[SciPy-User] problems building scipy on Yosemite.

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[SciPy-User] problems building scipy on Yosemite.

Andrew Nelson
Dear list,
I've updated to Yosemite (clean install) and am having problems building scipy from source (python setup.py build)

The complete build log is at:

$gfortran --version
GNU Fortran (GCC) 4.2.3
$gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
$echo FFLAGS
-ff2c


Is anyone able to give me any tips as to what I'm doing wrong?

cheers,
Andrew
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Re: problems building scipy on Yosemite.

Matthew Brett
Hi,

On Mon, Nov 10, 2014 at 11:29 PM, Andrew Nelson <[hidden email]> wrote:

> Dear list,
> I've updated to Yosemite (clean install) and am having problems building
> scipy from source (python setup.py build)
>
> The complete build log is at:
> https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2
>
> $gfortran --version
> GNU Fortran (GCC) 4.2.3
> $gcc --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
> Target: x86_64-apple-darwin14.0.0
> Thread model: posix
> $echo FFLAGS
> -ff2c
>
> gfortran was from http://cran.r-project.org/bin/macosx/tools/.
>
> Is anyone able to give me any tips as to what I'm doing wrong?

I think you may have to use clang - see :
http://www.scipy.org/scipylib/building/macosx.html#os-x-10-7-lion-and-10-8-mountain-lion

$ export CC=clang
$ export CXX=clang++
$ export FFLAGS=-ff2c

Does that work?

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Andrew Nelson
It may not have been clear in my original post, I was using clang and clang++.

On 13 November 2014 14:51, Matthew Brett <[hidden email]> wrote:
Hi,

On Mon, Nov 10, 2014 at 11:29 PM, Andrew Nelson <[hidden email]> wrote:
> Dear list,
> I've updated to Yosemite (clean install) and am having problems building
> scipy from source (python setup.py build)
>
> The complete build log is at:
> https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2
>
> $gfortran --version
> GNU Fortran (GCC) 4.2.3
> $gcc --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
> Target: x86_64-apple-darwin14.0.0
> Thread model: posix
> $echo FFLAGS
> -ff2c
>
> gfortran was from http://cran.r-project.org/bin/macosx/tools/.
>
> Is anyone able to give me any tips as to what I'm doing wrong?

I think you may have to use clang - see :
http://www.scipy.org/scipylib/building/macosx.html#os-x-10-7-lion-and-10-8-mountain-lion

$ export CC=clang
$ export CXX=clang++
$ export FFLAGS=-ff2c

Does that work?

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Sturla Molden-3
In reply to this post by Andrew Nelson
Have you tried the latest official "unofficial" gfortran binaries?

https://gcc.gnu.org/wiki/GFortranBinaries#MacOS


Sturla


Andrew Nelson <[hidden email]> wrote:

> Dear list,
> I've updated to Yosemite (clean install) and am having problems building
> scipy from source (python setup.py build)
>
> The complete build log is at:
> <a
> href="https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2">https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2</a>
>
> $gfortran --version
> GNU Fortran (GCC) 4.2.3
> $gcc --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
> Target: x86_64-apple-darwin14.0.0
> Thread model: posix
> $echo FFLAGS
> -ff2c
>
> gfortran was from <a
> href="http://cran.r-project.org/bin/macosx/tools/.">http://cran.r-project.org/bin/macosx/tools/.</a>
>
> Is anyone able to give me any tips as to what I'm doing wrong?
>
> cheers,
> Andrew
>
> --
> _____________________________________
> Dr. Andrew Nelson
>
> _____________________________________
>
> _______________________________________________
> SciPy-User mailing list
> [hidden email]
> <a
> href="http://mail.scipy.org/mailman/listinfo/scipy-user">http://mail.scipy.org/mailman/listinfo/scipy-user</a>

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Re: problems building scipy on Yosemite.

