Sage FreeBSD 8.x build notes for Sage 4.5

Note that this is a work-in-progress and not currently complete. If you wish to assist, please contact me via [email protected]

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, though additional work will be required on cephes.

• 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

• Run Sage

  • LD_LIBRARY_PATH=/usr/local/lib/gcc45 sage

Note that the LD_LIBRARY_PATH is needed to work around 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

Sage currently builds on FreeBSD but consistently reports a segmentation violation on exit (though it seems to run). Running sage -gdb gives:

$ LD_LIBRARY_PATH=/usr/local/lib/gcc45  ./sage -gdb
----------------------------------------------------------------------
| Sage Version 4.5, Release Date: 2010-07-16                         |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
/mnt/sage-4.5/local/bin/sage-ipython
GNU gdb 6.6 [GDB v6.6 for FreeBSD]
Copyright (C) 2006 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-portbld-freebsd8.1"...
Python 2.6.4 (r264:75706, Jul 27 2010, 07:47:11)
[GCC 4.5.1 20100722 (prerelease)] on freebsd8
Type "help", "copyright", "credits" or "license" for more information.
sage:
Exiting Sage (CPU time 0m0.15s, Wall time 1m21.93s).

Program received signal SIGSEGV, Segmentation fault.
0x000000081fe4b861 in ~Commentator (this=0x81fe32c60) at commentator.C:59
59                                      err = -err;
Current language:  auto; currently c++
(gdb) where
#0  0x000000081fe4b861 in ~Commentator (this=0x81fe32c60) at commentator.C:59
#1  0x0000000800f252a6 in __cxa_finalize () from /lib/libc.so.7
#2  0x0000000800ed20f7 in exit () from /lib/libc.so.7
#3  0x00000008008514cf in Py_Exit (sts=0) at Python/pythonrun.c:1618
#4  0x00000008008515d9 in handle_system_exit () at Python/pythonrun.c:1618
#5  0x000000000037bc40 in ?? ()
#6  0x000000080146b998 in ?? ()
#7  0x0000000000000000 in ?? ()
(gdb) p *this
$1 = {_vptr.Commentator = 0x82005a3b0,
  cnull = {<std::basic_ios<char, std::char_traits<char> >> = {<std::ios_base> = {_vptr.ios_base = 0x82005a3b0, static boolalpha = std::_S_boolalpha,
        static dec = std::_S_dec, static fixed = std::_S_fixed,
        static hex = std::_S_hex, static internal = std::_S_internal,
        static left = std::_S_left, static oct = std::_S_oct,
        static right = 4294967168, static scientific = std::_S_scientific,
        static showbase = std::_S_showbase,
        static showpoint = std::_S_showpoint,
        static showpos = std::_S_showpos, static skipws = std::_S_skipws,
        static unitbuf = std::_S_unitbuf,
        static uppercase = std::_S_uppercase, static adjustfield = 4294967216,
        static basefield = std::_S_basefield,
        static floatfield = std::_S_floatfield,
        static badbit = std::_S_badbit, static eofbit = std::_S_eofbit,
        static failbit = std::_S_failbit, static goodbit = std::_S_goodbit,
        static app = std::_S_app, static ate = std::_S_ate,
        static binary = std::_S_bin, static in = std::_S_in,
        static out = std::_S_out, static trunc = std::_S_trunc,
        static beg = std::_S_beg, static cur = std::_S_cur,
        static end = std::_S_end, _M_precision = 34470410560, _M_width = 6,
        _M_flags = 0, _M_exception = std::_S_goodbit,
        _M_streambuf_state = 4098, _M_callbacks = 0x0, _M_word_zero = {
          _M_pword = 0x0, _M_iword = 0}, _M_local_word = {{_M_pword = 0x0,
            _M_iword = 0}, {_M_pword = 0x0, _M_iword = 0}, {_M_pword = 0x0,
            _M_iword = 0}, {_M_pword = 0x0, _M_iword = 0}, {_M_pword = 0x0,
            _M_iword = 0}, {_M_pword = 0x0, _M_iword = 0}, {_M_pword = 0x0,
            _M_iword = 0}, {_M_pword = 0x0, _M_iword = 0}}, _M_word_size = 0,
        _M_word = 0x8, _M_ios_locale = {static none = 0, static ctype = 1,
          static numeric = 2, static collate = 4, static time = 8,
          static monetary = 16, static messages = 32, static all = 63,
          _M_impl = 0x81fe32ca8, static _S_classic = 0x806993920,
          static _S_global = 0x806993920, static _S_categories = 0x806987ec0,
          static _S_once = {state = 1, mutex = 0x0}} }, _M_tie = 0x806993920,
      _M_fill = 0 '\0', _M_fill_init = false, _M_streambuf = 0x0,
      _M_ctype = 0x804dc6d40, _M_num_put = 0x8069926e0,
      _M_num_get = 0x806992a00}, _vptr.basic_ostream = 0x80698b940},
  _activities = {
    c = {<std::_Deque_base<LinBox::Commentator::Activity*, std::allocator<LinBox::Commentator::Activity*> >> = {
        _M_impl = {<std::allocator<LinBox::Commentator::Activity*>> = {<__gnu_cxx::new_allocator<LinBox::Commentator::Activity*>> = {<No data fields>}, <No data fields>}, _M_map = 0x0, _M_map_size = 1, _M_start = {_M_cur = 0x8012b38b0,
            _M_first = 0xffffffff00000001, _M_last = 0x8012b38b8,
            _M_node = 0x0}, _M_finish = {_M_cur = 0x0, _M_first = 0x0,
            _M_last = 0x0, _M_node = 0x0}} }, <No data fields>}},
  _messageClasses = {_M_t = {
      _M_impl = {<std::allocator<std::_Rb_tree_node<std::pair<const char* const, LinBox::MessageClass*> > >> = {<__gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<const char* const, LinBox::MessageClass*> > >> = {<No data fields>}, <No data fields>}, _M_key_compare = {<No data fields>}, _M_header = {
          _M_color = std::_S_red, _M_parent = 0x0, _M_left = 0x0,
          _M_right = 0x0}, _M_node_count = 0}} },
  _estimationMethod = LinBox::Commentator::BEST_ESTIMATE,
  _format = LinBox::Commentator::OUTPUT_CONSOLE, _show_timing = false,
  _show_progress = false, _show_est_time = false, _last_line_len = 0,
  _report = {<std::basic_ostream<char, std::char_traits<char> >> = {<error reading variable>, _iteration_str = {static npos = 18446744073709551615,
    _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, _M_p = 0x0}} }
(gdb)

spkg/build/linbox-1.1.6.p3/src/linbox/util/commentator.C line 59 is in Linbox:nroot() which is not referenced from Commentator~ so further investigation into this error is required.

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.

atlas-3.8.3.p12

liblapack.so includes undefined references to __powidf2 and __powisf2, which are defined in libgcc (no other Sage shared libraries appear to rely on libgcc helper functions). Unfortunately, for reasons I don't fully understand, linking liblapack.so against libgcc.a fails, even when building a normal executable. One example of the resultant error occurs when configuring numpy:

gcc _configtest.o -L/tank/obj/sage/sage-4.5/local/lib -llapack -lf77blas -lcblas -latlas -o _configtest
/usr/local/bin/ld: _configtest: hidden symbol `__powidf2' in /usr/local/lib/gcc45/gcc/x86_64-portbld-freebsd8.1/4.5.1/libgcc.a(_powidf2.o) is referenced by DSO
/usr/local/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
/usr/local/bin/ld: _configtest: hidden symbol `__powidf2' in /usr/local/lib/gcc45/gcc/x86_64-portbld-freebsd8.1/4.5.1/libgcc.a(_powidf2.o) is referenced by DSO
/usr/local/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255

The fix is to add a dependency on libgcc_s.so when (re-)building liblapack.so in make_correct_shared.sh.

