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ggventurini / python-deltasigma

A port of the MATLAB Delta Sigma Toolbox based on free software and very little sleep
python-deltasigma.io
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/usr/bin/ld: cannot find -lcblas #61

Open snelgar opened 8 years ago

snelgar commented 8 years ago

deltasigma is working nicely for me on a Mac 10.9 setup, but not on 10.11 and not on Ubuntu. The problems are all to do with cblas. On Mac OS 10.11 and up /usr/include is "restricted", and opencblas puts things in a weird place (/opt/local/include/cblas.h). On my linux 4.5.3-x86_64 I have /usr/include/cblas.h, and instead get the message in the title when I "import deltasigma" Any help appreciated; your python version of deltasigma is much more useful than the Matlab one.

itdaniher commented 8 years ago

HI @snelgar - can you include what version you're using of deltasigma and the minimum commands to trigger the error on Linux? I'll take a look.

snelgar commented 8 years ago

Hi Ian: Just importing is good enough to trigger the problem:

$ python3 Python 3.5.2 (default, Sep 10 2016, 08:21:44) [GCC 5.4.0 20160609] on linux Type "help", "copyright", "credits" or "license" for more information.

import deltasigma /usr/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status /usr/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status

and here’s the version number

deltasigma.version ‘0.2.2'

I installed via “pip3 install deltasigma”, if that’s relevant.

thanks
    martin snelgrove

On Sep 30, 2016, at 10:32 PM, Ian Daniher notifications@github.com wrote:

HI @snelgar https://github.com/snelgar - can you include what version you're using of deltasigma and the minimum commands to trigger the error on Linux? I'll take a look.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ggventurini/python-deltasigma/issues/61#issuecomment-250887427, or mute the thread https://github.com/notifications/unsubscribe-auth/AORFaUuAfq4mGvHcmhg-MobBJpdnw_g6ks5qvcZXgaJpZM4KLo1B.

snelgar commented 8 years ago

Hi again Ian:

FYI, on Mac OS 10.11 (“El Capitan”), which is the rootless thing that doesn’t allow installations into /usr/include, the bad news looks like this:

$ python3 Python 3.5.2 (default, Sep 28 2016, 18:08:09) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.38)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import deltasigma /var/folders/l3/lf01jzh90mg0f5dc_mdd4nl00000gp/T/tmprk8tjx8r/source.c:1:10: fatal error: 'cblas.h' file not found

include 

     ^

1 error generated. /var/folders/l3/lf01jzh90mg0f5dc_mdd4nl00000gp/T/tmprk8tjx8r/source.c:1:10: fatal error: 'cblas.h' file not found

include 

     ^

1 error generated. /usr/local/lib/python3.5/site-packages/deltasigma/_config.py:54: UserWarning: Cannot find the path for 'cblas.h'. You may set it using the environment variable BLAS_H. NOTE: You need to pass the path to the directories were the header files are, not the path to the files. warn("Cannot find the path for 'cblas.h'. You may set it using the environment variable " deltasigma.version '0.2.2'

and a lot of that is coming from “get_info", per

$ python3 Python 3.5.2 (default, Sep 28 2016, 18:08:09) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.38)] on darwin Type "help", "copyright", "credits" or "license" for more information.

from numpy.distutils.system_info import get_info get_info("blas") /var/folders/l3/lf01jzh90mg0f5dc_mdd4nl00000gp/T/tmp7v2u8_xn/source.c:1:10: fatal error: 'cblas.h' file not found

include 

     ^

1 error generated. /var/folders/l3/lf01jzh90mg0f5dc_mdd4nl00000gp/T/tmp7v2u8_xn/source.c:1:10: fatal error: 'cblas.h' file not found

include 

     ^

1 error generated. {'library_dirs': ['/usr/lib'], 'libraries': ['blas', 'blas']}

I muddled through the code in _config and found it guessing that /usr/include might work. Setting BLAS_H didn’t do much for me either.

thanks
    martin s.

