Merge in sage-5.13.beta5

VERSION.txt

@@ -1 +1 @@
-Sage version 5.13.beta4, released 2013-11-24
+Sage version 5.13.beta5, released 2013-12-05

build/pkgs/atlas/SPKG.txt

@@ -95,6 +95,13 @@ The package can be configured via three environment variables:
 
 == ChangeLog ==
 
+=== atlas-3.10.1.p7, lapack-3.4.2 (Jean-Pierre Flori, 25 November 2013) ===
+ * Trac #14410: Let ATLAS build and install shared libraries on Cygwin.
+ * Bunch of modifications to the autotools project generating shared libraries
+   so that it does not invoke libtool on Cygwin.
+ * Fix a bug in spkg-install.
+ * Cleanup spkg-check.
+
 === atlas-3.10.1.p6, lapack-3.4.2 (Volker Braun, 11 October 2013) ===
  * Trac #15270: Do not give up if the upstream shared library build
    fails

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.1.p6
+3.10.1.p7

build/pkgs/atlas/patches/ATLAS-lib/Makefile.am

@@ -5,9 +5,9 @@ SO_VERSION=3:0
 
 # You shouldn't have to customize anything from here on
 
-ATLAS_SERIAL_LIBS=libatlas.la libcblas.la libf77blas.la liblapack.la
+ATLAS_SERIAL_LIBS=atlas cblas f77blas lapack
 
-ATLAS_PARALLEL_LIBS=libptcblas.la libptf77blas.la libptlapack.la
+ATLAS_PARALLEL_LIBS=ptcblas ptf77blas ptlapack
 
 all: all_parallel
 
@@ -16,105 +16,103 @@ all_serial: $(ATLAS_SERIAL_LIBS)
 all_parallel: all_serial $(ATLAS_PARALLEL_LIBS)
 
 clean:
-	$(RM) -r -f .libs *.la *-obj
+	$(RM) -r -f .libs *.la *.dll *.dll.a *-obj
 
 install: install_parallel
 
 install_serial: $(ATLAS_SERIAL_LIBS)
 	$(MKDIR_P) @libdir@
-	@LIBTOOL@ --mode=install $(INSTALL) -c libatlas.la @libdir@/libatlas.la
-	@LIBTOOL@ --mode=install $(INSTALL) -c libcblas.la @libdir@/libcblas.la
-	@LIBTOOL@ --mode=install $(INSTALL) -c libf77blas.la @libdir@/libf77blas.la
-	@LIBTOOL@ --mode=install $(INSTALL) -c liblapack.la @libdir@/liblapack.la
+	$(MKDIR_P) @bindir@
+	for module in $(ATLAS_SERIAL_LIBS); do \
+		@LTINSTALL@; \
+	done;
 	@LIBTOOL@ --finish @libdir@
+	@LIBTOOL@ --finish @bindir@
 
 install_parallel: install_serial $(ATLAS_PARALLEL_LIBS)
 	$(MKDIR_P) @libdir@
-	@LIBTOOL@ --mode=install $(INSTALL) -c libptcblas.la @libdir@/libptcblas.la
-	@LIBTOOL@ --mode=install $(INSTALL) -c libptf77blas.la @libdir@/libptf77blas.la
-	@LIBTOOL@ --mode=install $(INSTALL) -c libptlapack.la @libdir@/libptlapack.la
+	$(MKDIR_P) @bindir@
+	for module in $(ATLAS_PARALLEL_LIBS); do \
+		@LTINSTALL@; \
+	done;
 	@LIBTOOL@ --finish @libdir@
-
+	@LIBTOOL@ --finish @bindir@
 
 # In presence of multiple definitions of thread related functions, use the ones from *_mut.o
 # Works with all nm output formats (BSD/POSIX/System V)
-libatlas.la: libatlas.a
+atlas: libatlas.a
 	-$(RM) -r -f libatlas-obj
 	$(MKDIR) libatlas-obj
-	cd libatlas-obj && $(AR) x ../$<
+	cd libatlas-obj && $(AR) x ../$< && cd ..
 	if [ `$(NM) -g $< | $(EGREP) -w 'ATL_(Set|Reset|Free|Dec)AtomicCount' | $(GREP) -w T | wc -l` -gt 4 ]; then \
 	  $(RM) `ls -1 libatlas-obj/ATL_{Set,Reset,Free,Dec}AtomicCount_*.o | $(GREP) -v '_mut.o$$'`; \
 	fi
-	@LIBTOOL@ --tag=CC --mode=link $(CC) @LIBTOOL_TYPE@ \
-	    -o $@ libatlas-obj/*.o \
+	@LTCLINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libatlas-obj/*.o \
 	    @PTHREAD_LIB@ -lm \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
-
+	    @LTLINKFLAGS@
 