Trac ticket: #9600

cephes-2.8

FreeBSD does not yet include a full C99 libm so cephes is also used on FreeBSD. The overall approach used on the FreeBSD is for cephes to create complex.h, math.h and libm.so which are installed under $SAGE_LOCAL and contain the missing C99 functions then fall back to the FreeBSD base versions for functions existing in FreeBSD. This mean that references to <math.h>, <complex.h> or -lm will appear to reference a complete set of C99 functions, split over two physical locations.

Other changes:

• C99 defines lgammal as the long double natural log of the absolute value of the gamma function, with the sign of the result returned in the int variable signgam. cephes uses lgaml and sgnnaml (though it's documented as sgngam) instead. Rename the lgaml to lgammal and sgnnaml to signgam.

• C99 defines tgammal as the long double value of the gamma function, which does not affect signgam. cephes uses gammal, which does affect sgnnaml. Rename the gammal to tgammal and localize the use of signgam within tgammal.

• Enable '-e' option on spkg-install to catch errors

(tgammal and lgammal are required by sage/symbolic/pynac.cpp)

Areas still needing work:

• cephes-2.8 is known to fail a number of its self-tests (when they are enabled).
• Missing self-test sources need to be re-added and an appropriate test suite created. Possibly mpfr could be used as a reference library.

• The lgammal, signgam and tgammal changes above need to be reflected both in the self-test sources and in the double and float versions of those functions.

• Based on a standalone test of cephes-2.8 on FreeBSD-7.1, the following C99 functions are currently missing: carg, cargf, cargl, cproj, cprojf, cprojl, fmodl, llrintl, logbl, lrintl, nan, nanf, nanl, nearbyintl, remainderl, remquol, rintl and tgammaf.

Trac ticket: #9543

cvxopt-0.9.p8

Needs patch to ensure that $SAGE_LOCAL/include is included in the search path to correctly pick up the C99 functions that do not exist in the FreeBSD base system (see comments on cephes).

Trac ticket: #9601

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

gap-4.4.12.p4

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: #9602

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.

• $SAGE_LOCAL/include needs to be added to the search path to pick up the correct <math.h> (see cephes).

Trac ticket: #7831

pari-2.3.5.p1

The Configure script does not detect log2, which it should. (This appears to be an intrinsic bug because it doesn't detect either exp2 or log2 on Linux). The top line of spkg-install is also corrupt.

These are left for now because #9343 includes a new pari - which I have not checked yet.

sage-4.5

• 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

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.

scipy-0.7.p5

scipy uses local/lib/python2.5/site-packages/numpy/distutils/fcompiler/gnu.py to locate a Fortran compiler. This code only looks for g77, f77, gfortran and f95. Whilst it has some patches to look in sage_fortran, this does not appear to work for scipy, at least on FreeBSD. The work-around is to create a symlink to the actual Fortran compiler in local/bin, otherwise the scipy build fails with:

building 'mach' library
using additional config_fc from setup script for fortran compiler: {'noopt': ('scipy/integrate/setup.py', 1)}
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
Traceback (most recent call last):
  File "setup.py", line 92, in <module>
    setup_package()
  File "setup.py", line 84, in setup_package
    configuration=configuration )
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/tmp/sage-4.5/local/lib/python/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/tmp/sage-4.5/local/lib/python/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/tmp/sage-4.5/local/lib/python/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/tmp/sage-4.5/local/lib/python/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
  File "/tmp/sage-4.5/local/lib/python/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/tmp/sage-4.5/local/lib/python/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/command/build_clib.py", line 93, in run
    self.build_libraries(self.libraries)
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/command/build_clib.py", line 104, in build_libraries
    self.build_a_library(build_info, lib_name, libraries)
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/command/build_clib.py", line 157, in build_a_library
    fcompiler.customize(base_config_fc)
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/fcompiler/__init__.py", line 449, in customize
    self.find_executables()
  File "/tmp/sage-4.5/local/lib/python2.6/site-packages/numpy/distutils/fcompiler/__init__.py", line 342, in find_executables
    raise CompilerNotFound('%s: f90 nor f77' % ctype)
numpy.distutils.fcompiler.CompilerNotFound: gnu95: f90 nor f77
Error building scipy.

Further investigation is required to identify the underlying cause (since there doesn't appear to be a problem on Linux).

Trac ticket: #?

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