Sage FreeBSD 8.x build notes for Sage 4.3
Note that this is a work-in-progress and not currently complete
Overall build environment differences
sh and /bin/sh are a POSIX shell, rather than bash.
make is the BSD make, not GNU make
- Install ports/shells/bash or ports/shells/bash3 (I used 4.0.24)
- Install ports/devel/gmake
- Install ports/lang/gcc44 - FreeBSD no longer ships with a Fortran compiler by default.
- Install ports/devel/autoconf262
- Install ports/converters/libiconv
Ensure POSIX semaphores are available. This is required for ecl (at least). These are not available by default before FreeBSD 7.3 or 8.0 and should be enabled by either kldload sem or building a kernel with options P1003_1B_SEMAPHORES. If they are not available, building ecl will fail with Bad system call.
It's possible there are other dependencies, I haven't tried building sage in a clean (tinderbox) environment.
On FreeBSD 8.x
FreeBSD 7.x hasn't been tested with Sage 4.3 but is expected to work.
- Unpack sage-4.3.tar
Unpack sage-4.3.patch which includes the following:
- Create symlinks to mask name differences.
ln -s /usr/local/bin/gmake local/bin/make
ln -s /usr/local/bin/bash local/bin/sh
ln -s /usr/local/bin/gfortran44 local/bin/gfortran
Various patches as described below into spkg/patches
- Build Sage
SAGE_PORT=yes SAGE_FORTRAN=/usr/local/bin/gfortran44 SAGE_FORTRAN_LIB=/usr/local/lib/gcc44/libgfortran.so gmake
Note that it's not currently possible to use gcc44/g++44 to build Sage - configuration errors in the FreeBSD port of gcc44 means that the wrong shared libraries get used if this is attempted. See http://www.freebsd.org/cgi/query-pr.cgi?pr=129518
The gmake to make symlink is necessary to compile (eg) eclib - which is documented as requiring GNU make, and has this symlink as a suggested workaround.
Currently, the following tests fail on FreeBSD 8.0-STABLE/amd64. Full logs at sage-4.3.freebsd8.0-amd64.test.log.
The actual failures indicate that the port still needs significant work and include:
- Failed coercions in coercion.rst
- python/site-packages/sage/rings/polynomial/pbori.so runtime linking against the wrong C++ library.
- Invalid polymonials reported by scheme.py
- FreeBSD memory usage patch is incomplete
Notes on spkgs and attached patches
- The patch to base/sage-spkg enables the local patching that the rest of the patches rely on. Note that this patch is not intended to be merged into sage but provides a convenient mechanism to apply local patches without requiring that the spkg files are locally re-rolled.
- The patch to standard/deps ensures that bash is used. By default, gmake will use /bin/sh to execute commands and the patched line sources local/bin/sage-env - which includes the bash'ism 'source' instead of '.'. Whilst that file begins with a #! line invoking bash, because it must be sourced, it will actually execute in the invoking shell.
Various fixes to make it compile on FreeBSD
FreeBSD uses an '_fbsd' suffix on the ELF format supported by ld - prevents ld: unrecognised emulation mode: elf_x86_64 error during atlas build. Reported upstream as https://sourceforge.net/tracker/index.php?func=detail&aid=2728930&group_id=23725&atid=379482
- Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific)
Trac ticket: #7827
FreeBSD uses the same invocation as Linux to build shared libraries. This patch is necessary to allow cliquer to build.
Trac ticket: #7824
Patches (mostly taken from the FreeBSD port) to make gap compile on FreeBSD 8.x. These patches should be optional on FreeBSD/7.x.
Trac ticket: #?
Chase shared library name difference on FreeBSD. Sage local patch. Otherwise the gnutls build fails similar to:
(cd /home/peter/sage/sage-4.3/spkg/build/gnutls-2.2.1.p4/src/libextra; /bin/sh ../libtool --tag=CC --mode=relink gcc -std=gnu99 -g -O2 -D_REENTRANT -D_THREAD_SAFE -pipe -I/home/peter/sage/sage-4.3/local/include -g -O2 -D_REENTRANT -D_THREAD_SAFE -Wno-pointer-sign -no-undefined -L../lib/.libs -L/home/peter/sage/sage-4.3/local/lib -lopencdk -L/usr/local/lib -L/usr/local/lib -lgcrypt -L/usr/local/lib -lgpg-error -L/usr/local/lib -lintl -L/usr/local/lib -liconv -L/home/peter/sage/sage-4.3/local/lib -lz -R/home/peter/sage/sage-4.3/local/lib -R/usr/local/lib -version-info 27:2:1 -o libgnutls-extra.la -rpath /home/peter/sage/sage-4.3/local/lib gnutls_extra.lo gnutls_openpgp.lo gnutls_ia.lo openpgp/libgnutls_openpgp.la ../lgl/liblgnu.la ../lib/libgnutls.la minilzo/libminilzo.la ) gcc -std=gnu99 -shared .libs/gnutls_extra.o .libs/gnutls_openpgp.o .libs/gnutls_ia.o -Wl,--whole-archive openpgp/.libs/libgnutls_openpgp.a ../lgl/.libs/liblgnu.a minilzo/.libs/libminilzo.a -Wl,--no-whole-archive -Wl,--rpath -Wl,/home/peter/sage/sage-4.3/local/lib -Wl,--rpath -Wl,/usr/local/lib -L/home/peter/sage/sage-4.3/spkg/build/gnutls-2.2.1.p4/src/lib/.libs -L/home/peter/sage/sage-4.3/local/lib -lopencdk -L/usr/local/lib -lz -lgcrypt -lintl -liconv -lgpg-error -lgnutls -Wl,-soname -Wl,libgnutls-extra.so.27 -o .libs/libgnutls-extra.so.27 /usr/bin/ld: /home/peter/sage/sage-4.3/local/lib/libgcrypt.a(libgcrypt_la-visibility.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC /home/peter/sage/sage-4.3/local/lib/libgcrypt.a: could not read symbols: Bad value libtool: install: error: relink `libgnutls-extra.la' with the above command before installing it *** Error code 1 Stop in /home/peter/sage/sage-4.3/spkg/build/gnutls-2.2.1.p4/src/libextra. *** Error code 1
Trac ticket: #7823
Add support for FreeBSD later than 6.x. Otherwise you get :
BUILDING MATPLOTLIB matplotlib: 0.99.1 python: 2.6.2 (r262:71600, Jan 3 2010, 12:58:40) [GCC 4.2.1 20070719 [FreeBSD]] platform: freebsd8 REQUIRED DEPENDENCIES Traceback (most recent call last): File "setup.py", line 123, in <module> if not check_for_numpy(): File "/home/peter/sage/sage-4.3/spkg/build/matplotlib-0.99.1.p2/src/setupext.py", line 506, in check_for_numpy add_base_flags(module) File "/home/peter/sage/sage-4.3/spkg/build/matplotlib-0.99.1.p2/src/setupext.py", line 327, in add_base_flags [os.path.join(p, 'include') for p in basedir[sys.platform] ]) KeyError: 'freebsd8'
__init__.py needs a sage-specific patch to prefer sage_fortran on FreeBSD. This is necessary to prevent matplotlib dying with:
BUILDING MATPLOTLIB matplotlib: 0.99.1 python: 2.6.2 (r262:71600, Jan 3 2010, 12:58:40) [GCC 4.2.1 20070719 [FreeBSD]] platform: freebsd8 REQUIRED DEPENDENCIES numpy: no * You must install numpy 1.1 or later to build * matplotlib.
By default, numpy references threaded atlas libraries, as well as a custom variant on the lapack library, on FreeBSD. The reasoning behind this is unclear - there is nothing in the numpy documentation to indicate whether a threaded or non-threaded atlas is needed and the publicly available SVN logs do not mention this code. A query to the numpy mailing list elicited a response that either threaded or non-threaded atlas can be used and suggesting that the special-casing for FreeBSD may be obsolete. By default, atlas is built non-threaded and r-2.6.1.p23 assumes a non-threaded atlas and fails when only the threaded libraries are installed. Based on this, the special casing for FreeBSD was removed from numpy - it now uses the same libraries irrespective of the host OS.
Trac ticket: #7831
FreeBSD refers to the x86_64 architecture under its original name of 'amd64' so use this as an alias for x86_64. The `-fPIC' fix is needed to correct:
gcc -o libpari-gmp.so.2.3.3 -shared -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -Wl,-shared,-soname=libpari-gmp.so.2 mp.o mpinl.o Flx.o Qfb.o RgX.o alglin1.o alglin2.o arith1.o arith2.o base1.o base2.o base3.o base4.o base5.o bibli1.o bibli2.o buch1.o buch2.o buch3.o buch4.o galconj.o gen1.o gen2.o gen3.o ifactor1.o perm.o polarit1.o polarit2.o polarit3.o rootpol.o subcyclo.o subgroup.o trans1.o trans2.o trans3.o anal.o compat.o default.o errmsg.o es.o init.o intnum.o members.o sumiter.o aprcl.o elldata.o elliptic.o galois.o groupid.o kummer.o mpqs.o nffactor.o part.o stark.o subfield.o thue.o -lc -lm -L/home/peter/sage/sage-4.3/local/lib -lgmp /usr/bin/ld: mp.o: relocation R_X86_64_32S can not be used when making a shared object; recompile with -fPIC mp.o: could not read symbols: Bad value *** Error code 1 Stop in /home/peter/sage/sage-4.3/spkg/build/pari-2.3.3.p5/src/Ofreebsd-amd64.
Trac ticket: #7825 Reported upstream as http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1022
Pass CFLAGS, CPPFLAGS and LDFLAGS from the environment into the build process. This also corrects a typo in CPPFLAGS.
Note that FreeBSD needs the path to libiconv to be explicitly specified. In theory, --with-libiconv-prefix should work but configure script is broken and ignores that path when looking for libiconv. Hard-wire /usr/local/include and /usr/local/lib via xxFLAGS. Without this change, you get:
checking iconv.h usability... no checking iconv.h presence... no checking for iconv.h... no checking for iconv... no checking for iconvlist... no configure: error: --with-iconv=yes (default) and a suitable iconv is not available Error configuring R.
Note that the X11 detection in spkg-install will not work anywhere other than Linux. This needs future work.
These patches are all local to Sage.
Trac ticket: #7833
readline-6.0.p1/spkg-install contains a typo in some FreeBSD-specific code, leading to the following error:
... /bin/sh ../support/shlib-install -O freebsd8.0 -d /home/peter/sage/sage-4.3/local/lib -b /home/peter/sage/sage-4.3/local/bin -i "/usr/bin/install -c -m 644" libreadline.so.6.0 install: you may need to run ldconfig make: Leaving directory `/home/peter/sage/sage-4.3/spkg/build/readline-6.0.p1/src/shlib' ln: SAGE_LOCAL/lib/libreadline.so: No such file or directory
The affected code is no longer required with readline-6.0 so delete it.
FreeBSD 3.x and later default to ELF, rather then a.out. A utility objformat(1) was temporarily introduced to enable third-party applications to determine te object format. This has now been deleted and code should assume ELF format if it does not exist. Explicitly linking libreadline against libtermcap is necessary to ensure that dependencies are picked up.
Trac ticket #7821
Compiling sage/combinat/partitions_c.cc fails because FreeBSD 7.x does not define sqrtl (it was introduced in FreeBSD 8.0). As a hackish workaround, define sqrtl to be sqrt.
- FreeBSD does not include a definition for log2() in libm. Use a simplistic definition of log2(x) = log2(e) * ln(x) - this is numerically poor but can be cleaned up later if required.
sage/groups/perm_gps/permgroup_element.c fails to compile because LONG_LONG_MAX is not available on FreeBSD. Some googling suggests that this macro is either a GNU extension or is deprecated in C99 and has been replaced by LLONG_MAX - I have not been able to find a direct reference but indirect references include the following links: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=168346#19 http://linux.softpedia.com/progChangelog/GNU-ddrescue-Changelog-6106.html http://clang.llvm.org/doxygen/limits_8h-source.html
Remaining issues include:
sage/symbolic/pynac.cpp fails to compile because FreeBSD libm is mostly missing long double functions - specifically tgammal() and lgammal() in this case.
Trac ticket: #?
Patch sage-spkg to apply local patches. This patch also disables deletion of the spkg/build/FOO temporary directories - which was useful during porting. This latter patch can be safely removed.
By default, you get the following, which is corrected by the patch to singuname.sh:
make: Entering directory `/home/peter/sage/sage-4.3/spkg/build/singular-3-1-0-4-20090818.p2/src' make: *** No rule to make target `distclean'. Stop. make: Leaving directory `/home/peter/sage/sage-4.3/spkg/build/singular-3-1-0-4-20090818.p2/src' rm: /home/peter/sage/sage-4.3/local/bin/Singular*: No such file or directory creating cache ./config.cache checking uname for singular... unknown configure: error: Unknown architecture: Check singuname.sh Unable to configure Singular.
Correct configure script for amd64 by patching the autoconf inputs and re-running autoconf. This corrects a problem where linking libsingular.so reports lots of undefined references to both internal om* functions and functions within libncurses.
Several other trivial fixes to support dynamic linking on FreeBSD/amd64.
Trac ticket: #7832