
number_elements = "_N"
for k, v in codeobj.variables.iteritems():
#code objects which only run once
if k == "_python_randn" and codeobj.runs_every_tick == False and codeobj.template_name != "synapses_create":
additional_code.append('''
//genenerate an array of random numbers on the device
float* dev_array_randn;
cudaMalloc((void**)&dev_array_randn, sizeof(float)*''' + number_elements + ''' * ''' + str(codeobj.randn_calls) + ''');
if(!dev_array_randn)
{
printf("ERROR while allocating device memory with size %ld\\n", sizeof(float)*''' + number_elements + '''*''' + str(codeobj.randn_calls) + ''');
}
curandGenerator_t uniform_gen;
curandCreateGenerator(&uniform_gen, CURAND_RNG_PSEUDO_DEFAULT);
curandSetPseudoRandomGeneratorSeed(uniform_gen, time(0));
curandGenerateNormal(uniform_gen, dev_array_randn, ''' + number_elements + '''*''' + str(codeobj.randn_calls) + ''', 0, 1);''')
line = "float* _array_{name}_randn".format(name=codeobj.name)
device_parameters_lines.append(line)
host_parameters_lines.append("dev_array_randn")
elif k == "_python_rand" and codeobj.runs_every_tick == False and codeobj.template_name != "synapses_create":
additional_code.append('''
//genenerate an array of random numbers on the device
float* dev_array_rand;
cudaMalloc((void**)&dev_array_rand, sizeof(float)*''' + number_elements + '''*''' + str(codeobj.rand_calls) + ''');
if(!dev_array_rand)
{
printf("ERROR while allocating device memory with size %ld\\n", sizeof(float)*''' + number_elements + '''*''' + str(codeobj.rand_calls) + ''');
}
curandGenerator_t normal_gen;
curandCreateGenerator(&normal_gen, CURAND_RNG_PSEUDO_DEFAULT);
curandSetPseudoRandomGeneratorSeed(normal_gen, time(0));
curandGenerateUniform(normal_gen, dev_array_rand, ''' + number_elements + '''*''' + str(codeobj.rand_calls) + ''');''')
line = "float* _array_{name}_rand".format(name=codeobj.name)
device_parameters_lines.append(line)
host_parameters_lines.append("dev_array_rand")
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = thrust::raw_pointer_cast(&dev{dyn_array_name}[0]);'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
code_object_defs_lines.append(line)
line = 'const int _num{k} = dev{dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
code_object_defs_lines.append(line)
host_parameters_lines.append(array_name)
host_parameters_lines.append("_num" + k)
line = "{c_type}* par_{array_name}"
device_parameters_lines.append(line.format(c_type=c_data_type(v.dtype), array_name=array_name))
line = "int par_num_{array_name}"
device_parameters_lines.append(line.format(array_name=k))
line = "{c_type}* _ptr{array_name} = par_{array_name};"
kernel_variables_lines.append(line.format(c_type=c_data_type(v.dtype), array_name=array_name))
line = "const int _num{array_name} = par_num_{array_name};"
kernel_variables_lines.append(line.format(array_name=k))
else:
host_parameters_lines.append("dev"+self.get_array_name(v))
device_parameters_lines.append("%s* par_%s" % (c_data_type(v.dtype), self.get_array_name(v)))
kernel_variables_lines.append("%s* _ptr%s = par_%s;" % (c_data_type(v.dtype), self.get_array_name(v), self.get_array_name(v)))
code_object_defs_lines.append('const int _num%s = %s;' % (k, v.size))
kernel_variables_lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
for line in code_object_defs_lines:
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
for line in host_parameters_lines:
if not line in host_parameters[codeobj.name]:
host_parameters[codeobj.name].append(line)
for line in device_parameters_lines:
if not line in device_parameters[codeobj.name]:
device_parameters[codeobj.name].append(line)
for line in kernel_variables_lines:
