Differences between revisions 6 and 7
Revision 6 as of 2010-07-18 20:26:24
Size: 25196
Editor: PeterJeremy
Comment: Add trac tickets for cepes and flintqs
Revision 7 as of 2010-07-22 12:00:03
Size: 25398
Editor: PeterJeremy
Comment: Note that cephes port to FreeBSD will provide functions missing from sage-4.5
Deletions are marked like this. Additions are marked like this.
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 * 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 on older versions of FreeBSD.
 * 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.
 * 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 on older versions of FreeBSD. This will be removed once the cephes integration is complete.
 * 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. This will be removed once the cephes integration is complete.
Line 304: Line 304:
 * `sage/symbolic/pynac.cpp` fails to compile because FreeBSD libm is mostly missing long double functions - specifically tgammal() and lgammal() in this case.  * `sage/symbolic/pynac.cpp` fails to compile because FreeBSD libm is mostly missing long double functions - specifically tgammal() and lgammal() in this case.  This is being resolved by integrating cephes into the FreeBSD build of sage.

Sage FreeBSD 8.x build notes for Sage 4.5

Note that this is a work-in-progress and not currently complete

Contents

Overall build environment differences

  • sh and /bin/sh are a POSIX shell, rather than bash.

  • make is the BSD make, not GNU make

Preparatory work

  • Install ports/shells/bash or ports/shells/bash3 (I used 4.1.7)
  • Install ports/devel/gmake
  • Install ports/lang/gcc45 - 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.

Building Sage

On FreeBSD 8.x

FreeBSD 7.x hasn't been tested with Sage 4.5 but is expected to work.

  • Unpack sage-4.5.tar
  • cd sage-4.5

  • Unpack sage-4.5.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/gfortran45 local/bin/gfortran

    • Various patches as described below into spkg/patches

  • Build Sage
    • LD_LIBRARY_PATH=/usr/local/lib/gcc45 SAGE_PORT=yes SAGE_FORTRAN=/usr/local/bin/gfortran45 SAGE_FORTRAN_LIB=/usr/local/lib/gcc45/libgfortran.so gmake

Note that the LD_LIBRARY_PATH is needed to work arounf configuration errors in the FreeBSD port of gcc45 - 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.

Current Status

Currently, the following tests fail on FreeBSD 8.1-PRERELEASE/amd64. Full logs at sage-4.4.4.freebsd8.1-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

base.patch

  • 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.

cephes-2.8

  • FreeBSD does not yet include a full C99 libm so enable cephes on FreeBSD.
  • Correct error in the patched c9x-complex/makefile that refers to non-existent test sources.
  • Enable '-e' option on spkg-install to catch errors

Trac ticket: #9543

flintqs-20070817.p5

TonelliShanks.h references int32_t but does not directly include <stdint.h>. On FreeBSD using gcc45 (but not the base gcc), this causes compilation to fail with:

g++ -ansi -c TonelliShanks.cpp -o TonelliShanks.o -I/tank/obj/sage/sage-4.5/local/include -Wall -Wno-sign-compare -fomit-frame-pointer -O2
In file included from TonelliShanks.cpp:31:0:
TonelliShanks.h:41:8: error: 'int32_t' does not name a type
TonelliShanks.h:43:51: error: 'int32_t' has not been declared
TonelliShanks.cpp:67:1: error: 'int32_t' does not name a type
TonelliShanks.cpp:136:54: error: 'int32_t' has not been declared
TonelliShanks.cpp: In function 'void sqrtmodpk(__mpz_struct*, __mpz_struct*, __mpz_struct*, __mpz_struct*, int)':
TonelliShanks.cpp:140:11: error: 'int32_t' was not declared in this scope
TonelliShanks.cpp:140:19: error: expected ';' before 'i'
TonelliShanks.cpp:140:25: error: 'i' was not declared in this scope
make[2]: *** [TonelliShanks.o] Error 1
make[2]: Leaving directory `/tank/obj/sage/sage-4.5/spkg/build/flintqs-20070817.p5/src'
Error building William Hart's Quadratic Sieve

As a work-around, make TonelliShanks.h idempotent on FreeBSD (it probably should be on all architectures but making the patch FreeBSD-specific simplifies testing).

Trac ticket: #9545

matplotlib-0.99.3

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-4.4.4/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-4.4.4/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'

Trac #5873 Reported upstream as https://sourceforge.net/tracker/?func=detail&aid=3031051&group_id=80706&atid=560722

numpy-1.3.0.p3

  • __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

sage-4.5

  • 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 on older versions of FreeBSD. This will be removed once the cephes integration is complete.

  • 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. This will be removed once the cephes integration is complete.
  • 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. This is being resolved by integrating cephes into the FreeBSD build of sage.

Trac ticket: #?

sage_scripts-4.5

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.

singular-3.1.0.4.p7

By default, you get the following, which is corrected by the patch to singuname.sh:

make[2]: Entering directory `/home/peter/sage/sage-4.4.4/spkg/build/singular-3-1-0-4-20090818.p2/src'
make[2]: *** No rule to make target `distclean'.  Stop.
make[2]: Leaving directory `/home/peter/sage/sage-4.4.4/spkg/build/singular-3-1-0-4-20090818.p2/src'
rm: /home/peter/sage/sage-4.4.4/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