Preferences

Brian has a system of global preferences that affect how certain objects behave. These can be set either in scripts by using the prefs object or in a file. Each preference looks like codegen.cpp.compiler, i.e. dotted names.

Accessing and setting preferences

Preferences can be accessed and set either keyword-based or attribute-based. The following are equivalent:

prefs['codegen.cpp.compiler'] = 'unix'
prefs.codegen.cpp.compiler = 'unix'

Using the attribute-based form can be particulary useful for interactive work, e.g. in ipython, as it offers autocompletion and documentation. In ipython, prefs.codegen.cpp? would display a docstring with all the preferences available in the codegen.cpp category.

Preference files

Preferences are stored in a hierarchy of files, with the following order (each step overrides the values in the previous step but no error is raised if one is missing):

• The user default are stored in ~/.brian/user_preferences (which works on Windows as well as Linux). The ~ symbol refers to the user directory.

• The file brian_preferences in the current directory.

The preference files are of the following form:

a.b.c = 1
# Comment line
[a]
b.d = 2
[a.b]
b.e = 3

This would set preferences a.b.c=1, a.b.d=2 and a.b.e=3.

File setting all preferences to their default values

#-------------------------------------------------------------------------------
# Logging system preferences
#-------------------------------------------------------------------------------

[logging]

# What log level to use for the log written to the console.
# 
# Has to be one of CRITICAL, ERROR, WARNING, INFO, DEBUG or DIAGNOSTIC.

console_log_level = 'INFO'

# Whether to delete the log and script file on exit.
# 
# If set to ``True`` (the default), log files (and the copy of the main
# script) will be deleted after the brian process has exited, unless an
# uncaught exception occurred. If set to ``False``, all log files will be
# kept.

delete_log_on_exit = True

# Whether to display a text for uncaught errors, mentioning the location
# of the log file, the mailing list and the github issues.
# 
# Defaults to ``True``.

display_brian_error_message = True

# Whether to log to a file or not.
# 
# If set to ``True`` (the default), logging information will be written
# to a file. The log level can be set via the `logging.file_log_level`
# preference.

file_log = True

# What log level to use for the log written to the log file.
# 
# In case file logging is activated (see `logging.file_log`), which log
# level should be used for logging. Has to be one of CRITICAL, ERROR,
# WARNING, INFO, DEBUG or DIAGNOSTIC.

file_log_level = 'DEBUG'

# The maximum size for the debug log before it will be rotated.
# 
# If set to any value ``> 0``, the debug log will be rotated once
# this size is reached. Rotating the log means that the old debug log
# will be moved into a file in the same directory but with suffix ``".1"``
# and the a new log file will be created with the same pathname as the
# original file. Only one backup is kept; if a file with suffix ``".1"``
# already exists when rotating, it will be overwritten.
# If set to ``0``, no log rotation will be applied.
# The default setting rotates the log file after 10MB.

file_log_max_size = 10000000

# Whether to save a copy of the script that is run.
# 
# If set to ``True`` (the default), a copy of the currently run script
# is saved to a temporary location. It is deleted after a successful
# run (unless `logging.delete_log_on_exit` is ``False``) but is kept after
# an uncaught exception occured. This can be helpful for debugging,
# in particular when several simulations are running in parallel.

save_script = True

# Whether or not to redirect stdout/stderr to null at certain places.
# 
# This silences a lot of annoying compiler output, but will also hide
# error messages making it harder to debug problems. You can always
# temporarily switch it off when debugging. If
# `logging.std_redirection_to_file` is set to ``True`` as well, then the
# output is saved to a file and if an error occurs the name of this file
# will be printed.

std_redirection = True

# Whether to redirect stdout/stderr to a file.
# 
# If both ``logging.std_redirection`` and this preference are set to
# ``True``, all standard output/error (most importantly output from
# the compiler) will be stored in files and if an error occurs the name
# of this file will be printed. If `logging.std_redirection` is ``True``
# and this preference is ``False``, then all standard output/error will
# be completely suppressed, i.e. neither be displayed nor stored in a
# file.
# 
# The value of this preference is ignore if `logging.std_redirection` is
# set to ``False``.

