#10508: Update ATLAS to stable version 3.10
-----------------------------------------------------------------------------------------+
Reporter: vbraun
| Owner: tbd
Type: enhancement
| Status: needs_work
Priority: major
| Milestone: sage-5.8
Component: packages
| Resolution:
Keywords: ATLAS
| Work issues:
Report Upstream: Reported upstream. No feedback yet.
| Reviewers: Benjamin Jones, Karl-Dieter Crisman, Dmitrii
Pasechnik, Georg Weber, François Bissey, John Palmieri
Authors: Volker Braun, Jeroen Demeyer
| Merged in:
Dependencies: #13160, #13395, #13392, #13416, #12994, #9906, #12883,
#13123, #13415 | Stopgaps:
-----------------------------------------------------------------------------------------+
Comment (by kcrisman):
On Cygwin with this ticket, apparently Scipy doesn't know where to find
lapack any more.
{{{
$ ./sage -i scipy
Found package scipy in spkg/standard/scipy-0.11.0.p1.spkg
scipy-0.11.0.p1
====================================================
Extracting package
/home/sagetest/sage-5.9.beta0/spkg/standard/scipy-0.11.0.p1.spkg
-rw-r--r-- 1 Administrator None 5480829 Jan 29 19:13
/home/sagetest/sage-5.9.beta0/spkg/standard/scipy-0.11.0.p1.spkg
Finished extraction
****************************************************
Host system:
CYGWIN_NT-6.1-WOW64 CETGORD-J5FGIPM 1.7.17(0.262/5/3) 2012-10-19 14:39
i686 Cygwin
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.5.3/lto-wrapper.exe
Target: i686-pc-cygwin
Configured with:
/gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3/configure
--srcdir=/gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3
--prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin
--libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var
--sysconfdir=/etc --datarootdir=/usr/share --docdir=/usr/share/doc/gcc4 -C
--datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v
--with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-
specific-runtime-libs --libexecdir=/usr/lib --enable-static --enable-
shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-
gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-
languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite
--enable-lto --enable-java-awt=gtk --disable-symvers --enable-libjava
--program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada
--enable-threads=posix --with-arch=i686 --with-tune=generic --enable-
libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4
GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-
jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.5.3 (GCC)
****************************************************
Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from distutils,
so their current settings are ignored.
patching file scipy/weave/catalog.py
Running from scipy source directory.
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in
/home/sagetest/sage-5.9.beta0/local/lib
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local
libraries ptf77blas,ptcblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local/include
libraries ptf77blas,ptcblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local/lib
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local
libraries f77blas,cblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local/include
libraries f77blas,cblas,atlas not found in
/home/sagetest/sage-5.9.beta0/local/lib
NOT AVAILABLE
}}}
<snip a lot of similar stuff>
{{{
File "/home/sagetest/sage-5.9.beta0/local/lib/python2.7/site-
packages/numpy/distutils/system_info.py", line 461, in get_info
raise self.notfounderror(self.notfounderror.__doc__)
numpy.distutils.system_info.LapackNotFoundError:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
Error building scipy.
real 0m0.827s
user 0m0.264s
sys 0m0.542s
************************************************************************
Error installing package scipy-0.11.0.p1
************************************************************************
}}}
Indeed, local/lib has liblapack.a and libblas.a when I don't use this
ticket, but not with this ticket (though both have libblas.dll.a).
And I guess this is unsurprising, because we don't really do anything on
Cygwin!
{{{
Copying /usr/lib/libblas.dll.a to /home/sagetest/sage-5.9.beta0/local/lib
}}}
is the extent of the log for atlas in both cases, whereas before lapack
was definitely built (lots of `sage_fortran` etc. in the log) and of
course now it's MIA by design.
So... do we have to now ''build'' atlas on Cygwin? I can do
{{{
cp /usr/lib/liblapack.a /home/sagetest/sage-5.9.beta0/local/lib
}}}
for now, hopefully that will work...
Note that this ticket has removed the following.
{{{
# On Cygwin we simply require that the system-wide lapack is installed.
# This includes BLAS and is enough to build the rest of Sage.
if conf['CYGWIN?']:
lib = '/usr/lib/libblas.dll.a'
if not os.path.exists(lib):
print '*'*75
print 'On Cygwin you must install the standard LAPACK Cygwin
package'
print 'via the Cygwin setup.exe program in the "Math" category.'
print '*'*75
sys.exit(1)
cp(lib, os.path.join(conf['SAGE_LOCAL'], 'lib'))
sys.exit(0)
}}}
So I think that probably some update to this needs to be included. Maybe
this would still be enough?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/10508#comment:362>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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