Problem compiling bob.measure

[Victor Costa]

Hello

I'm trying to compile a bob.bio.spear system using the zc.buildout method on Ubuntu 14.04 for use in some experiments. When the build reaches bob.measure, I get the error:

error: /tmp/easy_install-bIMO3W/bob.measure-2.3.0/.eggs/bob.math-2.1.0-py2.7-linux-x86_64.egg/bob/math/libbob_math.so: undefined symbol: dggsvd3_

An error occurred when trying to install /tmp/tmpsVbOJqget_dist/bob.measure-2.3.0.zip. Look above this message for any errors that were output by easy_install.

From searching around, it seems dggsvd3_ is related to LAPACK. The version I have is the one from the default Ubuntu repository.

Attached is the whole output of ./bin/buildout. Any help is appreciated

Thanks

Victor

[Manuel Günther]

Dear Victor,

this is the same issue that was reported here: https://groups.google.com/forum/#!topic/bob-devel/bRKjZTRZ8Rc

bob.math seems to be broken at the moment. I would suggest to downgrade bob.math to the previous version, simply remove `bob.math-2.1.0-py2.7-linux-x86_64.egg` from your eggs directory, and overwrite "bob.math" with  "bob.math < 2.1" inside of your `requirements.txt` or inside the eggs section of `buildout.cfg`.

Manuel

[Amir Mohammadi]

Hi Victor,

Have you gone through our binary installation of bob? I.e. Installing bob with conda first.

Which installation instructions did you follow? 

Bob.math is not broken btw. You have to follow our installation instructions.

Thanks,
Amir

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[Victor Costa]

Hello,

The conda installation works, but I would prefer not to use conda if possible.

I'm using the instructions on this page. From what I understood of the install page, this method is independent from the conda install, is this not the case?

2017-03-08 18:59 GMT-03:00 Amir Mohammadi <183....@gmail.com>:

Hi Victor,

Have you gone through our binary installation of bob? I.e. Installing bob with conda first.

Which installation instructions did you follow? 

Bob.math is not broken btw. You have to follow our installation instructions.

Thanks,
Amir

On Wed, Mar 8, 2017, 10:29 PM Victor Costa <vic...@gmail.com> wrote:

Hello

I'm trying to compile a bob.bio.spear system using the zc.buildout method on Ubuntu 14.04 for use in some experiments. When the build reaches bob.measure, I get the error:

error: /tmp/easy_install-bIMO3W/bob.measure-2.3.0/.eggs/bob.math-2.1.0-py2.7-linux-x86_64.egg/bob/math/libbob_math.so: undefined symbol: dggsvd3_

An error occurred when trying to install /tmp/tmpsVbOJqget_dist/bob.measure-2.3.0.zip. Look above this message for any errors that were output by easy_install.

From searching around, it seems dggsvd3_ is related to LAPACK. The version I have is the one from the default Ubuntu repository.

Attached is the whole output of ./bin/buildout. Any help is appreciated

Thanks

Victor

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Victor P da Costa

M.Sc. Student - Electrical Engineering

SMT - Sinais, Multimídia e Telecomunicações

PEE - COPPE - UFRJ - Brazil

[André Anjos]

This is reported here: https://gitlab.idiap.ch/bob/bob.math/issues/11

TL;DR make sure you have openblas >= 0.2.16 (or LAPACK 3.6+, if no optimization required).

André

Dr. André Anjos
Idiap Research Institute
Centre du Parc - rue Marconi 19
CH-1920 Martigny, Suisse
Phone: +41 27 721 7763
Fax: +41 27 721 7712
http://andreanjos.org

[QA Collective]

FYI - This depdendency is satisfied by openblas, not lapack.

I just ran a build on Python3.5 Ubuntu 16.10 (Xenial) and got this exact same error.  I had lapack 3.6.0 installed but not openblas.  After installing libopenblas-base libopenblas-dev (0.2.18), the error went away and build completed successfully.

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Victor P da Costa

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SMT - Sinais, Multimídia e Telecomunicações

PEE - COPPE - UFRJ - Brazil

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[Amir Mohammadi]

Hi Viktor,

We develop (compile from source) bob in a conda environment: https://pythonhosted.org/bob/install.html#setting-up-a-development-environment-using-conda

Also, we compile and release binaries of bob on a centos 5 docker image using conda to make sure it works in ALL linux machines.

We really have no reason to support or test any Linux distribution besides conda anymore.

This does not mean that bob does not work on say Ubuntu 14.04 anymore but getting it to work falls in your responsibility.

So what you can do if you really want to install bob in Ubuntu 14.04 is to install the dependencies first using Ubuntu's package manager: https://pythonhosted.org/bob/install.html#dependencies

Then, if some dependencies do not satisfy our requirements like openblas here. You need to compile that from source and point its location to bob: https://pythonhosted.org/bob/temp/bob.extension/doc/buildout.html#hooking-in-privately-compiled-externals so it can pick that up instead.

All in all, I really am interested to know why you do not want to use conda.

Best,

Amir

On Thu, Mar 9, 2017 at 12:15 AM Victor Costa <vic...@gmail.com> wrote:

Hello,

The conda installation works, but I would prefer not to use conda if possible.

I'm using the instructions on this page. From what I understood of the install page, this method is independent from the conda install, is this not the case?

2017-03-08 18:59 GMT-03:00 Amir Mohammadi <183....@gmail.com>:

Hi Victor,

Have you gone through our binary installation of bob? I.e. Installing bob with conda first.

Which installation instructions did you follow? 

Bob.math is not broken btw. You have to follow our installation instructions.

Thanks,
Amir

On Wed, Mar 8, 2017, 10:29 PM Victor Costa <vic...@gmail.com> wrote:

Hello

I'm trying to compile a bob.bio.spear system using the zc.buildout method on Ubuntu 14.04 for use in some experiments. When the build reaches bob.measure, I get the error:

error: /tmp/easy_install-bIMO3W/bob.measure-2.3.0/.eggs/bob.math-2.1.0-py2.7-linux-x86_64.egg/bob/math/libbob_math.so: undefined symbol: dggsvd3_

An error occurred when trying to install /tmp/tmpsVbOJqget_dist/bob.measure-2.3.0.zip. Look above this message for any errors that were output by easy_install.

From searching around, it seems dggsvd3_ is related to LAPACK. The version I have is the one from the default Ubuntu repository.

Attached is the whole output of ./bin/buildout. Any help is appreciated

Thanks

Victor

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Victor P da Costa

M.Sc. Student - Electrical Engineering

SMT - Sinais, Multimídia e Telecomunicações

PEE - COPPE - UFRJ - Brazil

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