[fbsd62/amd64] scipy 0.5.1 fails to build - BSD

This is a discussion on [fbsd62/amd64] scipy 0.5.1 fails to build - BSD ; Hi all, I'm trying to build scipy 0.5.1 on freebsd/amd64 box. atlas take more than 12 hours to build (!) but successful. Building scipy fails with the following message: ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/python2.4/site-packages/numpy/core/numeric.p y - found ===> py24-scipy-0.5.1 ...

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Thread: [fbsd62/amd64] scipy 0.5.1 fails to build

  1. [fbsd62/amd64] scipy 0.5.1 fails to build


    Hi all,

    I'm trying to build scipy 0.5.1 on freebsd/amd64 box.

    atlas take more than 12 hours to build (!) but successful.

    Building scipy fails with the following message:

    ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/python2.4/site-packages/numpy/core/numeric.p
    y - found
    ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/libdjbfft.a - found
    ===> py24-scipy-0.5.1 depends on file: /usr/local/bin/python - found
    ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/python2.4/site-packages/wx-2.6-gtk2-ansi/wx/
    __init__.py - found
    ===> py24-scipy-0.5.1 depends on shared library: fftw.2 - found
    ===> py24-scipy-0.5.1 depends on shared library: atlas.1 - found
    ??? Makefile says that scipy needs atlas static lib
    So why this message ?

    ===> Configuring for py24-scipy-0.5.1
    Traceback (most recent call last):
    File "setup.py", line 55, in ?
    setup_package()
    File "setup.py", line 28, in setup_package
    from numpy.distutils.core import setup
    File "/usr/local/lib/python2.4/site-packages/numpy/__init__.py", line 40, in ?
    import linalg
    File "/usr/local/lib/python2.4/site-packages/numpy/linalg/__init__.py", line 4, in ?
    from linalg import *
    File "/usr/local/lib/python2.4/site-packages/numpy/linalg/linalg.py", line 25, in ?
    from numpy.linalg import lapack_lite
    ImportError: /usr/local/lib/libalapack_r.so.1: Undefined symbol "csqrt"
    *** Error code 1

    Stop in /usr/ports/science/py-scipy.

    What's going on with csqrt ???

    Any idea ?

    PS : scipy ports builds fine on my freebsd i386 box,
    but does not need gcc 4.2 and so on...


    Thanks in advance.


    Cheers,

    --
    Fred.

  2. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    fred wrote:
    >
    > Hi all,
    >
    > I'm trying to build scipy 0.5.1 on freebsd/amd64 box.
    >
    > atlas take more than 12 hours to build (!) but successful.
    >
    > Building scipy fails with the following message:
    >
    > ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/python2.4/site-packages/numpy/core/numeric.p
    > y - found
    > ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/libdjbfft.a - found
    > ===> py24-scipy-0.5.1 depends on file: /usr/local/bin/python - found
    > ===> py24-scipy-0.5.1 depends on file: /usr/local/lib/python2.4/site-packages/wx-2.6-gtk2-ansi/wx/
    > __init__.py - found
    > ===> py24-scipy-0.5.1 depends on shared library: fftw.2 - found
    > ===> py24-scipy-0.5.1 depends on shared library: atlas.1 - found
    > ??? Makefile says that scipy needs atlas static lib
    > So why this message ?


    Been there done that :-(

    Note the following in the Makefile:

    OPTIONS= ATLAS "Use optimized blas library" OFF

    --

    Michel TALON


  3. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    talon@lpthe.jussieu.fr (Michel Talon) a écrit :

    > Note the following in the Makefile:
    >
    > OPTIONS= ATLAS "Use optimized blas library" OFF

    And ?

    In fact, I have atlas-3.6.0,1 on my i386, which works fine.
    And atlas-3.6.0_1,1 on my amd64, which fails.

    So I want to try atlas-3.6.0,1 on my amd64.

    But how can I get this old port ?


    Cheers,

    --
    Fred.

