Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv915
Modified Files:
atlas.info
Log Message:
update to 3.10.1, refactor to only build libsatlas/libtatlas with --dylibs
configure option, upgrade to gcc48-compiler and link dylibs with same rather
than libtool to fix ppc build
Index: atlas.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/atlas.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- atlas.info 2 Jun 2012 16:19:53 -0000 1.4
+++ atlas.info 4 Apr 2013 19:07:25 -0000 1.5
@@ -1,6 +1,6 @@
Package: atlas
-Version: 3.9.76
-Revision: 3
+Version: 3.10.1
+Revision: 1
Description: Portable optimal linear algebra software
DescDetail: <<
The current version provides a complete BLAS and LAPACK API.
@@ -25,20 +25,32 @@
The optimized subset of LAPACK provided by ATLAS is merged
with the full LAPACK from http://www.netlib.org/lapack.
-Tuning and building is done independenly for static and for shared libs,
-to avoid hampering the static libs with -fPIC .
+The --dylib configure option is used to build both static and shared libs
+with -fPIC in both cases for ASLR compatibility. The main atlas package
+provides symlinks for libptlapack.dylib, libptf77blas.dylib and
+libptcblas.dylib to libtatlas.dylib as well as for liblapack.dylib,
+libf77blas.dylib and libcblas.dylib to libsatlas.dylib. This unfortunately
+breaks backward compatibilty with the previous packaging which incorrectly
+blocked compiling against the system lapack and blas libraries without
+completely deinstalling atlas (and anything that depended on it). Packages
+should now BuildDepends on atlas (>= 3.10.1-1) and Depends on atlas-shlibs
+(>= 3.10.1-1). The symlinks in atlas will allow code to build against
+atlas but result in linkages are to libsatlas rather than liblapack and
+libcblas, etc.
<<
DescUsage: <<
Order is important when linking! Use:
-L%p/lib -lptlapack -lptcblas -lptf77blas -latlas
+or
+-L%p/lib -ltatlas
(or the analogue without "pt" in pkgs that handle parallelism on their own).
Also decide carefully whether you want to link to static or to shared libs.
<<
Source: mirror:sourceforge:math-atlas/files/%n%v.tar.bz2
-Source-MD5: 1d60c9b4d142e2bce87ff7a08c781fe1
-Source2: http://www.netlib.org/lapack/lapack-3.4.1.tgz
-Source2-MD5: 44c3869c38c8335c2b9c2a8bb276eb55
+Source-MD5: 78753e869231cc1417a92eebaa076718
+Source2: http://www.netlib.org/lapack/lapack-3.4.2.tgz
+Source2-MD5: 61bf1a8a4469d4bdb7604f5897179478
PatchFile: %n.patch
PatchFile-MD5:06ec47ef569a02980b9f9f5dbaf3c134
@@ -49,7 +61,8 @@
SetMAKEFLAGS: -j1
UseMaxBuildJobs: false
BuildDependsOnly: true
-BuildDepends: gcc47-compiler, doxygen, graphviz | graphviz-nox
+BuildDepends: gcc48-compiler, doxygen, graphviz | graphviz-nox
+Depends: %N-shlibs (=%v-%r)
# The whole previous patchscript is in the srcs for %v 3.9.4
PatchScript: <<
@@ -57,10 +70,15 @@
patch -p1 < %{PatchFile}
chmod ugo+x ar2
perl -pi -e "s|XXXXX|%b/ar2|g" CONFIG/src/SpewMakeInc.c
+if [ "%m" = 'powerpc' ]
+ then perl -pi -e 's,cMVFLAGS=\\"%%s,cMVFLAGS=\\"-force_cpusubtype_ALL\ %%s,'
include/atlas_mvtesttime.h
+fi
+
## put srcs in logical dirs, version independent
+
cd ..
if [ -e LAPACK ] ; then mv LAPACK LAPACK-strange; fi
-mv lapack-3.4.1 LAPACK
+mv lapack-3.4.2 LAPACK
# first need the tarball of lapack (and no % will give the path to the
original;
# not worth to check the user's fink.conf for a FetchAltDir entry etc)
tar -czf lapack.tgz LAPACK
@@ -76,6 +94,11 @@
# use correct fink prefix
sed -i.bak -e 's,/sw,%p,' CONFIG/src/{config,probe_comp}.c
+# Link with gcc-fsf-4.8 to obtain correct libgcc related linkages to resolve
symbols on ppc
+perl -pi -e 's,\$\(LIBTOOL\) -dynamic,gcc-fsf-4.8 -dynamiclib,g' makes/Make.lib
+# force GOODGCC to gcc-fsf-4.8
+perl -pi -e "s|GOODGCC =.*|GOODGCC = gcc-fsf-4.8\");|" CONFIG/src/SpewMakeInc.c
+
cd ..
cd LAPACK
sed -e 's,\.\./.\./librefblas\.a,%b/../bld/lib/libf77blas.a
%b/../bld/lib/libcblas.a %b/../bld/lib/libatlas.a,' \
@@ -92,20 +115,20 @@
#!/bin/sh -ev
cd ..