if not line in kernel_variables[codeobj.name]:
kernel_variables[codeobj.name].append(line)
for line in additional_code:
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = self.freeze(codeobj.code.cu_file, ns)
if len(host_parameters[codeobj.name]) == 0:
host_parameters[codeobj.name].append("0")
device_parameters[codeobj.name].append("int dummy")
code = code.replace('%CONSTANTS%', '\n\t\t'.join(code_object_defs[codeobj.name]))
code = code.replace('%HOST_PARAMETERS%', ',\n\t\t\t'.join(host_parameters[codeobj.name]))
code = code.replace('%DEVICE_PARAMETERS%', ',\n\t'.join(device_parameters[codeobj.name]))
code = code.replace('%KERNEL_VARIABLES%', '\n\t'.join(kernel_variables[codeobj.name]))
code = code.replace('%CODEOBJ_NAME%', codeobj.name)
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cu', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
def atomics_parallelisation(self, statement, conditional_write_vars,
used_variables):
if not self._use_atomics:
raise ParallelisationError()
# Avoids circular import
from brian2.devices.device import device
# See https://github.com/brian-team/brian2/pull/531 for explanation
used = set(get_identifiers(statement.expr))
used = used.intersection(k for k in self.variables.keys()
if k in self.variable_indices
and self.variable_indices[k] != '_idx')
used_variables.update(used)
if statement.var in used_variables:
raise ParallelisationError()
expr = self.translate_expression(statement.expr)
if statement.op == ':=' or self.variable_indices[statement.var] == '_idx' or not statement.inplace:
if statement.op == ':=':
decl = self.c_data_type(statement.dtype) + ' '
op = '='
if statement.constant:
decl = 'const ' + decl
else:
decl = ''
op = statement.op
line = '{decl}{var} {op} {expr};'.format(decl=decl,
var=statement.var, op=op,
expr=expr)
line = [line]
elif statement.inplace:
sign = ''
if statement.op == '+=':
atomic_op = '_brian_atomicAdd'
elif statement.op == '-=':
# CUDA has hardware implementations for float (and for CC>=6.0
# for double) only for atomicAdd, which is faster then our
# software implementation
atomic_op = '_brian_atomicAdd'
sign = '-'
elif statement.op == '*=':
atomic_op = '_brian_atomicMul'
elif statement.op == '/=':
atomic_op = '_brian_atomicDiv'
else:
# TODO: what other inplace operations are possible? Can we
# implement them with atomicCAS ?
logger.info("Atomic operation for operation {op} is not implemented."
"".format(op=statement.op))
raise ParallelisationError()
line = '{atomic_op}(&{array_name}[{idx}], ({array_dtype}){sign}({expr}));'.format(
atomic_op=atomic_op,
array_name=self.get_array_name(self.variables[statement.var]),
idx=self.variable_indices[statement.var],
array_dtype=c_data_type(self.variables[statement.var].dtype),
sign=sign, expr=expr)
# this is now a list of 1 or 2 lines (potentially with if(...))
line = self.conditional_write(line, statement, conditional_write_vars)
else:
raise ParallelisationError()
if len(statement.comment):
line[-1] += ' // ' + statement.comment
return line
def build(
self,
project_dir='output',
compile_project=True,
run_project=False,
debug=True,
with_output=True,
native=True,
additional_source_files=None,
additional_header_files=None,
main_includes=None,
run_includes=None,
run_args=None,
):
'''
Build the project
TODO: more details
Parameters
----------
project_dir : str
The output directory to write the project to, any existing files will be overwritten.
compile_project : bool
Whether or not to attempt to compile the project using GNU make.
run_project : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile natively using the ``--march=native`` gcc option.
