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Atlas and NumPy Problems

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

Jul 18 '05 #1
2 3581
Justin Lemkul wrote:
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


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

--
Robert Kern
rk***@ucsd.edu

"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter
Jul 18 '05 #2
Robert Kern wrote:
Justin Lemkul wrote:
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

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


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
rk***@ucsd.edu

"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter
Jul 18 '05 #3

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