-libcblas.la: libcblas.a libatlas.la
+cblas: libcblas.a @LTPREFIX@atlas@LTSUFFIX@
 	-$(RM) -r -f libcblas-obj
 	$(MKDIR) libcblas-obj
-	cd libcblas-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=CC --mode=link $(CC) @LIBTOOL_TYPE@ \
-	    -o $@ libcblas-obj/*.o \
+	cd libcblas-obj && $(AR) x ../$< && cd ..
+	@LTCLINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libcblas-obj/*.o \
 	    -latlas \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
-
+	    @LTLINKFLAGS@
 
-libptcblas.la: libptcblas.a libatlas.la
+ptcblas: libptcblas.a @LTPREFIX@atlas@LTSUFFIX@
 	-$(RM) -r -f libptcblas-obj
 	$(MKDIR) libptcblas-obj
-	cd libptcblas-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=CC --mode=link $(CC) @LIBTOOL_TYPE@ \
-	    -o $@ libptcblas-obj/*.o \
+	cd libptcblas-obj && $(AR) x ../$< && cd ..
+	@LTCLINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libptcblas-obj/*.o \
 	    @PTHREAD_LIB@ -latlas \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
+	    @LTLINKFLAGS@
 
-
-libf77blas.la: libf77blas.a libatlas.la
+f77blas: libf77blas.a @LTPREFIX@atlas@LTSUFFIX@
 	-$(RM) -r -f libf77blas-obj
 	$(MKDIR) libf77blas-obj
-	cd libf77blas-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=F77 --mode=link $(F77) @LIBTOOL_TYPE@ \
-	    -o $@ libf77blas-obj/*.o \
+	cd libf77blas-obj && $(AR) x ../$< && cd ..
+	@LTF77LINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libf77blas-obj/*.o \
 	    -latlas \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
+	    @LTLINKFLAGS@
 
-libptf77blas.la: libptf77blas.a libatlas.la
+ptf77blas: libptf77blas.a @LTPREFIX@atlas@LTSUFFIX@
 	-$(RM) -r -f libptf77blas-obj
 	$(MKDIR) libptf77blas-obj
-	cd libptf77blas-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=F77 --mode=link $(F77) @LIBTOOL_TYPE@ \
-	    -o $@ libptf77blas-obj/*.o \
+	cd libptf77blas-obj && $(AR) x ../$< && cd ..
+	@LTF77LINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libptf77blas-obj/*.o \
 	    @PTHREAD_LIB@ -latlas \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
+	    @LTLINKFLAGS@
 
-libf77refblas.la: libf77refblas.a
+f77refblas: libf77refblas.a
 	-$(RM) -r -f libf77refblas-obj
 	$(MKDIR) libf77refblas-obj
-	cd libf77refblas-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=F77 --mode=link $(F77) @LIBTOOL_TYPE@ \
-	    -o $@ libf77refblas-obj/*.o \
+	cd libf77refblas-obj && $(AR) x ../$< && cd ..
+	@LTF77LINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libf77refblas-obj/*.o \
 	    -latlas \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
+	    @LTLINKFLAGS@
 
-liblapack.la: liblapack.a libatlas.la libcblas.la libf77blas.la
+lapack: liblapack.a @LTPREFIX@atlas@LTSUFFIX@ @LTPREFIX@cblas@LTSUFFIX@ @LTPREFIX@f77blas@LTSUFFIX@
 	-$(RM) -r -f liblapack-obj
 	$(MKDIR) liblapack-obj
-	cd liblapack-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=F77 --mode=link $(F77) @LIBTOOL_TYPE@ \
-	    -o $@ liblapack-obj/*.o \
-	    -latlas -lcblas -lf77blas -lm \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
+	cd liblapack-obj && $(AR) x ../$< && cd ..
+	@LTF77LINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ liblapack-obj/*.o \
+	    -lcblas -lf77blas -latlas -lm \
+	    @LTLINKFLAGS@
 
-libptlapack.la: libptlapack.a libatlas.la libptcblas.la libptf77blas.la
+ptlapack: libptlapack.a @LTPREFIX@atlas@LTSUFFIX@ @LTPREFIX@ptcblas@LTSUFFIX@ @LTPREFIX@ptf77blas@LTSUFFIX@
 	-$(RM) -r -f libptlapack-obj
 	$(MKDIR) libptlapack-obj
-	cd libptlapack-obj && $(AR) x ../$<
-	@LIBTOOL@ --tag=F77 --mode=link $(F77) @LIBTOOL_TYPE@ \
-	    -o $@ libptlapack-obj/*.o \
-	    @PTHREAD_LIB@ -latlas -lptcblas -lptf77blas -lm \
-	    -rpath @libdir@ -version-info $(SO_VERSION)
-
+	cd libptlapack-obj && $(AR) x ../$< && cd ..
+	@LTF77LINK@ \
+	    -o @LTPREFIX@$@@LTSUFFIX@ libptlapack-obj/*.o \
+	    @PTHREAD_LIB@ -lptcblas -lptf77blas -latlas -lm \
+	    @LTLINKFLAGS@
 