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = project_dir
ensure_directory(project_dir)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(project_dir, d))
writer = CPPWriter(project_dir)
logger.debug("Writing C++ standalone project to directory " +
os.path.normpath(project_dir))
arange_arrays = sorted(
[(var, start) for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: " +
str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(project_dir, 'static_arrays', name))
static_array_specs.append(
(name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [
net() for net in Network.__instances__()
if net().name != '_fake_network'
]
synapses = [S() for S in Synapses.__instances__()]
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None,
None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks,
)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func == 'run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func == 'run_network':
net, netcode = args
main_lines.extend(netcode)
elif func == 'set_by_array':
arrayname, staticarrayname = args
code = '''
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname,
staticarrayname=staticarrayname)
main_lines.extend(code.split('\n'))
elif func == 'set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname,
staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value)
main_lines.extend(code.split('\n'))
elif func == 'insert_code':
main_lines.append(args)
elif func == 'start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func == 'end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type " +
func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(
line.format(c_type=c_data_type(v.dtype),
varname=k,
objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(
c_type=c_data_type(v.dtype),
array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(
k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' %
(k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%',
'\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n' + code
writer.write('code_objects/' + codeobj.name + '.cpp', code)
writer.write('code_objects/' + codeobj.name + '.h',
codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(
None,
None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(
None,
None,
run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(
os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir,
os.path.join(project_dir, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/' + file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/' + file)
# Copy the CSpikeQueue implementation
spikequeue_h = os.path.join(project_dir, 'brianlib', 'spikequeue.h')
shutil.copy2(
os.path.join(
os.path.split(inspect.getsourcefile(Synapses))[0],
'cspikequeue.cpp'), spikequeue_h)
#writer.header_files.append(spikequeue_h)
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
# Generate the makefile
if os.name == 'nt':
rm_cmd = 'del'
else:
rm_cmd = 'rm'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(
None,
None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile_project:
with in_directory(project_dir):
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x == 0:
if run_project:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name == 'nt':
x = subprocess.call(['main'] + run_args,
stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args,
stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
else:
raise RuntimeError("Project compilation failed")
def determine_keywords(self):
# set up the restricted pointers, these are used so that the compiler
# knows there is no aliasing in the pointers, for optimisation
pointers = []
# Add additional lines inside the kernel functions
kernel_lines = []
# It is possible that several different variable names refer to the
# same array. E.g. in gapjunction code, v_pre and v_post refer to the
# same array if a group is connected to itself
handled_pointers = set()
template_kwds = {}
# Again, do the import here to avoid a circular dependency.
from brian2.devices.device import get_device
device = get_device()
for varname, var in self.variables.iteritems():
if isinstance(var, ArrayVariable):
# This is the "true" array name, not the restricted pointer.
array_name = device.get_array_name(var)
pointer_name = self.get_array_name(var)
if pointer_name in handled_pointers:
continue
if getattr(var, 'ndim', 1) > 1:
continue # multidimensional (dynamic) arrays have to be treated differently
restrict = self.restrict
# turn off restricted pointers for scalars for safety
if var.scalar:
restrict = ' '
line = '{0}* {1} {2} = {3};'.format(
self.c_data_type(var.dtype), restrict, pointer_name,
array_name)
pointers.append(line)
handled_pointers.add(pointer_name)
# set up the functions
user_functions = []
support_code = []
hash_defines = []
for varname, variable in self.variables.items():
if isinstance(variable, Function):
hd, ps, sc, uf, kl = self._add_user_function(varname, variable)
user_functions.extend(uf)
support_code.extend(sc)
pointers.extend(ps)
hash_defines.extend(hd)
kernel_lines.extend(kl)
support_code.append(self.universal_support_code)