std_redirection_to_file = True

#-------------------------------------------------------------------------------
# Runtime codegen preferences (see subcategories for individual targets)
#-------------------------------------------------------------------------------

[codegen.runtime]

#-------------------------------------------------------------------------------
# Codegen generator preferences (see subcategories for individual languages)
#-------------------------------------------------------------------------------

[codegen.generators]

#-------------------------------------------------------------------------------
# C++ compilation preferences
#-------------------------------------------------------------------------------

[codegen.cpp]

# Compiler to use (uses default if empty).
# Should be ``'unix'`` or ``'msvc'``.
# 
# To specify a specific compiler binary on unix systems, set the `CXX` environment
# variable instead.

compiler = ''

# List of macros to define; each macro is defined using a 2-tuple,
# where 'value' is either the string to define it to or None to
# define it without a particular value (equivalent of "#define
# FOO" in source or -DFOO on Unix C compiler command line).

define_macros = []

# Extra arguments to pass to compiler (if None, use either
# ``extra_compile_args_gcc`` or ``extra_compile_args_msvc``).

extra_compile_args = None

# Extra compile arguments to pass to GCC compiler

extra_compile_args_gcc = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11']

# Extra compile arguments to pass to MSVC compiler (the default
# ``/arch:`` flag is determined based on the processor architecture)

extra_compile_args_msvc = ['/Ox', '/w', '', '/MP']

# Any extra platform- and compiler-specific information to use when
# linking object files together.

extra_link_args = []

# A list of strings specifying header files to use when compiling the
# code. The list might look like ["<vector>","'my_header'"]. Note that
# the header strings need to be in a form than can be pasted at the end
# of a #include statement in the C++ code.

headers = []

# Include directories to use.
# The default value is ``$prefix/include`` (or ``$prefix/Library/include``
# on Windows), where ``$prefix`` is Python's site-specific directory
# prefix as returned by `sys.prefix`. This will make compilation use
# library files installed into a conda environment.

include_dirs = ['/path/to/your/Python/environment/include']

# List of library names (not filenames or paths) to link against.

libraries = []

# List of directories to search for C/C++ libraries at link time.
# The default value is ``$prefix/lib`` (or ``$prefix/Library/lib``
# on Windows), where ``$prefix`` is Python's site-specific directory
# prefix as returned by `sys.prefix`. This will make compilation use
# library files installed into a conda environment.

library_dirs = ['/path/to/your/Python/environment/lib']

# MSVC architecture name (or use system architectue by default).
# 
# Could take values such as x86, amd64, etc.

msvc_architecture = ''

# Location of the MSVC command line tool (or search for best by default).

msvc_vars_location = ''

# List of directories to search for C/C++ libraries at run time.
# The default value is ``$prefix/lib`` (not used on Windows), where
# ``$prefix`` is Python's site-specific directory prefix as returned by
# `sys.prefix`. This will make compilation use library files installed
# into a conda environment.

runtime_library_dirs = ['/path/to/your/Python/environment/lib']

#-------------------------------------------------------------------------------
# C++ codegen preferences
#-------------------------------------------------------------------------------

[codegen.generators.cpp]

# Adds code to flush denormals to zero.
# 
# The code is gcc and architecture specific, so may not compile on all
# platforms. The code, for reference is::
# 
#     #define CSR_FLUSH_TO_ZERO         (1 << 15)
#     unsigned csr = __builtin_ia32_stmxcsr();
#     csr |= CSR_FLUSH_TO_ZERO;
#     __builtin_ia32_ldmxcsr(csr);
# 
# Found at `<http://stackoverflow.com/questions/2487653/avoiding-denormal-values-in-c>`_.

flush_denormals = False

# The keyword used for the given compiler to declare pointers as restricted.
# 
# This keyword is different on different compilers, the default works for
# gcc and MSVS.