  4. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    Begin <8764bgbm3i.fsf@free.fr>
    On 2007-01-09, fred wrote:
    > In fact, I have atlas-3.6.0,1 on my i386, which works fine.
    > And atlas-3.6.0_1,1 on my amd64, which fails.
    >
    > So I want to try atlas-3.6.0,1 on my amd64.


    The difference between atlas-3.6.0,1 and atlas-3.6.0_1,1, that is,
    the _1 bit, is a change local to the port. From a quick look, the
    most significant changes were more specific compiler support (in the
    Makefile) and some fiddling with compiler flags.

    I expect you'll be better off building using the latest version, only
    this time pay close attention to building with the right CPU support. It
    appears to have quite a few options there, and your settings may easily
    be wrong -- in fact, it tells you to correct it if its autodetection fails.


    > But how can I get this old port ?


    Pull it out of CVS.


    --
    j p d (at) d s b (dot) t u d e l f t (dot) n l .
    This message was originally posted on Usenet in plain text.
    Any other representation, additions, or changes do not have my
    consent and may be a violation of international copyright law.

  5. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    fred wrote:
    > talon@lpthe.jussieu.fr (Michel Talon) a écrit :
    >
    > > Note the following in the Makefile:
    > >
    > > OPTIONS= ATLAS "Use optimized blas library" OFF

    > And ?
    >
    > In fact, I have atlas-3.6.0,1 on my i386, which works fine.
    > And atlas-3.6.0_1,1 on my amd64, which fails.
    >
    > So I want to try atlas-3.6.0,1 on my amd64.
    >
    > But how can I get this old port ?
    >

    http://www.freebsd.org/cgi/cvsweb.cg...=RELEASE_6_2_0

    Note the:
    ..if !defined(WITH_STATICLIB)
    @${ECHO_MSG} "You can build static libraries with"
    @${ECHO_MSG} "make -DWITH_STATICLIB"
    @${ECHO_MSG}
    ..endif

    >
    > Cheers,
    >


    --

    Michel TALON


  6. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    fred wrote:
    > talon@lpthe.jussieu.fr (Michel Talon) a écrit :
    >
    >> Note the following in the Makefile:
    >>
    >> OPTIONS= ATLAS "Use optimized blas library" OFF

    > And ?
    >
    > In fact, I have atlas-3.6.0,1 on my i386, which works fine.
    > And atlas-3.6.0_1,1 on my amd64, which fails.
    >
    > So I want to try atlas-3.6.0,1 on my amd64.
    >
    > But how can I get this old port ?


    /usr/ports/sysutils/portdowngrade can help.

    --
    Warren Block * Rapid City, South Dakota * USA

  7. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    Warren Block a écrit :

    > fred wrote:


    >> But how can I get this old port ?

    >
    > /usr/ports/sysutils/portdowngrade can help.

    Thanks !

    --
    Fred.

  8. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    talon@lpthe.jussieu.fr (Michel Talon) a écrit :

    > Note the:
    > .if !defined(WITH_STATICLIB)
    > @${ECHO_MSG} "You can build static libraries with"
    > @${ECHO_MSG} "make -DWITH_STATICLIB"
    > @${ECHO_MSG}
    > .endif

    Ok, I did not understand I could build scipy with atlas _or_ blas/lapack
    libs. Sorry.

    So... forget atlas, ok.

    I built lapack & blas, which need gcc4.2.