# Clock variables (t, dt, timestep) are passed by value to kernels and
# need to be translated back into pointers for scalar/vector code.
for varname, variable in self.variables.iteritems():
if hasattr(variable, 'owner') and isinstance(
variable.owner, Clock):
# get arrayname without _ptr suffix (e.g. _array_defaultclock_dt)
arrayname = self.get_array_name(variable, pointer=False)
line = "const {dtype}* _ptr{arrayname} = &_value{arrayname};"
line = line.format(dtype=c_data_type(variable.dtype),
arrayname=arrayname)
if line not in kernel_lines:
kernel_lines.append(line)
keywords = {
'pointers_lines':
stripped_deindented_lines('\n'.join(pointers)),
'support_code_lines':
stripped_deindented_lines('\n'.join(support_code)),
'hashdefine_lines':
stripped_deindented_lines('\n'.join(hash_defines)),
'denormals_code_lines':
stripped_deindented_lines('\n'.join(
self.denormals_to_zero_code())),
'kernel_lines':
stripped_deindented_lines('\n'.join(kernel_lines)),
'uses_atomics':
self.uses_atomics
}
keywords.update(template_kwds)
return keywords
def generate_codeobj_source(self, writer):
#check how many random numbers are needed per step
for code_object in self.code_objects.itervalues():
num_occurences_rand = code_object.code.cu_file.count("_rand(")
num_occurences_randn = code_object.code.cu_file.count("_randn(")
if num_occurences_rand > 0:
# synapses_create_generator uses host side random number generation
if code_object.template_name != "synapses_create_generator":
#first one is alway the definition, so subtract 1
code_object.rand_calls = num_occurences_rand - 1
for i in range(0, code_object.rand_calls):
code_object.code.cu_file = code_object.code.cu_file.replace(
"_rand(_vectorisation_idx)",
"_rand(_vectorisation_idx + {i} * _N)".format(i=i),
1)
if num_occurences_randn > 0 and code_object.template_name != "synapses_create_generator":
#first one is alway the definition, so subtract 1
code_object.randn_calls = num_occurences_randn - 1
for i in range(0, code_object.randn_calls):
code_object.code.cu_file = code_object.code.cu_file.replace(
"_randn(_vectorisation_idx)",
"_randn(_vectorisation_idx + {i} * _N)".format(i=i), 1)
code_object_defs = defaultdict(list)
host_parameters = defaultdict(list)
device_parameters = defaultdict(list)
kernel_variables = defaultdict(list)
# Generate data for non-constant values
for codeobj in self.code_objects.itervalues():
code_object_defs_lines = []
host_parameters_lines = []
device_parameters_lines = []
kernel_variables_lines = []
additional_code = []
number_elements = ""
if hasattr(codeobj, 'owner') and hasattr(
codeobj.owner, '_N') and codeobj.owner._N != 0:
number_elements = str(codeobj.owner._N)
else:
number_elements = "_N"
for k, v in codeobj.variables.iteritems():
#code objects which only run once
if k == "_python_randn" and codeobj.runs_every_tick == False and codeobj.template_name != "synapses_create_generator":
additional_code.append('''
//genenerate an array of random numbers on the device
float* dev_array_randn;
cudaMalloc((void**)&dev_array_randn, sizeof(float)*'''
+ number_elements + ''' * ''' +
str(codeobj.randn_calls) + ''');
if(!dev_array_randn)
{
printf("ERROR while allocating device memory with size %ld\\n", sizeof(float)*'''
+ number_elements + '''*''' +
str(codeobj.randn_calls) + ''');
}
curandGenerateNormal(random_float_generator, dev_array_randn, '''
+ number_elements + '''*''' +
str(codeobj.randn_calls) +
''', 0, 1);''')
line = "float* _array_{name}_randn".format(
name=codeobj.name)
device_parameters_lines.append(line)
host_parameters_lines.append("dev_array_randn")
elif k == "_python_rand" and codeobj.runs_every_tick == False and codeobj.template_name != "synapses_create_generator":
additional_code.append('''
//genenerate an array of random numbers on the device
float* dev_array_rand;
cudaMalloc((void**)&dev_array_rand, sizeof(float)*''' +
number_elements + '''*''' +
str(codeobj.rand_calls) + ''');
if(!dev_array_rand)
{