restrict_keyword = '__restrict'

#-------------------------------------------------------------------------------
# Device preferences
#-------------------------------------------------------------------------------

[devices]

#-------------------------------------------------------------------------------
# Directory containing GSL code
#-------------------------------------------------------------------------------

[GSL]

# Set path to directory containing GSL header files (gsl_odeiv2.h etc.)
# If this directory is already in Python's include (e.g. because of conda installation), this path can be set to None.

directory = None

#-------------------------------------------------------------------------------
# Numpy runtime codegen preferences
#-------------------------------------------------------------------------------

[codegen.runtime.numpy]

# Whether to change the namespace of user-specifed functions to remove
# units.

discard_units = False

#-------------------------------------------------------------------------------
# Cython runtime codegen preferences
#-------------------------------------------------------------------------------

[codegen.runtime.cython]

# Location of the cache directory for Cython files. By default,
# will be stored in a ``brian_extensions`` subdirectory
# where Cython inline stores its temporary files
# (the result of ``get_cython_cache_dir()``).

cache_dir = None

# Whether to delete source files after compiling. The Cython
# source files can take a significant amount of disk space, and
# are not used anymore when the compiled library file exists.
# They are therefore deleted by default, but keeping them around
# can be useful for debugging.

delete_source_files = True

# Whether to use a lock file to prevent simultaneous write access
# to cython .pyx and .so files.

multiprocess_safe = True

#-------------------------------------------------------------------------------
# Code generation preferences
#-------------------------------------------------------------------------------

[codegen]

# Whether to pull out scalar expressions out of the statements, so that
# they are only evaluated once instead of once for every neuron/synapse/...
# Can be switched off, e.g. because it complicates the code (and the same
# optimisation is already performed by the compiler) or because the
# code generation target does not deal well with it. Defaults to ``True``.

loop_invariant_optimisations = True

# The size of a directory (in MB) with cached code for Cython that triggers
# a warning. Set to 0 to never get a warning.

max_cache_dir_size = 1000

# Default target for the evaluation of string expressions (e.g. when
# indexing state variables). Should normally not be changed from the
# default numpy target, because the overhead of compiling code is not
# worth the speed gain for simple expressions.
# 
# Accepts the same arguments as `codegen.target`, except for ``'auto'``

string_expression_target = 'numpy'

# Default target for code generation.
# 
# Can be a string, in which case it should be one of:
# 
# * ``'auto'`` the default, automatically chose the best code generation
#   target available.
# * ``'cython'``, uses the Cython package to generate C++ code. Needs a
#   working installation of Cython and a C++ compiler.
# * ``'numpy'`` works on all platforms and doesn't need a C compiler but
#   is often less efficient.
# 
# Or it can be a ``CodeObject`` class.

target = 'auto'

#-------------------------------------------------------------------------------
# Network preferences
#-------------------------------------------------------------------------------

[core.network]

# Default schedule used for networks that
# don't specify a schedule.

default_schedule = ['start', 'groups', 'thresholds', 'synapses', 'resets', 'end']

#-------------------------------------------------------------------------------
# C++ standalone preferences
#-------------------------------------------------------------------------------

[devices.cpp_standalone]

# Additional flags to pass to the GNU make command on Linux/OS-X.
# Defaults to "-j" for parallel compilation.

extra_make_args_unix = ['-j']

# Additional flags to pass to the nmake command on Windows. By default, no
# additional flags are passed.

extra_make_args_windows = []

# The make command used to compile the standalone project. Defaults to the
# standard GNU make commane "make".

make_cmd_unix = 'make'

# DEPRECATED. Previously used to chose the strategy to parallelize the
# solution of the three tridiagonal systems for multicompartmental
# neurons. Now, its value is ignored.

openmp_spatialneuron_strategy = None

# The number of threads to use if OpenMP is turned on. By default, this value is set to 0 and the C++ code
# is generated without any reference to OpenMP. If greater than 0, then the corresponding number of threads
# are used to launch the simulation.

openmp_threads = 0

# The command used to run the compiled standalone project. Defaults to executing
# the compiled binary with "./main". Must be a single binary as string or a list
# of command arguments (e.g. ["./binary", "--key", "value"]).

run_cmd_unix = './main'

# Dictionary of environment variables and their values that will be set
# during the execution of the standalone code.

run_environment_variables = {'LD_BIND_NOW': '1'}

#-------------------------------------------------------------------------------
# Core Brian preferences
#-------------------------------------------------------------------------------

[core]

# Default dtype for all arrays of scalars (state variables, weights, etc.).

default_float_dtype = float64

# Default dtype for all arrays of integer scalars.

default_integer_dtype = int32

# Whether to raise an error for outdated dependencies (``True``) or just
# a warning (``False``).

outdated_dependency_error = True

#-------------------------------------------------------------------------------
# Preferences to enable legacy behaviour
#-------------------------------------------------------------------------------

[legacy]

# Whether to use the semantics for checking the refractoriness condition
# that were in place up until (including) version 2.1.2. In that
# implementation, refractory periods that were multiples of dt could lead
# to a varying number of refractory timesteps due to the nature of
# floating point comparisons). This preference is only provided for exact
# reproducibility of previously obtained results, new simulations should
# use the improved mechanism which uses a more robust mechanism to
# convert refractoriness into timesteps. Defaults to ``False``.

refractory_timing = False

List of preferences

Brian itself defines the following preferences (including their default values):

GSL

Directory containing GSL code

GSL.directory = None

Set path to directory containing GSL header files (gsl_odeiv2.h etc.) If this directory is already in Python’s include (e.g. because of conda installation), this path can be set to None.

codegen

Code generation preferences

codegen.loop_invariant_optimisations = True

Whether to pull out scalar expressions out of the statements, so that they are only evaluated once instead of once for every neuron/synapse/… Can be switched off, e.g. because it complicates the code (and the same optimisation is already performed by the compiler) or because the code generation target does not deal well with it. Defaults to True.

codegen.max_cache_dir_size = 1000

The size of a directory (in MB) with cached code for Cython that triggers a warning. Set to 0 to never get a warning.

codegen.string_expression_target = 'numpy'

Default target for the evaluation of string expressions (e.g. when indexing state variables). Should normally not be changed from the default numpy target, because the overhead of compiling code is not worth the speed gain for simple expressions.

Accepts the same arguments as codegen.target, except for 'auto'

codegen.target = 'auto'

Default target for code generation.

Can be a string, in which case it should be one of:

• 'auto' the default, automatically chose the best code generation target available.

• 'cython', uses the Cython package to generate C++ code. Needs a working installation of Cython and a C++ compiler.

• 'numpy' works on all platforms and doesn’t need a C compiler but is often less efficient.

Or it can be a CodeObject class.

codegen.cpp

C++ compilation preferences

codegen.cpp.compiler = ''

Compiler to use (uses default if empty). Should be 'unix' or 'msvc'.

To specify a specific compiler binary on unix systems, set the CXX environment variable instead.

codegen.cpp.define_macros = []

List of macros to define; each macro is defined using a 2-tuple, where ‘value’ is either the string to define it to or None to define it without a particular value (equivalent of “#define FOO” in source or -DFOO on Unix C compiler command line).

codegen.cpp.extra_compile_args = None

Extra arguments to pass to compiler (if None, use either extra_compile_args_gcc or extra_compile_args_msvc).

codegen.cpp.extra_compile_args_gcc = ['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11']

Extra compile arguments to pass to GCC compiler

codegen.cpp.extra_compile_args_msvc = ['/Ox', '/w', '', '/MP']

Extra compile arguments to pass to MSVC compiler (the default /arch: flag is determined based on the processor architecture)

codegen.cpp.extra_link_args = []

Any extra platform- and compiler-specific information to use when linking object files together.

codegen.cpp.headers = []

A list of strings specifying header files to use when compiling the code. The list might look like [“<vector>”,“‘my_header’”]. Note that the header strings need to be in a form than can be pasted at the end of a #include statement in the C++ code.

