Atlas and NumPy Problems

[Justin Lemkul]

Hello all,

I am hoping someone out there will be able to help me. I am trying to install
a program that utilizes NumPy. In installing NumPy, I realized that I was
lacking Atlas. I ran into the following problems installing Atlas and NumPy,
as I realized that NumPy could be installed using the Mac OSX veclib already
built in. If anyone has any ideas on how to fix either of these, I would be
most grateful.

I am fairly new to Python (I've been learning it myself), so I apologize if
these questions are a bit foolish. I've been fighting these problems for
days, and I'm out of ideas.

I am running OS X v10.3, gcc v3.3, Python v2.3, ScientificPytho n v2.4.3, and
am attempting to install NumPy 23.7

Thank you!

-Justin


ATLAS install problem:

n file included from
/Users/jalemkul/Desktop/ATLAS/include/
atlas_prefetch. h:8, from
.../ATL_col2blk.c:3 3:/Users/jalemkul/Desktop/ATLAS/
include/atlas_altivec.h :6:27: altivec.h: No such file or
directory../ATL_col2blk.c: In function
`ATL_dcol2blk_a X':../ATL_col2blk.c:7 9: error: `vector' undeclared (first use
in this
function)../ATL_col2blk.c:7 9: error: (Each undeclared identifier is reported
only once../
ATL_col2blk.c:7 9: error: for each function it appears in.)../ATL_col2blk.c:7 9:
error: parse
error before "float"../ATL_col2blk.c:8 0: error: parse error before
"float"make[7]: ***
[ATL_dcol2blk_aX .o] Error 1make[7]: *** Waiting for unfinished
jobs....make[6]: *** [dlib]
Error 2make[5]: *** [dmmlib]
Error 2make[4]: *** [res/atlas_cacheedge .h]
Error2make[3]: *** [dinstall]
Error 2make[2]: *** [MMinstall]
Error 2 STAGE2-1-2: CacheEdge
DETECTIONmake -f Makefile INSTALL_LOG/atlas_cacheedge .h pre=d 2>&1 |
../xatlas_tee
INSTALL_LOG/dMMCACHEEDGE.LO Gcd /Users/jalemkul/Desktop/ATLAS/tune/blas/gemm/
OSX_UNKNOWNAlti Vec_2 ; make res/atlas_cacheedge .h pre=dmake dRunFindCEcd
/Users/
jalemkul/Desktop/ATLAS/src/blas/gemm/OSX_UNKNOWNAlti Vec_2 ; make dlibmake
auxillib
dcleanuplib dusergemmcd /Users/jalemkul/Desktop/ATLAS/src/auxil/
OSX_UNKNOWNAlti Vec_2 ; make libmake[7]: Nothing to be done for `lib'.cd KERNEL
; make
-f dMakefile dlibmake[7]: Nothing to be done for `dlib'.cd
/Users/jalemkul/Desktop/ATLAS/
src/blas/gemm/OSX_UNKNOWNAlti Vec_2 ; make dusermmmake[7]: `dusermm' is up to
date.make -j 2 dlib.grd/usr/bin//gcc -o ATL_dcol2blk_aX .o -c -DL2SIZE=4194304
-I/Users/
jalemkul/Desktop/ATLAS/include -I/Users/jalemkul/Desktop/ATLAS/include/
OSX_UNKNOWNAlti Vec_2 -I/Users/jalemkul/Desktop/ATLAS/include/contrib
-DATL_OS_OSX -DATL_AltiVec -DATL_AVgcc -DATL_AS_OSX_PPC -DATL_NCPU=2 -O
-maltivec -mabi=altivec -DDREAL -DALPHAX ../ATL_col2blk.c
/usr/bin//gcc -o ATL_drow2blkT_a X.o -c -DL2SIZE=4194304
-I/Users/jalemkul/Desktop/
ATLAS/include -I/Users/jalemkul/Desktop/ATLAS/include/OSX_UNKNOWNAlti Vec_2
-I/Users/