Matthew Brett
On Wed, Nov 12, 2014 at 9:40 PM, Sturla Molden <[hidden email]> wrote:

> Have you tried the latest official "unofficial" gfortran binaries?
>
> https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
>
>
> Sturla
>
>
> Andrew Nelson <[hidden email]> wrote:
>> Dear list,
>> I've updated to Yosemite (clean install) and am having problems building
>> scipy from source (python setup.py build)
>>
>> The complete build log is at:
>> <a
>> href="https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2">https://gist.github.com/andyfaff/5a433d0585e8dae1dfc2</a>
>>
>> $gfortran --version
>> GNU Fortran (GCC) 4.2.3
>> $gcc --version
>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
>> Target: x86_64-apple-darwin14.0.0
>> Thread model: posix
>> $echo FFLAGS
>> -ff2c
>>
>> gfortran was from <a
>> href="http://cran.r-project.org/bin/macosx/tools/.">http://cran.r-project.org/bin/macosx/tools/.</a>
>>
>> Is anyone able to give me any tips as to what I'm doing wrong?
>>
>> cheers,
>> Andrew

Scipy builds OK for me with the cran gfortran, current trunk, numpy
1.9.1 via pip install, and

$ export CC=clang
$ export CXX=clang++
$ export FFLAGS=-ff2c

Can you give more detail about your system?  Numpy, scipy version?

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Sturla Molden-3
Matthew Brett <[hidden email]> wrote:

> Scipy builds OK for me with the cran gfortran, current trunk, numpy
> 1.9.1 via pip install, and
>
> $ export CC=clang
> $ export CXX=clang++
> $ export FFLAGS=-ff2c

The last flag is interesting. It instructs gfortran to use g77 ABI. But
SciPy is supposed to have ABI wrappers for g77 ABI in Accelerate. If it is
still needed it means that the ABI wrappers don't do what they are supposed
to do. The ABI wrapper code in SciPy is so convoluted (and confused?) that
it would not surprise me. If so, we should create ABI wrappers in the same
way as libVecFort.

Sturla

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Re: problems building scipy on Yosemite.

Andrew Nelson
In reply to this post by Matthew Brett

Scipy builds OK for me with the cran gfortran, current trunk, numpy
1.9.1 via pip install, and

$ export CC=clang
$ export CXX=clang++
$ export FFLAGS=-ff2c

Can you give more detail about your system?  Numpy, scipy version?

Cheers,

Matthew


I'm trying to build scipy trunk. numpy was installed into a virtualenv with 'pip install numpy'. Python is :

Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35) 
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin

>>> np.version.full_version

'1.9.1'

>>> np.version.git_revision

'd44b9c61499f8bc5a9fc94286cd52f05e15e003f' 

OSX 10.10.

(development)$ clang --version

Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)

Target: x86_64-apple-darwin14.0.0

Thread model: posix

(development)$ clang++ --version

Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)

Target: x86_64-apple-darwin14.0.0

Thread model: posix



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Re: problems building scipy on Yosemite.

Matthew Brett
On Thu, Nov 13, 2014 at 12:08 AM, Andrew Nelson <[hidden email]> wrote:

>>
>> Scipy builds OK for me with the cran gfortran, current trunk, numpy
>> 1.9.1 via pip install, and
>>
>> $ export CC=clang
>> $ export CXX=clang++
>> $ export FFLAGS=-ff2c
>>
>> Can you give more detail about your system?  Numpy, scipy version?
>>
>> Cheers,
>>
>> Matthew
>>
>
> I'm trying to build scipy trunk. numpy was installed into a virtualenv with
> 'pip install numpy'. Python is :
>
> Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
>
>>>> np.version.full_version
>
> '1.9.1'
>
>>>> np.version.git_revision
>
> 'd44b9c61499f8bc5a9fc94286cd52f05e15e003f'
>
> OSX 10.10.
>
> (development)$ clang --version
>
> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
>
> Target: x86_64-apple-darwin14.0.0
>
> Thread model: posix
>
> (development)$ clang++ --version
>
> Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
>
> Target: x86_64-apple-darwin14.0.0
>
> Thread model: posix

That's strange, I have the exact same configuration.  You used the
same build environment variables too?

Matthew
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Re: problems building scipy on Yosemite.

Andrew Nelson
In reply to this post by Sturla Molden-3
On 13 November 2014 16:40, Sturla Molden <[hidden email]> wrote:
Have you tried the latest official "unofficial" gfortran binaries?

https://gcc.gnu.org/wiki/GFortranBinaries#MacOS


This finally worked for me.  I downloaded the gfortran 4.9.0 from a link on that page that Sturla provided. I had the CC=clang, CXX=clang++ environment variables (no FFLAGS set), and the build worked.

Thanks Sturla for that suggestion.  I can't help feeling that the build process is a little fragile if one has to find the exact gfortran compiler that works for given C compiler/OS combination.

cheers,
Andrew.

