[SciPy-Dev] ANN: Scipy 0.13.0 beta 1 release

Jack Howarth howarth@bromo.med.uc....
Fri Aug 30 09:27:23 CDT 2013


On Sat, Aug 24, 2013 at 11:11:36AM +0200, Ralf Gommers wrote:
> On Sat, Aug 24, 2013 at 1:58 AM, Jack Howarth <howarth@bromo.med.uc.edu>wrote:
> 
> > On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
> > > Hi all,
> > >
> > > I'm happy to announce the availability of the first beta release of Scipy
> > > 0.13.0. Please try this beta and report any issues on the scipy-dev
> > mailing
> > > list.
> > >
> > > Source tarballs and release notes can be found at
> > > https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows
> > and
> > > OS X installers will follow later (we have a minor infrastructure issue
> > to
> > > solve, and I'm at EuroScipy now).
> > >
> > > Cheers,
> > > Ralf
> >
> > Ralf,
> >    FYI, if the proposed elimination of support for the Accelerate
> > framework on
> > darwin was implemented in scipy 0.13, you will definietely want to
> > consider reverting that
> > change. It appears that the issues in the Accelerate framework (at least as
> > tested with scipy 0.12.0) are resolved in the next darwin release...
> >
> 
> Hi Jack, the issues appear to have been resolved completely (thanks to
> Michael Wimmer and Pauli), so we didn't drop support or used OpenBLAS for
> the binaries.
> 
> Ralf

Ralf,
   Unfortunately, I am seeing a linkage failure in 0.13.0 beta1 on darwin13 using
the same build recipe that we use in fink for 0.12.0...

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build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddp_rid_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddp_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddp_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_aid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_aid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_aid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_aid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_asvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_asvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_rid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_rid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/iddr_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_frm_subr_6.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_house_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_house_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_house_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_6.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id_subr_7.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_id2svd_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_qrpiv_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_sfft_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_snorm_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idz_svd_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_aid_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_asvd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rid_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzp_rsvd_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_aid_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_asvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_asvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rid_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rid_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_0.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_1.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_2.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_3.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_4.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_5.o build/temp.macosx-10.9-x86_64-2.7/scipy/linalg/src/id_dist/src/prini_subr_6.o -L/sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.0.0/4.8.1 -Lbuild/temp.macosx-10.9-x86_64-2.7 -lgfortran -o build/lib.macosx-10.9-x86_64-2.7/scipy/linalg/_interpolative.so -Wl,-framework -Wl,Accelerate
Undefined symbols for architecture x86_64:
  "_PyArg_ParseTupleAndKeywords", referenced from:
      _f2py_rout__interpolative_id_srand in _interpolativemodule.o
      _f2py_rout__interpolative_id_srandi in _interpolativemodule.o
      _f2py_rout__interpolative_id_srando in _interpolativemodule.o
      _f2py_rout__interpolative_idd_frm in _interpolativemodule.o
      _f2py_rout__interpolative_idd_sfrm in _interpolativemodule.o
      _f2py_rout__interpolative_idd_frmi in _interpolativemodule.o
      _f2py_rout__interpolative_idd_sfrmi in _interpolativemodule.o
      ...

etc. This is using...

a site.cfg with...

[amd]
library_dirs = /sw/lib
include_dirs = /sw/include/suitesparse
amd_libs = amd

[umfpack]
library_dirs = /sw/lib
include_dirs = /sw/include/suitesparse
umfpack_libs = umfpack

and

   export CC=clang
   export CXX=clang++
   export FFLAGS=-ff2c
   export FC=/sw/bin/gfortran

   unset LDFLAGS
   /sw/bin/python2.7 setup.py build --fcompiler gnu95

with a build against suitesparse 4.0.2 and numpy 1.7.1.
      Jack

 
> 
> 
> > Ran 6134 tests in 88.016s
> >
> > OK (KNOWNFAIL=15, SKIP=36)
> >
> > compared to darwin12...
> >
> > Ran 6134 tests in 96.886s
> >
> > FAILED (KNOWNFAIL=15, SKIP=36, failures=63)
> >
> > and darwin11...
> >
> > Ran 6134 tests in 118.346s
> >
> > FAILED (KNOWNFAIL=15, SKIP=36, failures=65)
> >
> >              Jack
> > ps I have looked at the proposed replacement of using openblas and it is
> > rather suboptimal. Please
> > don't inflict that on us.
> >
> > > _______________________________________________
> > > SciPy-Dev mailing list
> > > SciPy-Dev@scipy.org
> > > http://mail.scipy.org/mailman/listinfo/scipy-dev
> >
> > _______________________________________________
> > SciPy-Dev mailing list
> > SciPy-Dev@scipy.org
> > http://mail.scipy.org/mailman/listinfo/scipy-dev
> >

> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev@scipy.org
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