-.PHONY: all all_serial all_parallel build install install_serial install_parallel clean
+.PHONY: all all_serial all_parallel build install install_serial install_parallel clean $(ATLAS_SERIAL_LIBS) $(ATLAS_PARALLEL_LIBS)

build/pkgs/atlas/patches/ATLAS-lib/configure.ac

@@ -1,6 +1,8 @@
 AC_INIT([ATLAS],[3.10.1])
 AM_INIT_AUTOMAKE(foreign)
 
+AC_CANONICAL_HOST
+
 LT_INIT
 
 AC_PROG_CC
@@ -20,4 +22,30 @@ AS_IF([test "x$enable_static" = "xyes"],
     [libtool_type=-shared])
 AC_SUBST(LIBTOOL_TYPE, [$libtool_type])
 
+case $host in
+     *-*-cygwin*)
+        LTPREFIX=cyg
+        LTSUFFIX=.dll
+        LTCLINK="\$(CC) -L. -shared"
+        LTF77LINK="\$(F77) -L. -shared"
+        LTLINKFLAGS="-Wl,--out-implib=lib\$@.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import"
+        LTINSTALL="\$(CP) \$(LTPREFIX)\$\${module}\$(LTSUFFIX) \$(bindir)/\$(LTPREFIX)\$\${module}\$(LTSUFFIX); \$(CP) lib\$\${module}.dll.a \$(libdir)/lib\$\${module}.dll.a"
+        ;;
+     *)
+        LTPREFIX=lib
+        LTSUFFIX=.la
+        LTCLINK="\$(LIBTOOL) --tag=CC --mode=link \$(CC) \$(LIBTOOL_FLAG)"
+        LTF77LINK="\$(LIBTOOL) --tag=F77 --mode=link \$(F77) \$(LIBTOOL_FLAG)"
+        LTLINKFLAGS="-rpath \$(libdir) -version-info \$(SO_VERSION)"
+        LTINSTALL="\$(LIBTOOL) --mode=install \$(INSTALL) -c \$(LTPREFIX)\$\${module}\$(LTSUFFIX) \$(libdir)/\$(LTPREFIX)\$\${module}\$(LTSUFFIX)"
+        ;;
+esac
+
+AC_SUBST(LTPREFIX)
+AC_SUBST(LTSUFFIX)
+AC_SUBST(LTCLINK)
+AC_SUBST(LTF77LINK)
+AC_SUBST(LTLINKFLAGS)
+AC_SUBST(LTINSTALL)
+
 AC_OUTPUT

build/pkgs/atlas/spkg-check

@@ -4,26 +4,23 @@
 ### Sanity check
 ######################################################################
 
-if [ "$SAGE_LOCAL" = "" ]; then
-    echo "SAGE_LOCAL undefined ... exiting"
-    echo "Maybe run sage -sh?"
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
     exit 1
 fi
 
 ######################################################################
 ### Skip building ATLAS on specific systems
 ######################################################################
 
-if [ `uname` = "CYGWIN" ]; then
+if [ "$UNAME" = "Darwin" -a -z "$SAGE_ATLAS_ARCH" ]; then
+    echo "System-wide accelerate framework is used on Darwin; skipping ATLAS test suite."
     exit 0
 fi
 
-if [ `uname` = "Darwin" ]; then
-    exit 0
-fi
-
-if [ "x$SAGE_ATLAS_LIB" != "x" ]; then
-    echo "SAGE_ATLAS_LIB is set to \"$SAGE_ATLAS_LIB\"; skipping the test suite."
+if [ ! -z "$SAGE_ATLAS_LIB" ]; then
+    echo "SAGE_ATLAS_LIB is set to \"$SAGE_ATLAS_LIB\"; skipping ATLAS test suite."
     exit 0
 fi
 
@@ -35,32 +32,28 @@ fi
 make_check()
 {
     # make sure everything builds correctly
-    cd ATLAS-build
-    make check
-        if [ $? -ne 0 ]; then
-            echo "An error occurred when running the ATLAS self-tests."
-            exit 1
-        else
-            echo "The ATLAS self-tests successfully passed."
-        fi
-    cd ..
+    $MAKE check
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: The ATLAS self-tests failed."
+        exit 1
+    else
+        echo "The ATLAS self-tests successfully passed."
+    fi
 }
 
 
 make_time()
 {
     # collect some timings
-    cd ATLAS-build
-    make time
-        if [ $? -ne 0 ]; then
-            echo "The ATLAS timing data failed to be collected."
-            exit 1
-        else
-            echo "The ATLAS timing data was successfully collected."
-        fi
-    cd ..
+    $MAKE time
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: The ATLAS timing data failed to be collected."
+        exit 1
+    else
+        echo "The ATLAS timing data was successfully collected."
+    fi
 }
 