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Re: problems building scipy on Yosemite.

Matthew Brett
Hi,

On Thu, Nov 13, 2014 at 2:41 PM, Andrew Nelson <[hidden email]> wrote:

> On 13 November 2014 16:40, Sturla Molden <[hidden email]> wrote:
>>
>> Have you tried the latest official "unofficial" gfortran binaries?
>>
>> https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
>>
>
> This finally worked for me.  I downloaded the gfortran 4.9.0 from a link on
> that page that Sturla provided. I had the CC=clang, CXX=clang++ environment
> variables (no FFLAGS set), and the build worked.
>
> Thanks Sturla for that suggestion.  I can't help feeling that the build
> process is a little fragile if one has to find the exact gfortran compiler
> that works for given C compiler/OS combination.

Did you use the FFLAGS variable set with the cran Fortran compiler?

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Andrew Nelson

Yes.

On 14/11/2014 9:45 AM, "Matthew Brett" <[hidden email]> wrote:
Hi,

On Thu, Nov 13, 2014 at 2:41 PM, Andrew Nelson <[hidden email]> wrote:
> On 13 November 2014 16:40, Sturla Molden <[hidden email]> wrote:
>>
>> Have you tried the latest official "unofficial" gfortran binaries?
>>
>> https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
>>
>
> This finally worked for me.  I downloaded the gfortran 4.9.0 from a link on
> that page that Sturla provided. I had the CC=clang, CXX=clang++ environment
> variables (no FFLAGS set), and the build worked.
>
> Thanks Sturla for that suggestion.  I can't help feeling that the build
> process is a little fragile if one has to find the exact gfortran compiler
> that works for given C compiler/OS combination.

Did you use the FFLAGS variable set with the cran Fortran compiler?

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Sturla Molden-3
In reply to this post by Andrew Nelson
Andrew Nelson <[hidden email]> wrote:

> This finally worked for me.  I downloaded the gfortran 4.9.0 from a link on
> that page that Sturla provided. I had the CC=clang, CXX=clang++ environment
> variables (no FFLAGS set), and the build worked.

Run the test suite a s well.

Personally I use gfortran 4.8.2 from the same source. It seems to work
reliably and I trust the gfortran team to build a binary with the right
configurations.

The purpose of of the ABI wrappers in scipy/_build_utils is to avoid
building with FFLAGS=-ff2c with gfortran on OS X, so Matthew Brett's
suggestion to keep this flag made me worried.

> Thanks Sturla for that suggestion.  I can't help feeling that the build
> process is a little fragile if one has to find the exact gfortran compiler
> that works for given C compiler/OS combination.

Building SciPy on OS X has always been a bit fragile, at least without
Intel's Fortran compiler and MKL.

But downloading an official/unoffcial gfortran binary installer from the
gfortran wiki does not seem to be that fragile. Using an old gfortran build
from the R project seems more on the fragile side, though.

Sturla

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Re: problems building scipy on Yosemite.

Matthew Brett
Hi,

On Thu, Nov 13, 2014 at 8:01 PM, Sturla Molden <[hidden email]> wrote:

> Andrew Nelson <[hidden email]> wrote:
>
>> This finally worked for me.  I downloaded the gfortran 4.9.0 from a link on
>> that page that Sturla provided. I had the CC=clang, CXX=clang++ environment
>> variables (no FFLAGS set), and the build worked.
>
> Run the test suite a s well.
>
> Personally I use gfortran 4.8.2 from the same source. It seems to work
> reliably and I trust the gfortran team to build a binary with the right
> configurations.
>
> The purpose of of the ABI wrappers in scipy/_build_utils is to avoid
> building with FFLAGS=-ff2c with gfortran on OS X, so Matthew Brett's
> suggestion to keep this flag made me worried.

It certainly used to be necessary building on 10.9, but for a
different error : https://github.com/scipy/scipy/issues/3194

Actually, now I try and build on 10.9 with cran gfortran, I also get
this error, I believe same as OP:

/usr/local/bin/gfortran -Wall -g -arch i686 -arch x86_64 -Wall -g
-undefined dynamic_lookup -bundle
build/temp.macosx-10.6-intel-2.7/scipy/integrate/_odepackmodule.o
-Lbuild/temp.macosx-10.6-intel-2.7 -lodepack -lmach -lgfortran -o
build/lib.macosx-10.6-intel-2.7/scipy/integrate/_odepack.so
-Wl,-framework -Wl,Accelerate

ld: warning: can't find atom for N_GSYM stabs
ls0001:G(0,24)=s1900rowns:(0,25)=ar(0,6);0;208;(0,9),0,13376;ccmax:(0,9),13376,64;el0:(0,9),13440,64;h:(0,9),13504,64;hmin:(0,9),13568,64;hmxi:(0,9),13632,64;hu:(0,9),13696,64;rc:(0,9),13760,64;tn:(0,9),13824,64;uround:(0,9),13888,64;illin:(0,6),13952,32;init:(0,6),13984,32;lyh:(0,6),14016,32;lewt:(0,6),14048,32;lacor:(0,6),14080,32;lsavf:(0,6),14112,32;lwm:(0,6),14144,32;liwm:(0,6),14176,32;mxstep:(0,6),14208,32;mxhnil:(0,6),14240,32;nhnil:(0,6),14272,32;ntrep:(0,6),14304,32;nslast:(0,6),14336,32;nyh:(0,6),14368,32;iowns:(0,26)=ar(0,6);0;5;(0,6),14400,192;icf:(0,6),14592,32;ierpj:(0,6),14624,32;iersl:(0,6),14656,32;jcur:(0,6),14688,32;jstart:(0,6),14720,32;kflag:(0,6),14752,32;l:(0,6),14784,32;meth:(0,6),14816,32;miter:(0,6),14848,32;maxord:(0,6),14880,32;maxcor:(0,6),14912,32;msbp:(0,6),14944,32;mxncf:(0,6),14976,32;n:(0,6),15008,32;nq:(0,6),15040,32;nst:(0,6),15072,32;nfe:(0,6),15104,32;nje:(0,6),15136,32;nqu:(0,6),15168,32;;
in build/temp.macosx-10.6-intel-2.7/libodepack.a(lsoda.o)

I get this whether I use `export FFLAGS=-ff2c` or not, so maybe it is
an incompatibility of the old gfortran with recent clang.

>> Thanks Sturla for that suggestion.  I can't help feeling that the build
>> process is a little fragile if one has to find the exact gfortran compiler
>> that works for given C compiler/OS combination.
>
> Building SciPy on OS X has always been a bit fragile, at least without
> Intel's Fortran compiler and MKL.
>
> But downloading an official/unoffcial gfortran binary installer from the
> gfortran wiki does not seem to be that fragile. Using an old gfortran build
> from the R project seems more on the fragile side, though.

The cran fortran is the standard recommendation because it compiles
both 32 and 64 bit binaries, if given the correct -arch flags; I don't
think that's true with the official gfortran binary (it just builds
64-bit or 32-bit but not both).  Not many of us are using 32-bit on
Macs these days though: https://www.adium.im/sparkle/#cpu64bit

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Sturla Molden-3
Matthew Brett <[hidden email]> wrote:

> It certainly used to be necessary building on 10.9, but for a
> different error : https://github.com/scipy/scipy/issues/3194

Obviously not, as the error is reported when compiling with this flag.

The error here is a missing mmintrin.h when compiling with Apple's
llvm-gcc-4.2.


Sturla

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Re: problems building scipy on Yosemite.

David Cournapeau
In reply to this post by Andrew Nelson


On Tue, Nov 11, 2014 at 7:29 AM, Andrew Nelson <[hidden email]> wrote:
Dear list,
I've updated to Yosemite (clean install) and am having problems building scipy from source (python setup.py build)

The complete build log is at:

$gfortran --version
GNU Fortran (GCC) 4.2.3
$gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
$echo FFLAGS
-ff2c


I can reproduce the issue on 10.6, where I used to be able to build numpy/scipy before with the exact same configuration (10.6, gfortran from ATT, official gcc-4.2 compilers from Apple).

I reduced the issue to be related to 32 bits only, and when built against numpy 1.9.1. I don't have the issue when building scipy against 1.8.1.

This suggests some incompatibilities in compilation options that have changed in numpy between 1.8.1 and 1.9.1.

David

P.S: one should not use -ff2c flags.
 

Is anyone able to give me any tips as to what I'm doing wrong?

cheers,
Andrew
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Re: problems building scipy on Yosemite.

David Cournapeau


On Tue, Nov 18, 2014 at 11:44 AM, David Cournapeau <[hidden email]> wrote:


On Tue, Nov 11, 2014 at 7:29 AM, Andrew Nelson <[hidden email]> wrote:
Dear list,
I've updated to Yosemite (clean install) and am having problems building scipy from source (python setup.py build)

The complete build log is at:

$gfortran --version
GNU Fortran (GCC) 4.2.3
$gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
$echo FFLAGS
-ff2c


I can reproduce the issue on 10.6, where I used to be able to build numpy/scipy before with the exact same configuration (10.6, gfortran from ATT, official gcc-4.2 compilers from Apple).

I reduced the issue to be related to 32 bits only, and when built against numpy 1.9.1. I don't have the issue when building scipy against 1.8.1.

This suggests some incompatibilities in compilation options that have changed in numpy between 1.8.1 and 1.9.1.

Indeed, the problem is the added '-g' flag between 1.8.1 and 1.9.1. That flag is invalid for gcc 4.2.x on darwin, we should instead use -gdwarf-2: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=34719

David

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Re: problems building scipy on Yosemite.

Sturla Molden-3
In reply to this post by David Cournapeau
On 18/11/14 12:44, David Cournapeau wrote:

> P.S: one should not use -ff2c flags.

If it is needed your ABI wrappers are to blame ;-)


Sturla


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Re: problems building scipy on Yosemite.

Sturla Molden-3
In reply to this post by Matthew Brett
On 14/11/14 08:55, Matthew Brett wrote:

> The cran fortran is the standard recommendation because it compiles
> both 32 and 64 bit binaries, if given the correct -arch flags; I don't
> think that's true with the official gfortran binary

I just checked this, it actually builds both.

If I pass -m32 or -arch i386 it creates a 32-bit binary.

If I pass -m64 or -arch x86_64 it creates a 64-bit binary.

The default is 64 bit.


I really think we should start to recommend the gfortran wiki binaries:

- It is easy to download and install (.dmg installer)

- It is a recent gfortran (currently 4.9.0 and 4.8.2).

- It is configured and built by the gfortran team.

- It can build SciPy and the test suite passes.

- It is configured to be compatible with Apple's Xcode command line
utils (including clang and clang++).

- It builds 32-bit and 64-bit binaries.

https://gcc.gnu.org/wiki/GFortranBinaries


Sturla


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Re: problems building scipy on Yosemite.

Matthew Brett
Hi,

On Wed, Nov 19, 2014 at 7:11 PM, Sturla Molden <[hidden email]> wrote:

> On 14/11/14 08:55, Matthew Brett wrote:
>
>> The cran fortran is the standard recommendation because it compiles
>> both 32 and 64 bit binaries, if given the correct -arch flags; I don't
>> think that's true with the official gfortran binary
>
> I just checked this, it actually builds both.
>
> If I pass -m32 or -arch i386 it creates a 32-bit binary.
>
> If I pass -m64 or -arch x86_64 it creates a 64-bit binary.
>
> The default is 64 bit.
>
>
> I really think we should start to recommend the gfortran wiki binaries:
>
> - It is easy to download and install (.dmg installer)
>
> - It is a recent gfortran (currently 4.9.0 and 4.8.2).
>
> - It is configured and built by the gfortran team.
>
> - It can build SciPy and the test suite passes.
>
> - It is configured to be compatible with Apple's Xcode command line
> utils (including clang and clang++).
>
> - It builds 32-bit and 64-bit binaries.
>
> https://gcc.gnu.org/wiki/GFortranBinaries

Sorry, the point I was trying to make is that the CRAN gfortran builds
fat binaries (containing both i386 and x86_64), matching the (dual
arch) Python.org and system Python architectures.  Of course you can
do that with the gcc gfortran, but only by doing a complicated two
pass compile (that was how I was building the ATLAS binaries),

Cheers,

Matthew
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Re: problems building scipy on Yosemite.

Sturla Molden-3
On 20/11/14 07:39, Matthew Brett wrote:

> Sorry, the point I was trying to make is that the CRAN gfortran builds
> fat binaries (containing both i386 and x86_64), matching the (dual
> arch) Python.org and system Python architectures.

I see. But it is still a very old gfortran.

Modern Fortran code will e.g. use ISO C bindings (Fortran 2003) for
interfacing with C and the IEEE environment (Fortran 2008) for
consistent floating point arithmetics. It would be sad if an old CRAN
gfortran prevents future additions to SciPy from using these rather
essential Fortran tools.

Sturla





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