codegen.cpp.include_dirs = ['/path/to/your/Python/environment/include']

Include directories to use. The default value is $prefix/include (or $prefix/Library/include on Windows), where $prefix is Python’s site-specific directory prefix as returned by sys.prefix. This will make compilation use library files installed into a conda environment.

codegen.cpp.libraries = []

List of library names (not filenames or paths) to link against.

codegen.cpp.library_dirs = ['/path/to/your/Python/environment/lib']

List of directories to search for C/C++ libraries at link time. The default value is $prefix/lib (or $prefix/Library/lib on Windows), where $prefix is Python’s site-specific directory prefix as returned by sys.prefix. This will make compilation use library files installed into a conda environment.

codegen.cpp.msvc_architecture = ''

MSVC architecture name (or use system architectue by default).

Could take values such as x86, amd64, etc.

codegen.cpp.msvc_vars_location = ''

Location of the MSVC command line tool (or search for best by default).

codegen.cpp.runtime_library_dirs = ['/path/to/your/Python/environment/lib']

List of directories to search for C/C++ libraries at run time. The default value is $prefix/lib (not used on Windows), where $prefix is Python’s site-specific directory prefix as returned by sys.prefix. This will make compilation use library files installed into a conda environment.

codegen.generators

Codegen generator preferences (see subcategories for individual languages)

codegen.generators.cpp

C++ codegen preferences

codegen.generators.cpp.flush_denormals = False

Adds code to flush denormals to zero.

The code is gcc and architecture specific, so may not compile on all platforms. The code, for reference is:

#define CSR_FLUSH_TO_ZERO         (1 << 15)
unsigned csr = __builtin_ia32_stmxcsr();
csr |= CSR_FLUSH_TO_ZERO;
__builtin_ia32_ldmxcsr(csr);

Found at http://stackoverflow.com/questions/2487653/avoiding-denormal-values-in-c.

codegen.generators.cpp.restrict_keyword = '__restrict'

The keyword used for the given compiler to declare pointers as restricted.

This keyword is different on different compilers, the default works for gcc and MSVS.

codegen.runtime

Runtime codegen preferences (see subcategories for individual targets)

codegen.runtime.cython

Cython runtime codegen preferences

codegen.runtime.cython.cache_dir = None

Location of the cache directory for Cython files. By default, will be stored in a brian_extensions subdirectory where Cython inline stores its temporary files (the result of get_cython_cache_dir()).

codegen.runtime.cython.delete_source_files = True

Whether to delete source files after compiling. The Cython source files can take a significant amount of disk space, and are not used anymore when the compiled library file exists. They are therefore deleted by default, but keeping them around can be useful for debugging.

codegen.runtime.cython.multiprocess_safe = True

Whether to use a lock file to prevent simultaneous write access to cython .pyx and .so files.

codegen.runtime.numpy

Numpy runtime codegen preferences

codegen.runtime.numpy.discard_units = False

Whether to change the namespace of user-specifed functions to remove units.

core

Core Brian preferences

core.default_float_dtype = float64

Default dtype for all arrays of scalars (state variables, weights, etc.).

core.default_integer_dtype = int32

Default dtype for all arrays of integer scalars.

core.outdated_dependency_error = True

Whether to raise an error for outdated dependencies (True) or just a warning (False).

core.network

Network preferences

core.network.default_schedule = ['start', 'groups', 'thresholds', 'synapses', 'resets', 'end']

Default schedule used for networks that don’t specify a schedule.

devices

Device preferences

devices.cpp_standalone

C++ standalone preferences

devices.cpp_standalone.extra_make_args_unix = ['-j']

Additional flags to pass to the GNU make command on Linux/OS-X. Defaults to “-j” for parallel compilation.

devices.cpp_standalone.extra_make_args_windows = []

Additional flags to pass to the nmake command on Windows. By default, no additional flags are passed.

devices.cpp_standalone.make_cmd_unix = 'make'

