warnings after install brian 2
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Sandro Perrone
May 5, 2015, 5:14:32 AM5/5/15
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Hi,
I had to install again spyder, anaconda, and brian2 on my mac.
Unfortunately, runnig a brian code I got the following three warnings (see below), but I don't know what exactly they mean.
I installed cython 0.22, but it continue to appear, probably it is a warning related with dependencies.
Please could you help me to eliminate these warnings making a faster code runnig?
Many thanks in advance!
Sandro
WARNING brian2.codegen.runtime.weave_rt.weave_rt.failed_compile_test: Cannot use weave, a test compilation failed: error: Command "clang++ -fno-strict-aliasing -fno-common -dynamic -I/usr/local/include -I/usr/local/opt/sqlite/include -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/scipy/weave -I/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/scipy/weave/scxx -I/Applications/Spyder-Py2.app/Contents/Resources/lib/python2.7/numpy/core/include -I/Applications/Spyder-Py2.app/Contents/Resources/include/python2.7 -c /Users/sandro/.cache/scipy/python27_compiled/sc_302644cc5257b9feebbfde0f5856848e51.cpp -o /var/folders/c1/7pmwl23d1fg60ktvhd75vd840000gn/T/scipy-sandro-iP0pDP/python27_intermediate/compiler_10a3badd5737329477237726cc2e9ec1/Users/sandro/.cache/scipy/python27_compiled/sc_302644cc5257b9feebbfde0f5856848e51.o -w -O3" failed with exit status 1 (CompileError)
WARNING brian2.codegen.runtime.cython_rt.cython_rt.failed_compile_test: Cannot use Cython, a test compilation failed: Cython is not available (ImportError)
WARNING brian2.devices.device.codegen_fallback: Cannot use compiled code, falling back to the numpy code generation target. Note that this will likely be slower than using compiled code.
Marcel Stimberg
May 6, 2015, 5:55:57 AM5/6/15
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Hi Sandro,
as described here: http://brian2.readthedocs.org/en/2.0b3/user/computation.html Brian tries to use first weave, then Cython if no code generation target is specified. Apparently in your case, weave compilation does not work. Our testing on Mac OS is very limited, it might possibly work if you install gcc (if you don't have it already) and set the compiler preference accordingly (http://brian2.readthedocs.org/en/2.0b3/reference/brian2.codegen.html#module-brian2.codegen.cpp_prefs). Cython does not seem to work either, but there Brian can simply not find the Cython package, so this is probably just a path/installation issue.
Note that, as the warning says, simulations will still work but they will be somewhat slower. Set the code generation target explicitly (e.g. "prefs.codegen.target = 'numpy'") to avoid the warnings.
Best,
Marcel
as described here: http://brian2.readthedocs.org/en/2.0b3/user/computation.html Brian tries to use first weave, then Cython if no code generation target is specified. Apparently in your case, weave compilation does not work. Our testing on Mac OS is very limited, it might possibly work if you install gcc (if you don't have it already) and set the compiler preference accordingly (http://brian2.readthedocs.org/en/2.0b3/reference/brian2.codegen.html#module-brian2.codegen.cpp_prefs). Cython does not seem to work either, but there Brian can simply not find the Cython package, so this is probably just a path/installation issue.
Note that, as the warning says, simulations will still work but they will be somewhat slower. Set the code generation target explicitly (e.g. "prefs.codegen.target = 'numpy'") to avoid the warnings.
Best,
Marcel
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Sandro Perrone
May 6, 2015, 7:10:21 AM5/6/15
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Thank you Marcel,
Probably I would set some paths for cython, however with the trick "prefs.codegen.target = 'numpy' I could avoid warnings appear.
Kind regards,
Sandro
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Dan Goodman
May 7, 2015, 8:17:43 AM5/7/15
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As Marcel said, we don't do much testing on Mac, but I know that some
people have been able to get this working. Does anyone on the list have
any other suggestions? One possibility would be to install gcc rather
than using the built in clang compiler (which is mostly but not fully
compatible with gcc it seems).
Dan
On 06/05/2015 12:10, Sandro Perrone wrote:
> Thank you Marcel,
>
> Probably I would set some paths for cython, however with the trick
> "prefs.codegen.target = 'numpy' I could avoid warnings appear.
>
> Kind regards,
>
> Sandro
>
> 2015-05-06 11:55 GMT+02:00 Marcel Stimberg <marcel....@inserm.fr
> <mailto:marcel....@inserm.fr>>:
>> <mailto:brian-developm...@googlegroups.com>.
> www.sandroperrone.net <http://www.sandroperrone.net>
> cel. +39-331.61.87.867
people have been able to get this working. Does anyone on the list have
any other suggestions? One possibility would be to install gcc rather
than using the built in clang compiler (which is mostly but not fully
compatible with gcc it seems).
Dan
On 06/05/2015 12:10, Sandro Perrone wrote:
> Thank you Marcel,
>
> Probably I would set some paths for cython, however with the trick
> "prefs.codegen.target = 'numpy' I could avoid warnings appear.
>
> Kind regards,
>
> Sandro
>
> 2015-05-06 11:55 GMT+02:00 Marcel Stimberg <marcel....@inserm.fr
>> For more options, visit https://groups.google.com/d/optout.
>
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