- ln -s %p/lib/gcc4.7/bin/gcc-4 gcc
- ln -s %p/lib/gcc4.7/bin/gfortran gfortran
+ ln -s %p/lib/gcc4.8/bin/gcc-4 gcc
+ ln -s %p/lib/gcc4.8/bin/gfortran gfortran
GCCADDR=`pwd`
- export PATH=$GCCADDR:%p/lib/gcc4.7/bin:$PATH
+ export PATH=$GCCADDR:%p/lib/gcc4.8/bin:$PATH
### BUILDSCRIPT
BLD () {
confflags="-b 32"
- mflags="$mflags -fomit-frame-pointer -O2"
+ mflags="$mflags -fomit-frame-pointer -O3"
if [ "%m" = 'i386' ]
then mflags="$mflags -m32 -mfpmath=sse"
else if [ "%m" = 'x86_64' ]
then mflags="$mflags -m64 -mfpmath=sse"; confflags="-b 64"
- else mflags="$mflags -maltivec -mabi=altivec"
+ else mflags="$mflags -maltivec -mabi=altivec
-force_cpusubtype_ALL"
if [ `machine|sed -e 's,ppc,,' -e 's,\([0-9]\).*,\1,'` != 9 ]
then confflags='-Si cputhrchk 0 -D c -DATL_AVgcc -b 32'
fi
@@ -115,7 +138,11 @@
sed -e "/^OPTS /s;=;= $mflags;" -e "s,ATLAS/../bld,$1,g" <
LAPACK/make.inc.proto > LAPACK/make.inc
cd $1
- ../ATLAS/configure %c -C ac $GCCADDR/gcc -C if `which gfortran` -F alg
"$mflags" $confflags
+ if [ "%m" = 'powerpc' ]
+ then ../ATLAS/configure %c -C ac $GCCADDR/gcc -C if `which gfortran` -A 4
-F alg "$mflags" $confflags --dylibs
+ else ../ATLAS/configure %c -C ac $GCCADDR/gcc -C if `which gfortran` -F alg
"$mflags" $confflags --dylibs
+ fi
+
make
### Static Libs
@@ -130,56 +157,14 @@
cd ../..
}
-### BUILDING STATIC
- iflags=''
- mflags=''
- mkdir -p STAT_bld
- BLD STAT_bld
- cp -p LAPACK/make.inc LAPACK/make.inc_STAT
-
-### BUILDING SHARED
- iflags="-fPIC"
- mflags="-fPIC"
- mkdir -p SHAR_bld
- BLD SHAR_bld
-
-### MAKE DYLIBS
- cd SHAR_bld/lib
- # We now make shared libs (experimental); easier to just write the commands
here than to fix lib/Makefile ...
- # We link 'manually', with ld, to try avoid having unnecessary libs like
lgcc_s among the load commands.
- # This way the libs can be safely used in linking with any compiler: they
will not bring themselves
- # the wrong lgcc_s in the search list.
- mkdir -p tmp
- if [ `uname -r | cut -d. -f1` -ge 9 ] ; then flag=-dead_strip_dylibs ; else
flag='' ; fi
- ld="ld -arch `sed -e 's,powerpc,ppc,' <<<'%m'` -dynamic -dylib -single_module
$flag -dead_strip -x tmp/*.o -L. -L%p/lib/gcc4.7/lib -ldylib1.o
-dylib_install_name"
- lnk () {
- cd tmp; rm -f *; ar x ../lib$1.a; cd -
- echo $ld %p/lib/lib$1.dylib -o lib$1.dylib $2 -lSystem
- $ld %p/lib/lib$1.dylib -o lib$1.dylib $2 -lSystem
- }
- LNK () {
- lnk $1 "$2"
- l=pt$1; libs=`sed -e 's,atlas|cblas|f77blas,pt&,g' <<<"$2"`
- if [ -h "lib$l.a" ]
- then ln -s lib$1.dylib lib$l.dylib
- else lnk $l "$libs"
- fi
- }
- LNK atlas ''
- LNK cblas -latlas
- LNK f77blas '-lgfortran -latlas'
- LNK lapack "-lf77blas -lgfortran -lcblas -latlas -lgcc_s.1"
- rm -fR tmp
- ## the next 4 lines are optional _ no idea of a correct exported symbols list
for libatlas...
