Known issues¶
In addition to the issues noted below, you can refer to our bug tracker on GitHub.
List of known issues
- Cannot find msvcr90d.dll
- “AttributeError: MSVCCompiler instance has no attribute ‘compiler_cxx’”
- “Missing compiler_cxx fix for MSVCCompiler”
- Problems with numerical integration
- Jupyter notebooks and C++ standalone mode progress reporting
- Parallel Brian simulations with the
weave
code generation target - Slow standalone simulations
- Cython fails with compilation error on OS X:
error: use of undeclared identifier 'isinf'
Cannot find msvcr90d.dll¶
If you see this message coming up, find the file
PythonDir\Lib\site-packages\numpy\distutils\mingw32ccompiler.py
and modify the line msvcr_dbg_success = build_msvcr_library(debug=True)
to read
msvcr_dbg_success = False
(you can comment out the existing line and add the new line
immediately after).
“AttributeError: MSVCCompiler instance has no attribute ‘compiler_cxx’”¶
This is caused by a bug in some versions of numpy on Windows. The easiest solution is to update to the latest version of numpy.
If that isn’t possible, a hacky solution is to modify the numpy code directly to fix the
problem. The following change may work.
Modify line 388 of numpy/distutils/ccompiler.py
from elif not self.compiler_cxx:
to
elif not hasattr(self, 'compiler_cxx') or not self.compiler_cxx:
. If the line
number is different, it should be nearby. Search for elif not self.compiler_cxx
in
that file.
“Missing compiler_cxx fix for MSVCCompiler”¶
If you keep seeing this message, do not worry. It’s not possible for us to hide it, but doesn’t indicate any problems.
Problems with numerical integration¶
In some cases, the automatic choice of numerical integration method will not be appropriate, because of a choice of parameters that couldn’t be determined in advance. In this case, typically you will get nan (not a number) values in the results, or large oscillations. In this case, Brian will generate a warning to let you know, but will not raise an error.
Jupyter notebooks and C++ standalone mode progress reporting¶
When you run simulations in C++ standalone mode and enable progress reporting
(e.g. by using report='text'
as a keyword argument), the progress will not
be displayed in the jupyter notebook. If you started the notebook from a
terminal, you will find the output there. Unfortunately, this is a tricky
problem to solve at the moment, due to the details of how the jupyter notebook
handles output.
Parallel Brian simulations with the weave
code generation target¶
When using the weave
code generation target (the default runtime target on
Python 2.x, see Runtime code generation for details), you should avoid running multiple
Brian simulations in parallel. The weave
package caches compiled files,
but this cache is not prepared for multiple concurrent updates. If two Python
scripts (or two processes started from the same Python script, e.g. via the
multiprocessing
package) try to store compilation results at the same time,
weave
will crash with an error message. The numpy
and cython
targets
are not affected by this problem.
Slow standalone simulations¶
Some versions of the GNU standard library (in particular those used by recent
Ubuntu versions) have a bug that can dramatically slow down simulations in
C++ standalone mode on modern hardware (see #803). As a workaround, Brian will
set an environment variable LD_BIND_NOW
during the execution of standalone
stimulations which changes the way the library is linked so that it does not
suffer from this problem. If this environment variable leads to unwanted
behaviour on your machine, change the
prefs.devices.cpp_standalone.run_environment_variables
preference.
Cython fails with compilation error on OS X: error: use of undeclared identifier 'isinf'
¶
Try setting the environment variable MACOSX_DEPLOYMENT_TARGET=10.9
.