jalemkul/Desktop/ATLAS/include/contrib -DATL_OS_OSX -DATL_AltiVec
-DATL_AVgcc
-DATL_AS_OSX_PPC -DATL_NCPU=2 -O -maltivec -mabi=altivec -DDREAL -DALPHAX ../
ATL_row2blkT.c
In file included from
/Users/jalemkul/Desktop/ATLAS/include/atlas_prefetch. h:8,
from ../ATL_row2blkT.c: 32:
/Users/jalemkul/Desktop/ATLAS/include/atlas_altivec.h :6:27: altivec.h: No such
file or
directory
.../ATL_row2blkT.c: In function `ATL_drow2blkT_ NB_aX':
.../ATL_row2blkT.c: 64: error: `vector' undeclared (first use in this function)
.../ATL_row2blkT.c: 64: error: (Each undeclared identifier is reported only once
.../ATL_row2blkT.c: 64: error: for each function it appears in.)
.../ATL_row2blkT.c: 64: error: parse error before "float"
.../ATL_row2blkT.c: 65: error: parse error before "float"
.../ATL_row2blkT.c: 74: error: parse error before "float"
.../ATL_row2blkT.c: 75: error: parse error before "float"
In file included from
/Users/jalemkul/Desktop/ATLAS/include/atlas_prefetch. h:8,
from ../ATL_col2blk.c:3 3:
/Users/jalemkul/Desktop/ATLAS/include/atlas_altivec.h :6:27: altivec.h: No such
file or
directory
.../ATL_col2blk.c: In function `ATL_dcol2blk_a X':
.../ATL_col2blk.c:7 9: error: `vector' undeclared (first use in this function)
make[6]: *** [ATL_drow2blkT_a X.o] Error 1
make[6]: *** Waiting for unfinished jobs....
.../ATL_col2blk.c:7 9: error: (Each undeclared identifier is reported only once
.../ATL_col2blk.c:7 9: error: for each function it appears in.)
.../ATL_col2blk.c:7 9: error: parse error before "float"
.../ATL_col2blk.c:8 0: error: parse error before "float"
make[6]: *** [ATL_dcol2blk_aX .o] Error 1
make[5]: *** [dlib] Error 2
make[4]: *** [dmmlib] Error 2
make[3]: *** [res/atlas_cacheedge .h] Error 2
make[2]: ***
[/Users/jalemkul/Desktop/ATLAS/tune/blas/gemm/OSX_UNKNOWNAlti Vec_2/
res/atlas_cachedge. h] Error 2
ERROR 572 DURING CACHE EDGE DETECTION!!.
cd ../.. ; make error_report arch=OSX_UNKNOW NAltiVec_2
make -f Make.top error_report arch=OSX_UNKNOW NAltiVec_2
uname -a 2>&1 >> bin/OSX_UNKNOWNAlti Vec_2/INSTALL_LOG/ERROR.LOG
/usr/bin//gcc -v 2>&1 >> bin/OSX_UNKNOWNAlti Vec_2/INSTALL_LOG/ERROR.LOG
Reading specs from /usr/libexec/gcc/darwin/ppc/3.3/specs
Thread model: posix
gcc version 3.3 20030304 (Apple Computer, Inc. build 1495)
/usr/bin//gcc -V 2>&1 >> bin/OSX_UNKNOWNAlti Vec_2/INSTALL_LOG/ERROR.LOG
gcc: `-V' option must have argument
make[4]: [error_report] Error 1 (ignored)
/usr/bin//gcc --version 2>&1 >>
bin/OSX_UNKNOWNAlti Vec_2/INSTALL_LOG/ERROR.LOG
/usr/bin//tar cf error_OSX_UNKNO WNAltiVec_2.tar Make.OSX_UNKNOW NAltiVec_2
bin/
OSX_UNKNOWNAlti Vec_2/INSTALL_LOG/*
/usr/bin//gzip --best error_OSX_UNKNO WNAltiVec_2.tar
mv error_OSX_UNKNO WNAltiVec_2.tar .gz error_OSX_UNKNO WNAltiVec_2.tgz
Error report error_<ARCH>.tg z has been created in your top-level ATLAS
directory. Be sure to include this file in any help request.