-
+cd src/ATLAS-build
 make_check
 make_time

build/pkgs/atlas/spkg-install

@@ -25,7 +25,7 @@ PATCH_DIR = os.path.join(conf['SPKG_DIR'], 'patches')
 LAPACK_TARFILE = os.path.join(conf['SPKG_DIR'], 'src', 'lapack-3.4.2.tar')
 
 # temporary directory to build everything in
-BUILD_DIR = os.path.join(conf['SPKG_DIR'], 'ATLAS-build')
+BUILD_DIR = os.path.join(conf['SPKG_DIR'], 'src', 'ATLAS-build')
 
 # the shared library autotools stub project
 BUILD_LIB_DIR = os.path.join(conf['SPKG_DIR'], 'src', 'ATLAS-lib')
@@ -66,27 +66,12 @@ def assert_success(rc, good=None, bad=None):
 ### Skip building ATLAS on specific systems
 ######################################################################
 
-# On Cygwin we simply require that the system-wide lapack is installed.
-# This includes BLAS and LAPACK and is enough to build the rest of Sage.
-if conf['CYGWIN?'] and not os.environ.has_key('SAGE_ATLAS_ARCH'):
-    libraries = ['/usr/lib/libblas.dll.a', '/usr/lib/liblapack.dll.a']
-    for lib in libraries:
-        if not os.path.exists(lib):
-            print '*'*75
-            print 'Could not locate required file: "' + lib + '".'
-            print 'On Cygwin you must install the following standard LAPACK Cygwin packages'
-            print 'via the Cygwin setup.exe program in the "Math" category:'
-            print '* lapack,'
-            print '* liblapack-devel.'
-            print 'Alternatively you can try building your own ATLAS by setting'
-            print 'SAGE_ATLAS_ARCH to something sensible although that is not'
-            print 'officially supported.'
-            print '*'*75
-            sys.exit(1)
-    for lib in libraries:
-        cp(lib, os.path.join(conf['SAGE_LOCAL'], 'lib'))
-    sys.exit(0)
-
+# On Cygwin, we used to require that the system-wide lapack packages were
+# installed (this included the lapack-devel and lapack packages).
+# These packages indeed include BLAS and LAPACK and are enough to build
+# the rest of Sage, whereas building ATLAS was problematic.
+# For the record, the corresponding files to symlink from the system-wide
+# packages are: '/usr/lib/libblas.dll.a' and  '/usr/lib/liblapack.dll.a'.
 
 if conf['Darwin?'] and not os.environ.has_key('SAGE_ATLAS_ARCH'):
     print 'Skipping build of ATLAS on OS X, using system library instead.'
@@ -107,8 +92,12 @@ if conf['Darwin?'] and not os.environ.has_key('SAGE_ATLAS_ARCH'):
 
 if os.environ.has_key('SAGE_ATLAS_LIB'):
     ATLAS_LIB = os.environ['SAGE_ATLAS_LIB']
-    libraries = ['libatlas', 'liblapack', 'libcblas', 'libf77blas']
-    libraries_optional = ['libptcblas', 'libptf77blas']
+    if conf['CYGWIN?']:
+        libraries = ['libblas', 'liblapack']
+        libraries_optional = []
+    else:
+        libraries = ['libatlas', 'liblapack', 'libcblas', 'libf77blas']
+        libraries_optional = ['libptcblas', 'libptf77blas']
 
     def is_atlas_lib_path(path):
         if path is None:
@@ -164,7 +153,7 @@ if os.environ.has_key('SAGE_ATLAS_LIB'):
         for fname in filenames:
             source = os.path.join(ATLAS_LIB, fname)
             destination = os.path.join(SAGE_LOCAL_LIB, fname)
-            print 'Symlinking '+source+' -> '+destination
+            print 'Symlinking '+destination+' -> '+source
             try:
                 os.remove(destination)
             except OSError:
@@ -293,7 +282,7 @@ def configure(arch=None, isa_ext=None):
     else:
         CCbin, CCopt = CC, ''
 
-    cmd = '../src/ATLAS/configure'
+    cmd = '../ATLAS/configure'
     cmd += ' --prefix=' + conf['SAGE_LOCAL']
     cmd += ' --with-netlib-lapack-tarfile=' + LAPACK_TARFILE
     cmd += ' --cc="' + CC + '"'
@@ -563,7 +552,7 @@ if rc!=0:
         INSTALL_STATIC_LIBRARIES = True
     else:
         print 'Finished building serial shared ATLAS library (libtool).'
-    have_serial_libs = True
+        have_serial_libs = True
 else:
     have_parallel_libs = True