printf("ERROR while allocating device memory with size %ld\\n", sizeof(float)*'''
+ number_elements + '''*''' +
str(codeobj.rand_calls) + ''');
}
curandGenerateUniform(random_float_generator, dev_array_rand, '''
+ number_elements + '''*''' +
str(codeobj.rand_calls) + ''');''')
line = "float* _array_{name}_rand".format(
name=codeobj.name)
device_parameters_lines.append(line)
host_parameters_lines.append("dev_array_rand")
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = thrust::raw_pointer_cast(&dev{dyn_array_name}[0]);'
line = line.format(
c_type=c_data_type(v.dtype),
array_name=array_name,
dyn_array_name=dyn_array_name)
code_object_defs_lines.append(line)
line = 'const int _num{k} = dev{dyn_array_name}.size();'
line = line.format(
k=k, dyn_array_name=dyn_array_name)
code_object_defs_lines.append(line)
host_parameters_lines.append(array_name)
host_parameters_lines.append("_num" + k)
line = "{c_type}* par_{array_name}"
device_parameters_lines.append(
line.format(c_type=c_data_type(v.dtype),
array_name=array_name))
line = "int par_num_{array_name}"
device_parameters_lines.append(
line.format(array_name=k))
line = "{c_type}* _ptr{array_name} = par_{array_name};"
kernel_variables_lines.append(
line.format(c_type=c_data_type(v.dtype),
array_name=array_name))
line = "const int _num{array_name} = par_num_{array_name};"
kernel_variables_lines.append(
line.format(array_name=k))
else:
arrayname = self.get_array_name(v)
host_parameters_lines.append("dev" + arrayname)
device_parameters_lines.append(
"%s* par_%s" %
(c_data_type(v.dtype), arrayname))
kernel_variables_lines.append(
"%s* _ptr%s = par_%s;" %
(c_data_type(v.dtype), arrayname, arrayname))
code_object_defs_lines.append(
'const int _num%s = %s;' % (k, v.size))
kernel_variables_lines.append(
'const int _num%s = %s;' % (k, v.size))
if k.endswith('space'):
host_parameters_lines[
-1] += '[current_idx{arrayname}]'.format(
arrayname=arrayname)
except TypeError:
pass
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
for line in code_object_defs_lines:
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
for line in host_parameters_lines:
if not line in host_parameters[codeobj.name]:
host_parameters[codeobj.name].append(line)
for line in device_parameters_lines:
if not line in device_parameters[codeobj.name]:
device_parameters[codeobj.name].append(line)
for line in kernel_variables_lines:
if not line in kernel_variables[codeobj.name]:
kernel_variables[codeobj.name].append(line)
for line in additional_code:
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = self.freeze(codeobj.code.cu_file, ns)
if len(host_parameters[codeobj.name]) == 0:
host_parameters[codeobj.name].append("0")
device_parameters[codeobj.name].append("int dummy")
code = code.replace('%CONSTANTS%',
'\n\t\t'.join(code_object_defs[codeobj.name]))
code = code.replace(
'%HOST_PARAMETERS%',
',\n\t\t\t'.join(host_parameters[codeobj.name]))
code = code.replace('%DEVICE_PARAMETERS%',
',\n\t'.join(device_parameters[codeobj.name]))
code = code.replace('%KERNEL_VARIABLES%',
'\n\t'.join(kernel_variables[codeobj.name]))
code = code.replace('%CODEOBJ_NAME%', codeobj.name)
code = '#include "objects.h"\n' + code
writer.write('code_objects/' + codeobj.name + '.cu', code)
writer.write('code_objects/' + codeobj.name + '.h',
codeobj.code.h_file)
def determine_keywords(self):
# set up the restricted pointers, these are used so that the compiler
# knows there is no aliasing in the pointers, for optimisation
pointers = []
# Add additional lines inside the kernel functions
kernel_lines = []
# It is possible that several different variable names refer to the
# same array. E.g. in gapjunction code, v_pre and v_post refer to the
# same array if a group is connected to itself
handled_pointers = set()
template_kwds = {}
# Again, do the import here to avoid a circular dependency.
from brian2.devices.device import get_device
device = get_device()
for varname, var in self.variables.items():
if isinstance(var, ArrayVariable):
# This is the "true" array name, not the restricted pointer.
array_name = device.get_array_name(var)
pointer_name = self.get_array_name(var)
if pointer_name in handled_pointers:
continue
if getattr(var, 'ndim', 1) > 1:
continue # multidimensional (dynamic) arrays have to be treated differently
restrict = self.restrict
# turn off restricted pointers for scalars for safety
if var.scalar:
restrict = ' '
# Need to use correct dt type in pointers_lines for single precision,
# see #148
if varname == "dt" and prefs.core.default_float_dtype == np.float32:
# c_data_type(variable.dtype) is float, but we need double
dtype = "double"
else:
dtype = self.c_data_type(var.dtype)
line = '{0}* {1} {2} = {3};'.format(dtype,
restrict,
pointer_name,
array_name)
pointers.append(line)
handled_pointers.add(pointer_name)
# set up the functions
user_functions = []
support_code = []
hash_defines = []
added = set() # keep track of functions that were added
for varname, variable in list(self.variables.items()):
if isinstance(variable, Function):
user_func = self._add_user_function(varname, variable, added)
if user_func is not None:
hd, ps, sc, uf, kl = user_func
user_functions.extend(uf)
support_code.extend(sc)
pointers.extend(ps)
hash_defines.extend(hd)
kernel_lines.extend(kl)
# Generate universal_support_code once when the first codeobject is created.
# Can't do it at import time since need access to user preferences
# This is a class attribute (not instance attribute).
if CUDACodeGenerator.universal_support_code is None:
_atomic_support_code = _generate_atomic_support_code()
CUDACodeGenerator.universal_support_code = (
_hightype_support_code
+ _mod_support_code
+ _floordiv_support_code
+ _pow_support_code
+ _atomic_support_code
)
support_code.append(CUDACodeGenerator.universal_support_code)
# Clock variables (t, dt, timestep) are passed by value to kernels and
# need to be translated back into pointers for scalar/vector code.
for varname, variable in self.variables.items():
if hasattr(variable, 'owner') and isinstance(variable.owner, Clock):
# get arrayname without _ptr suffix (e.g. _array_defaultclock_dt)
arrayname = self.get_array_name(variable, prefix='')
# kernel_lines appear before dt is cast to float (in scalar_code), hence
# we need to still use double (used in kernel parameters), see #148
if varname == "dt" and prefs.core.default_float_dtype == np.float32:
# c_data_type(variable.dtype) is float, but we need double
dtype = "double"
else:
dtype = dtype=c_data_type(variable.dtype)
line = f"const {dtype}* _ptr{arrayname} = &_value{arrayname};"
if line not in kernel_lines:
kernel_lines.append(line)
keywords = {'pointers_lines': stripped_deindented_lines('\n'.join(pointers)),
'support_code_lines': stripped_deindented_lines('\n'.join(support_code)),
'hashdefine_lines': stripped_deindented_lines('\n'.join(hash_defines)),
'denormals_code_lines': stripped_deindented_lines('\n'.join(self.denormals_to_zero_code())),
'kernel_lines': stripped_deindented_lines('\n'.join(kernel_lines)),
'uses_atomics': self.uses_atomics
}
keywords.update(template_kwds)
return keywords
def build(self, project_dir='output', compile_project=True, run_project=False, debug=True,
with_output=True, native=True,
additional_source_files=None, additional_header_files=None,
main_includes=None, run_includes=None,
run_args=None,
):
'''
Build the project
TODO: more details
Parameters
----------
project_dir : str
The output directory to write the project to, any existing files will be overwritten.
compile_project : bool
Whether or not to attempt to compile the project using GNU make.
run_project : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile natively using the ``--march=native`` gcc option.
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = project_dir
ensure_directory(project_dir)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(project_dir, d))
writer = CPPWriter(project_dir)
logger.debug("Writing C++ standalone project to directory "+os.path.normpath(project_dir))
arange_arrays = sorted([(var, start)
for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(project_dir, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [net() for net in Network.__instances__() if net().name!='_fake_network']
synapses = [S() for S in Synapses.__instances__()]
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None, None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks,
)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func=='run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func=='run_network':
net, netcode = args
main_lines.extend(netcode)
elif func=='set_by_array':
arrayname, staticarrayname = args
code = '''
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname, staticarrayname=staticarrayname)
main_lines.extend(code.split('\n'))
elif func=='set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value)
main_lines.extend(code.split('\n'))
elif func=='insert_code':
main_lines.append(args)
elif func=='start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func=='end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type "+func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(line.format(c_type=c_data_type(v.dtype), varname=k, objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cpp', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(None, None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(None, None, run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir, os.path.join(project_dir, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/'+file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/'+file)
# Copy the CSpikeQueue implementation
spikequeue_h = os.path.join(project_dir, 'brianlib', 'spikequeue.h')
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'cspikequeue.cpp'),
spikequeue_h)
#writer.header_files.append(spikequeue_h)
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
# Generate the makefile
if os.name=='nt':
rm_cmd = 'del'
else:
rm_cmd = 'rm'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(None, None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile_project:
with in_directory(project_dir):
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x==0:
if run_project:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name=='nt':
x = subprocess.call(['main'] + run_args, stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args, stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
else:
raise RuntimeError("Project compilation failed")
def build(self, directory='output',
compile=True, run=True, debug=False, clean=True,
with_output=True, native=True,
additional_source_files=None, additional_header_files=None,
main_includes=None, run_includes=None,
run_args=None, **kwds):
'''
Build the project
TODO: more details
Parameters
----------
directory : str
The output directory to write the project to, any existing files will be overwritten.
compile : bool
Whether or not to attempt to compile the project
run : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile for the current machine's architecture (best for speed, but not portable)
clean : bool
Whether or not to clean the project before building
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
renames = {'project_dir': 'directory',
'compile_project': 'compile',
'run_project': 'run'}
if len(kwds):
msg = ''
for kwd in kwds:
if kwd in renames:
msg += ("Keyword argument '%s' has been renamed to "
"'%s'. ") % (kwd, renames[kwd])
else:
msg += "Unknown keyword argument '%s'. " % kwd
raise TypeError(msg)
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = directory
ensure_directory(directory)
compiler, extra_compile_args = get_compiler_and_args()
compiler_flags = ' '.join(extra_compile_args)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(directory, d))
writer = CPPWriter(directory)
# Get the number of threads if specified in an openmp context
nb_threads = prefs.devices.cpp_standalone.openmp_threads
# If the number is negative, we need to throw an error
if (nb_threads < 0):
raise ValueError('The number of OpenMP threads can not be negative !')
logger.debug("Writing C++ standalone project to directory "+os.path.normpath(directory))
if nb_threads > 0:
logger.warn("OpenMP code is not yet well tested, and may be inaccurate.", "openmp", once=True)
logger.debug("Using OpenMP with %d threads " % nb_threads)
for codeobj in self.code_objects.itervalues():
if not 'IS_OPENMP_COMPATIBLE' in codeobj.template_source:
raise RuntimeError(("Code object '%s' uses the template %s "
"which is not compatible with "
"OpenMP.") % (codeobj.name,
codeobj.template_name))
arange_arrays = sorted([(var, start)
for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(directory, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [net() for net in Network.__instances__()
if net().name != '_fake_network']
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
# We don't currently support pathways with scalar delays
for synapse_obj in net_synapses:
for pathway in synapse_obj._pathways:
if not isinstance(pathway.variables['delay'],
DynamicArrayVariable):
error_msg = ('The "%s" pathway uses a scalar '
'delay (instead of a delay per synapse). '
'This is not yet supported. Do not '
'specify a delay in the Synapses(...) '
'call but instead set its delay attribute '
'afterwards.') % (pathway.name)
raise NotImplementedError(error_msg)