- ## probably to be removed for a commit _ it gains an enormous decrease in the
# of symbols exported by the lib,
- ## but size goes down only from ~ 2.8M to 2.3M
- # nm -mfgu liblapack.dylib libcblas.dylib libf77blas.dylib|fgrep ' (from
libatlas'|sed -e 's, (from .*,,' -e 's,.* ,,'|sort -u > lst
- # install_name_tool -id %p/lib/libatlas_full.dylib libatlas.dylib
- # mv libatlas.dylib libatlas_full.dylib
- # $ld %p/lib/libatlas.dylib libatlas.a -o libatlas.dylib -ldylib1.o -lSystem
-exported_symbols_list lst
+### BUILDING
+ iflags='-fPIC'
+ mflags='-fPIC'
+ mkdir -p darwin_bld
+ BLD darwin_bld
### LAPACK-DOCS
- cd ../../LAPACK
+ cd %b/../LAPACK
make man html
<<
InfoTest: <<
@@ -190,11 +175,10 @@
cd ..
export PATH=`pwd`:$PATH
cd LAPACK
- cp -p make.inc_STAT make.inc
make -k blas_testing || :
# to get timing uncluttered by compilation times, we'll repeat the tests at
the end of the log:
rm BLAS/*.out
- cd ../STAT_bld
+ cd ../darwin_bld
make -k full_test || :
if test -f lib/libptcblas.a
then make -k lapack_test_al_pt || :; make -k ptcheck || :
@@ -204,7 +188,7 @@
# here: real 3m10.903s; user 2m55.622s; sys 0m15.570s (average of 3)
# with 3.8.2: real 3m19.518s; user 3m2.366s; sys 0m18.272s
egrep "fail|Error" BLAS/*.out
- cat ../STAT_bld/bin/LAPACK_TEST/SUMMARY_al_*.txt
+ cat ../darwin_bld/bin/LAPACK_TEST/SUMMARY_al_*.txt
<<
<<
InstallScript: <<
@@ -217,29 +201,30 @@
cp -pPR ../LAPACK/{LICENSE,README} %i/share/doc/%n/LAPACK
cp -pPR ../LAPACK/DOCS/explore-html %i/share/doc/%n/LAPACK/html
ln -s html/index.html %i/share/doc/%n/LAPACK/lapack.html
- cd ../STAT_bld
+ cd ../darwin_bld
make install DESTDIR=%i
+ # create symlinks to threaded atlas
+ ln -sf %p/lib/libtatlas.dylib %i/lib/libptlapack.dylib
+ ln -sf %p/lib/libtatlas.dylib %i/lib/libptf77blas.dylib
+ ln -sf %p/lib/libtatlas.dylib %i/lib/libptcblas.dylib
+ # create symlinks to serial atlas
+ ln -sf %p/lib/libsatlas.dylib %i/lib/liblapack.dylib
+ ln -sf %p/lib/libsatlas.dylib %i/lib/libf77blas.dylib
+ ln -sf %p/lib/libsatlas.dylib %i/lib/libcblas.dylib
# rm empty headers
cd %i/include/atlas; ls -1s|grep '^[[:space:]]*0[[:space:]]'|sed -e 's,.*
,,'|xargs rm -f; cd -
- cp -pPR lib/*.a ../SHAR_bld/lib/*.dylib %i/lib
- rm -f %i/lib/libtstatlas.a %i/lib/libf77refblas.a %i/lib/lapack_matgen.a
find %i/lib -type f -name '*.a' -exec ranlib \{\} \;
chmod -R a-x %i/lib/*
chmod -R a+rX %i/share
<<
Splitoff: <<
Package: %N-shlibs
- Depends: gcc47-shlibs
- Files: lib/*.dylib
+ Depends: gcc48-shlibs
+ Files: lib/libtatlas.dylib lib/libsatlas.dylib
InstallScript: mkdir -p %i/share/doc; ln -s %N %i/share/doc/%n
Shlibs: <<
- %p/lib/liblapack.dylib 0.0.0 %n (>= 3.8.0-6)
- %p/lib/libptlapack.dylib 0.0.0 %n (>= 3.9.63-1)
- %p/lib/libf77blas.dylib 0.0.0 %n (>= 3.8.0-6)
- %p/lib/libptf77blas.dylib 0.0.0 %n (>= 3.9.63-1)
- %p/lib/libcblas.dylib 0.0.0 %n (>= 3.8.0-6)
- %p/lib/libptcblas.dylib 0.0.0 %n (>= 3.9.63-1)
- %p/lib/libatlas.dylib 0.0.0 %n (>= 3.8.0-6)
+ %p/lib/libtatlas.dylib 0.0.0 %n (>= 3.11.8-1)
+ %p/lib/libsatlas.dylib 0.0.0 %n (>= 3.11.8-1)
<<
<<
SplitOff2: <<
@@ -248,4 +233,4 @@
InstallScript: mkdir -p %i/share/doc; ln -s %N %i/share/doc/%n
<<
Homepage: http://math-atlas.sourceforge.net
-Maintainer: None <fink-de...@lists.sourceforge.net>
+Maintainer: Jack Howarth <howa...@bromo.med.uc.edu>
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