The make command used to compile the standalone project. Defaults to the standard GNU make commane “make”.

devices.cpp_standalone.openmp_spatialneuron_strategy = None

DEPRECATED. Previously used to chose the strategy to parallelize the solution of the three tridiagonal systems for multicompartmental neurons. Now, its value is ignored.

devices.cpp_standalone.openmp_threads = 0

The number of threads to use if OpenMP is turned on. By default, this value is set to 0 and the C++ code is generated without any reference to OpenMP. If greater than 0, then the corresponding number of threads are used to launch the simulation.

devices.cpp_standalone.run_cmd_unix = './main'

The command used to run the compiled standalone project. Defaults to executing the compiled binary with “./main”. Must be a single binary as string or a list of command arguments (e.g. [“./binary”, “–key”, “value”]).

devices.cpp_standalone.run_environment_variables = {'LD_BIND_NOW': '1'}

Dictionary of environment variables and their values that will be set during the execution of the standalone code.

legacy

Preferences to enable legacy behaviour

legacy.refractory_timing = False

Whether to use the semantics for checking the refractoriness condition that were in place up until (including) version 2.1.2. In that implementation, refractory periods that were multiples of dt could lead to a varying number of refractory timesteps due to the nature of floating point comparisons). This preference is only provided for exact reproducibility of previously obtained results, new simulations should use the improved mechanism which uses a more robust mechanism to convert refractoriness into timesteps. Defaults to False.

logging

Logging system preferences

logging.console_log_level = 'INFO'

What log level to use for the log written to the console.

Has to be one of CRITICAL, ERROR, WARNING, INFO, DEBUG or DIAGNOSTIC.

logging.delete_log_on_exit = True

Whether to delete the log and script file on exit.

If set to True (the default), log files (and the copy of the main script) will be deleted after the brian process has exited, unless an uncaught exception occurred. If set to False, all log files will be kept.

logging.display_brian_error_message = True

Whether to display a text for uncaught errors, mentioning the location of the log file, the mailing list and the github issues.

Defaults to True.

logging.file_log = True

Whether to log to a file or not.

If set to True (the default), logging information will be written to a file. The log level can be set via the logging.file_log_level preference.

logging.file_log_level = 'DEBUG'

What log level to use for the log written to the log file.

In case file logging is activated (see logging.file_log), which log level should be used for logging. Has to be one of CRITICAL, ERROR, WARNING, INFO, DEBUG or DIAGNOSTIC.

logging.file_log_max_size = 10000000

The maximum size for the debug log before it will be rotated.

If set to any value > 0, the debug log will be rotated once this size is reached. Rotating the log means that the old debug log will be moved into a file in the same directory but with suffix ".1" and the a new log file will be created with the same pathname as the original file. Only one backup is kept; if a file with suffix ".1" already exists when rotating, it will be overwritten. If set to 0, no log rotation will be applied. The default setting rotates the log file after 10MB.

logging.save_script = True

Whether to save a copy of the script that is run.

If set to True (the default), a copy of the currently run script is saved to a temporary location. It is deleted after a successful run (unless logging.delete_log_on_exit is False) but is kept after an uncaught exception occured. This can be helpful for debugging, in particular when several simulations are running in parallel.

logging.std_redirection = True

Whether or not to redirect stdout/stderr to null at certain places.

This silences a lot of annoying compiler output, but will also hide error messages making it harder to debug problems. You can always temporarily switch it off when debugging. If logging.std_redirection_to_file is set to True as well, then the output is saved to a file and if an error occurs the name of this file will be printed.

logging.std_redirection_to_file = True

Whether to redirect stdout/stderr to a file.

If both logging.std_redirection and this preference are set to True, all standard output/error (most importantly output from the compiler) will be stored in files and if an error occurs the name of this file will be printed. If logging.std_redirection is True and this preference is False, then all standard output/error will be completely suppressed, i.e. neither be displayed nor stored in a file.

The value of this preference is ignore if logging.std_redirection is set to False.