First, make sure this error is not covered in the ATLAS errata file,

http://math-atlas.sourceforge.net/errata.html

All known errors, and most common mistakes/system problems are documented
in this file, so it will save everyone hassle in the long run if you take
the time to scope it out before sending e-mail to the help list.

If this does not have the solution to your problem, and you can't figure out
what went wrong, submit a support request to the ATLAS support tracker, as
discussed here:

http://math-atlas.sourceforge.net/faq.html#help

In the above examples, <ARCH> should be replaced with your architecture
string, such as "Linux_PIII " or "FreeBSD_21264" .

make[1]: *** [install] Error 255
make: *** [install] Error 2


NumPy install problem:

warning: no library file corresponding to '/System/Library' found (skipping)
gcc -Wl,-F. -Wl,-F. -bundle -framework Python
build/temp.darwin-7.7.0-Power_Macintosh
-2.3/Packages/dotblas/dotblas/_dotblas.o -L/System/Library -o
build/lib.darwin-7.7.0-
Power_Macintosh-2.3/_dotblas.so
ld: Undefined symbols:
_cblas_caxpy
_cblas_cdotc_su b
_cblas_cdotu_su b
_cblas_cgemm
_cblas_cgemv
_cblas_daxpy
_cblas_ddot
_cblas_dgemm
_cblas_dgemv
_cblas_saxpy
_cblas_sdot
_cblas_sgemm
_cblas_sgemv
_cblas_zaxpy
_cblas_zdotc_su b
_cblas_zdotu_su b
_cblas_zgemm
_cblas_zgemv
error: command 'gcc' failed with exit status 1

[Robert Kern]

Re: Atlas and NumPy Problems

Justin Lemkul wrote:[color=blue]
> Hello all,
>
> I am hoping someone out there will be able to help me. I am trying to install
> a program that utilizes NumPy. In installing NumPy, I realized that I was
> lacking Atlas. I ran into the following problems installing Atlas and NumPy,
> as I realized that NumPy could be installed using the Mac OSX veclib already
> built in. If anyone has any ideas on how to fix either of these, I would be
> most grateful.
>
> I am fairly new to Python (I've been learning it myself), so I apologize if
> these questions are a bit foolish. I've been fighting these problems for
> days, and I'm out of ideas.
>
> I am running OS X v10.3, gcc v3.3, Python v2.3, ScientificPytho n v2.4.3, and
> am attempting to install NumPy 23.7[/color]

Did you try to follow my advice from the other thread? What does your
setup.py look like?

--
Robert Kern
rkern@ucsd.edu

"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter

[Robert Kern]

Re: Atlas and NumPy Problems

Robert Kern wrote:[color=blue]
> Justin Lemkul wrote:
>[color=green]
>> Hello all,
>>
>> I am hoping someone out there will be able to help me. I am trying to
>> install a program that utilizes NumPy. In installing NumPy, I
>> realized that I was lacking Atlas. I ran into the following problems
>> installing Atlas and NumPy, as I realized that NumPy could be
>> installed using the Mac OSX veclib already built in. If anyone has
>> any ideas on how to fix either of these, I would be most grateful.
>>
>> I am fairly new to Python (I've been learning it myself), so I
>> apologize if these questions are a bit foolish. I've been fighting
>> these problems for days, and I'm out of ideas.
>>
>> I am running OS X v10.3, gcc v3.3, Python v2.3, ScientificPytho n
>> v2.4.3, and am attempting to install NumPy 23.7[/color]
>
>
> Did you try to follow my advice from the other thread? What does your
> setup.py look like?[/color]

For the record, he did in fact follow my advice (removing the
ATLAS-specific defaults and letting setup.py autodetect the vecLib
framework), and it turns out my advice was incomplete.

One also needs to add

extra_link_args =extra_link_arg s,

to the argument list of the Extension() call for the _dotblas module.

It worked fine on my machine because I had modified my Python config to
use "-undefined dynamic_lookup" instead of explicit -framework arguments
(this change is necessary for the neighborly cohabitation of different
Python versions, I believe. See the PythonMac-SIG archives for more
information).

--
Robert Kern
rkern@ucsd.edu

"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter