Known issues¶

In addition to the issues noted below, you can refer to our bug tracker on GitHub.

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.

Parallel Brian simulations with C++ standalone¶

Simulations using the C++ standalone device will create code and store results in a dedicated directory (output, by default). If you run multiple simulations in parallel, you have to take care that these simulations do not use the same directory – otherwise, everything from compilation errors to incorrect results can happen. Either chose a different directory name for each simulation and provide it as the directory argument to the set_device or build call, or use directory=None which will use a randomly chosen unique temporary directory (in /tmp on Unix-based systems) for each simulation. If you need to know the directory name, you can access it after the simulation run via device.project_dir.

Slow C++ 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 simulations 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.

CMD windows open when running Brian on Windows with the Spyder 3 IDE¶

This is due to the interaction with the integrated ipython terminal. Either change the run configuration to “Execute in an external system terminal” or patch the internal Python function used to spawn processes as described in github issue #1140.