# Not sure what the best place is to call Network.after_run -- at the
# moment the only important thing it does is to clear the objects stored
# in magic_network. If this is not done, this might lead to problems
# for repeated runs of standalone (e.g. in the test suite).
for net in networks:
net.after_run()
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None, None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func=='run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func=='run_network':
net, netcode = args
main_lines.extend(netcode)
elif func=='set_by_array':
arrayname, staticarrayname = args
code = '''
{pragma}
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname, staticarrayname=staticarrayname, pragma=openmp_pragma('static'))
main_lines.extend(code.split('\n'))
elif func=='set_by_single_value':
arrayname, item, value = args
code = '{arrayname}[{item}] = {value};'.format(arrayname=arrayname,
item=item,
value=value)
main_lines.extend([code])
elif func=='set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
{pragma}
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value, pragma=openmp_pragma('static'))
main_lines.extend(code.split('\n'))
elif func=='insert_code':
main_lines.append(args)
elif func=='start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func=='end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type "+func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(line.format(c_type=c_data_type(v.dtype), varname=k, objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cpp', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(None, None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
if compiler=='msvc':
std_move = 'std::move'
else:
std_move = ''
network_tmp = CPPStandaloneCodeObject.templater.network(None, None,
std_move=std_move)
writer.write('network.*', network_tmp)
synapses_classes_tmp = CPPStandaloneCodeObject.templater.synapses_classes(None, None)
writer.write('synapses_classes.*', synapses_classes_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(None, None, run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir, os.path.join(directory, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/'+file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/'+file)
# Copy the CSpikeQueue implementation
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'cspikequeue.cpp'),
os.path.join(directory, 'brianlib', 'spikequeue.h'))
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'stdint_compat.h'),
os.path.join(directory, 'brianlib', 'stdint_compat.h'))
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
if compiler=='msvc':
if native:
arch_flag = ''
try:
from cpuinfo import cpuinfo
res = cpuinfo.get_cpu_info()
if 'sse' in res['flags']:
arch_flag = '/arch:SSE'
if 'sse2' in res['flags']:
arch_flag = '/arch:SSE2'
except ImportError:
logger.warn('Native flag for MSVC compiler requires installation of the py-cpuinfo module')
compiler_flags += ' '+arch_flag
if nb_threads>1:
openmp_flag = '/openmp'
else:
openmp_flag = ''
# Generate the visual studio makefile
source_bases = [fname.replace('.cpp', '').replace('/', '\\') for fname in writer.source_files]
win_makefile_tmp = CPPStandaloneCodeObject.templater.win_makefile(
None, None,
source_bases=source_bases,
compiler_flags=compiler_flags,
openmp_flag=openmp_flag,
)
writer.write('win_makefile', win_makefile_tmp)
else:
# Generate the makefile
if os.name=='nt':
rm_cmd = 'del *.o /s\n\tdel main.exe $(DEPS)'
else:
rm_cmd = 'rm $(OBJS) $(PROGRAM) $(DEPS)'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(None, None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
compiler_flags=compiler_flags,
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile:
with in_directory(directory):
if compiler=='msvc':
# TODO: handle debug
if debug:
logger.warn('Debug flag currently ignored for MSVC')
vcvars_search_paths = [
# futureproofing!
r'c:\Program Files\Microsoft Visual Studio 15.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 15.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 14.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 13.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 13.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 12.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 11.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 10.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\vcvarsall.bat',
]
vcvars_loc = prefs['codegen.cpp.msvc_vars_location']
if vcvars_loc=='':
for fname in vcvars_search_paths:
if os.path.exists(fname):
vcvars_loc = fname
break
if vcvars_loc=='':
raise IOError("Cannot find vcvarsall.bat on standard search path.")
# TODO: copy vcvars and make replacements for 64 bit automatically
arch_name = prefs['codegen.cpp.msvc_architecture']
if arch_name=='':
mach = platform.machine()
if mach=='AMD64':
arch_name = 'x86_amd64'
else:
arch_name = 'x86'
vcvars_cmd = '"{vcvars_loc}" {arch_name}'.format(
vcvars_loc=vcvars_loc, arch_name=arch_name)
make_cmd = 'nmake /f win_makefile'
if os.path.exists('winmake.log'):
os.remove('winmake.log')
with std_silent(debug):
if clean:
os.system('%s >>winmake.log 2>&1 && %s clean >>winmake.log 2>&1' % (vcvars_cmd, make_cmd))
x = os.system('%s >>winmake.log 2>&1 && %s >>winmake.log 2>&1' % (vcvars_cmd, make_cmd))
if x!=0:
raise RuntimeError("Project compilation failed")
else:
with std_silent(debug):
if clean:
os.system('make clean')
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x!=0:
raise RuntimeError("Project compilation failed")
if run:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name=='nt':
x = subprocess.call(['main'] + run_args, stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args, stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