On Sep 30, 2016, at 10:32 PM, Ian Daniher notifications@github.com wrote:

HI @snelgar https://github.com/snelgar - can you include what version you're using of deltasigma and the minimum commands to trigger the error on Linux? I'll take a look.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ggventurini/python-deltasigma/issues/61#issuecomment-250887427, or mute the thread https://github.com/notifications/unsubscribe-auth/AORFaUuAfq4mGvHcmhg-MobBJpdnw_g6ks5qvcZXgaJpZM4KLo1B.

3mdj23 commented 8 years ago

Hi Ian,

Jut following up on the Linux (Linux d5d56fb00c3f 4.4.22-moby #1 SMP Sun Sep 25 22:54:41 UTC 2016 x86_64 GNU/Linux) import issue that Martin mentioned previously.

I installed deltasigma using pip. Then, I installed the libblas-dev package from Debian jessie and that solved the cblas.h not found issue. This then gave me the error:

root@d5d56fb00c3f:/work/software/algo# python
Python 2.7.11 (default, Apr 21 2016, 17:11:33)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import deltasigma as ds
/usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
/usr/bin/ld: cannot find -lcblas
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lcblas
collect2: error: ld returned 1 exit status
>>>

The blas library exists, but not cblas:

root@d5d56fb00c3f:/work/software/algo# ls /usr/lib/libcblas*
ls: cannot access /usr/lib/libcblas*: No such file or directory
root@d5d56fb00c3f:/work/software/algo# ls /usr/lib/libblas*
/usr/lib/libblas.a  /usr/lib/libblas.so  /usr/lib/libblas.so.3  /usr/lib/libblas.so.3gf

/usr/lib/libblas:
libblas.a  libblas.so  libblas.so.3  libblas.so.3.0
root@d5d56fb00c3f:/work/software/algo#

As a work-around I symlinked libblas.so to libcblas.so:

#> apt-get update
#> pip install deltasigma
#> apt-get install libblas-dev
#> cd /usr/lib
#> ln -s libblas.so libcblas.so

root@bf4be19467c9:/usr/lib# python
Python 2.7.11 (default, Apr 21 2016, 17:11:33)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import deltasigma as ds
>>>

Not sure if it's relevant but apparently there have been a few name changes in the atlas and/or blas libraries recently (see: https://www.centos.org/forums/viewtopic.php?t=48543).

Let me know if you need more information.

Kindest regards, Matthew

snelgar commented 6 years ago

I have this working on Sierra now, and the fix was reproduced by a colleague. Basically I gave up on trying to get numpy/Cython to look in the places officially allowed by Mac OS and overrode its "System Integrity Protection" -- Mac limitations on where anybody (even with sudo) can put files. Step 1 is to reboot the Mac into safe mode, with command-R, fire up a terminal and do

csrutil disable

That's dangerous stuff, so when you're done go back and do a csrutil enable. Once SIP-free, you set up symbolic links that make copies of the relevant files appear where Cython expects. In my case the originals were installed using homebrew, so

brew install openblas ln -s /usr/local/Cellar/openblas/0.2.20_2/include/openblas_config.h /usr/local/include ln -s /usr/local/Cellar/openblas/0.2.20_2/include/cblas.h /usr/local/include

A more tasteful fix would be welcome.

ma-laforge commented 3 years ago

Hi @snelgar,

My own (Julia) port of the ΔΣ library

Just wanted to mention there is a Julia version of Richard's toolbox. I've got a good portion of it ported, and I can probably port other portions if you give me minimum working examples to work from. -->https://github.com/ma-laforge/RSDeltaSigmaPort.jl

About Julia

If you don't already know, Julia is the MIT-seeded language that takes what Matlab gave us to a whole new level:

Known issues

At the moment, the biggest issue appears to be is in the conversion from ABCD -> zpk||rational.

(Same goes to the others on this thread :))