    scipy needs numpy so I tried to build numpy.
    But numpy fails to build :-(

    last lines:
    creating build/temp.freebsd-6.2-PRERELEASE-amd64-2.4/numpy/linalg
    compile options: '-DATLAS_WITHOUT_LAPACK -DNO_ATLAS_INFO=2 -Inumpy/core/include -Ibuild/src.freebsd-
    6.2-PRERELEASE-amd64-2.4/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/local/include/pytho
    n2.4 -c'
    cc: numpy/linalg/lapack_litemodule.c
    /usr/bin/f77 -g -Wall -shared build/temp.freebsd-6.2-PRERELEASE-amd64-2.4/numpy/linalg/lapack_litemo
    dule.o -L/usr/local/lib -L/usr/lib -llapack -lblas -lg2c -lm -lpthread -llapack -lg2c -o build/lib.f
    reebsd-6.2-PRERELEASE-amd64-2.4/numpy/linalg/lapack_lite.so
    /usr/bin/ld: /usr/local/lib/liblapack.a(zheevd.o): relocation R_X86_64_32 can not be used when makin
    g a shared object; recompile with -fPIC
    /usr/local/lib/liblapack.a: could not read symbols: Bad value
    /usr/bin/ld: /usr/local/lib/liblapack.a(zheevd.o): relocation R_X86_64_32 can not be used when makin
    g a shared object; recompile with -fPIC
    /usr/local/lib/liblapack.a: could not read symbols: Bad value
    error: Command "/usr/bin/f77 -g -Wall -shared build/temp.freebsd-6.2-PRERELEASE-amd64-2.4/numpy/lina
    lg/lapack_litemodule.o -L/usr/local/lib -L/usr/lib -llapack -lblas -lg2c -lm -lpthread -llapack -lg2
    c -o build/lib.freebsd-6.2-PRERELEASE-amd64-2.4/numpy/linalg/lapack_lite.so" failed with exit status
    1
    *** Error code 1

    Stop in /usr/ports/math/py-numpy.

    I put the full log (778 lines) here: http://fredantispam.free.fr/numpy.log.

    Thanks in advance for any help.

    PS : after installed blas, numpy fails to detect it installed !
    I had to comment the few lines regarding blas detection in the Makefile.

    Cheers,


    --
    Fred.

  9. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    In article <874pr1ovd9.fsf@free.fr>, fred wrote:
    >
    >
    >
    >Hi all,
    >
    >I'm trying to build scipy 0.5.1 on freebsd/amd64 box.
    >
    >atlas take more than 12 hours to build (!) but successful.
    >
    >Building scipy fails with the following message:
    >
    >===> py24-scipy-0.5.1 depends on file:
    >/usr/local/lib/python2.4/site-packages/numpy/core/numeric.p
    >y - found
    >===> py24-scipy-0.5.1 depends on file: /usr/local/lib/libdjbfft.a - found
    >===> py24-scipy-0.5.1 depends on file: /usr/local/bin/python - found
    >===> py24-scipy-0.5.1 depends on file:
    >/usr/local/lib/python2.4/site-packages/wx-2.6-gtk2-ansi/wx/
    >__init__.py - found
    >===> py24-scipy-0.5.1 depends on shared library: fftw.2 - found
    >===> py24-scipy-0.5.1 depends on shared library: atlas.1 - found
    >??? Makefile says that scipy needs atlas static lib


    Yes. Did you build atlas with "-DWITH_STATICLIB"?

    --
    Conrad J. Sabatier
    "In Unix veritas"

  10. Re: [fbsd62/amd64] scipy 0.5.1 fails to build

    conrads@cox.net (Conrad J. Sabatier) a écrit :

    > Yes. Did you build atlas with "-DWITH_STATICLIB"?

    Sure.

    --
    Fred.

  11. Re: [fbsd62/amd64] scipy 0.5.1 fails to build [fixed]

    So...

    I rebuilt all, after updated my ports tree: atlas, then numpy.

    scipy needs libblas.1 & liblapack.3.
    But blas & lapack have installed libblas.2 & liblapack.4,

    I have modified Makefile, and now, scipy builds successfully.


    Cheers,

    --
    Fred.

  12. [fbsd62/amd64/gcc4.2] scipy 0.5.1 fails to run...


    Ok, so I have built successfully atlas/scipy or lapack/blas/scipy.

    But for these two cases, scipy fails to run, because it does not find
    "csqrt" function in alapack or lapack libs :-(

    What am/was I doing wrong ??

    PS : I built scipy with the new ports, which need gcc 4.2, on my amd64
    box. Previous ports don't, and scipy works fine, on my i386.

    Thanks in advance for any help.


    Cheers,

    --
    Fred.

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