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Size: 27937
Comment: Create as copy of Sage 3.4 on FreeBSD page
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Comment: Note ecl needs POSIX semaphores
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| = Sage FreeBSD 7.x/amd64 and 8-current/amd64 build notes for Sage 3.4 = | = Sage FreeBSD 7.x and 8.x build notes for Sage 4.1 = Note that this page is under construction and currently incomplete. In particular, it still includes references to sage-3.4 in areas that have not been converted to sage-4.1. |
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| * Install ports/shells/bash or ports/shells/bash3 (I used 3.2.48) | * Install ports/shells/bash or ports/shells/bash3 (I used 4.0.24) |
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| * Install ports/lang/gcc43 - FreeBSD no longer ships with a Fortran compiler by default. I tried using g95 but ran into problems. | * Install ports/lang/gcc43 - FreeBSD no longer ships with a Fortran compiler by default. |
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| * Install ports/converters/libiconv - This may be optional but is definitely used if found It's likely there are other dependencies, I haven't tried building sage in a clean (tinderbox) environment. |
* 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. |
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| The Sage build chain automatically unpacks and builds each spkg, however in order to build on FreeBSD, a number of spkgs need patching. Rather than manually unpack, patch and repack each spkg, I have instead modified base/sage-spkg to automatically apply a local patch if it exists. |
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| * Unpack sage-3.4.tar * `cd sage-3.4` * Unpack [[attachment:sage-3.4.tgz]]. This installs the symlinks listed below as well as various patches. Note that the patches in spkg/patches.save are not currently applied. |
* Unpack sage-4.1.tar * `cd sage-4.1` * `mkdir -p local/bin spkg/patches` * 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/gcc43 local/bin/gcc` . `ln -s /usr/local/bin/g++43 local/bin/g++` . `ln -s /usr/local/bin/gfortran43 local/bin/gfortran` * Copy the patches listed below into `spkg/patches` |
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| . `SAGE_FORTRAN_LIB=/usr/local/lib/gcc-4.3.4/libgfortran.so gmake` | . `SAGE_FORTRAN=/usr/local/bin/gfortran43 SAGE_FORTRAN_LIB=/usr/local/lib/gcc43/libgfortran.so gmake` {{{#!wiki comment |
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| A number of the following patches change `make` to `${MAKE}` and/or use `gmake` instead of `make` on FreeBSD. The former is the recommended way to recursively invoke make to ensure that the subordinate make is the same as the parent make (and also ensures that the two make instances will communicate on things like '-jX'). The latter fixes date from early versions of this patchset before I decided to symlink GNU make as local/bin/make and should no longer be necessary (though I haven't verified this). | A number of the following patches change `make` to `${MAKE}`. This the recommended way to recursively invoke make to ensure that the subordinate make is the same as the parent make (and also ensures that the two make instances will communicate on things like '-jX'). |
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| * The patch to standard/deps ensures that bash is used. === atlas-3.8.3.p0 === |
/* * The patch to standard/deps ensures that bash is used. */ === atlas-3.8.3.p5 === [[attachment:atlas-3.8.3.p5.patch]] |
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| * 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/?func=detail&atid=379483&aid=2728930&group_id=23725 * Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific) {{{#!wiki comment |
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| * 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/?func=detail&atid=379483&aid=2728930&group_id=23725 * Building the `libclapack.so` should result in a `libclapack.so` being created. This appears to be a copy-and-paste error in atlas and has been reported as https://sourceforge.net/tracker/?func=detail&atid=379483&aid=2728935&group_id=23725 * Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific) |
* Building the `libclapack.so` should result in a `libclapack.so` being created. This appears to be a copy-and-paste error in atlas and has been reported as https://sourceforge.net/tracker/?func=detail&atid=379483&aid=2728935&group_id=23725 (Note that this is not relevant to sage as libclapack is not built or used). * numpy on FreeBSD expects atlas to build different and (according to the FreeBSD numpy port, static) threaded libraries: libatlas_r instead of libatlas and libalapack_r instead of liblapack. libatlas_r is built as part of the threaded version of atlas. libalapack_r is a FreeBSD special which explicitly combines all of liblapack from the atlas lapack build with the threaded atlas version of liblapack. |
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| libraries f77blas,cblas,atlas_r not found in /home/pjeremy/sage-3.4/local/lib | libraries f77blas,cblas,atlas_r not found in /usr/home/peter/sage-4.1/local/lib |
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| /home/pjeremy/sage-3.4/spkg/build/numpy-1.2.0.p0/src/numpy/distutils/system_info.py:1340: UserWarning: | /usr/home/peter/sage-4.1/spkg/build/numpy-1.3.0.p0/src/numpy/distutils/system_info.py:1383: UserWarning: |
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| libraries f77blas,cblas,atlas_r not found in /home/pjeremy/sage-3.4/local/lib libraries lapack_atlas not found in /home/pjeremy/sage-3.4/local/lib |
libraries f77blas,cblas,atlas_r not found in /usr/home/peter/sage-4.1/local/lib libraries lapack_atlas not found in /usr/home/peter/sage-4.1/local/lib |
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| /home/pjeremy/sage-3.4/spkg/build/numpy-1.2.0.p0/src/numpy/distutils/system_info.py:1247: UserWarning: | /usr/home/peter/sage-4.1/spkg/build/numpy-1.3.0.p0/src/numpy/distutils/system_info.py:1290: UserWarning: |
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| /home/pjeremy/sage-3.4/local/bin/gfortran -Wall build/temp.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/lapack_litemodule.o build/temp.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/python_xerbla.o -L/home/pjeremy/sage-3.4/local/lib -L/usr/local/lib/gcc-4.3.4/gcc/x86_64-portbld-freebsd7.0/4.3.4 -llapack -lblas -lgfortran -o build/lib.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/lapack_lite.so build/temp.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/lapack_litemodule.o(.text+0x41): In function `check_object': numpy/linalg/lapack_litemodule.c:103: undefined reference to `PyType_IsSubtype' build/temp.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/lapack_litemodule.o(.text+0x7b):numpy/linalg/lapack_litemodule.c:114: undefined reference to `PyErr_Format' build/temp.freebsd-7.0-STABLE-amd64-2.5/numpy/linalg/lapack_litemodule.o(.text+0xb7):numpy/linalg/lapack_litemodule.c:109: undefined reference to `PyErr_Format' ... }}} |
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=== matplotlib-0.98.5.3rc0-svn6910.p3 === |
}}} === matplotlib-0.98.5.3rc0-svn6910.p4 === |
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| Correctly pass `-fPIC` when building the shared library. Various fixes to handle correct fortran and library detection on FreeBSD. |
[[attachment:numpy-1.3.0.p0.patch]] * `__init__.py` needs a sage-specific patch to prefer sage_fortran on FreeBSD. * 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 [[http://mail.scipy.org/pipermail/numpy-discussion/2009-August/044523.html|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. {{{#!wiki comment |
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| 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/pjeremy/sage-3.4/local/lib -lgmp | 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/pjeremy/sage-3.4/local/lib -lgmp |
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=== r-2.6.1.p22 === Pass CFLAGS, CPPFLAGS and LDFLAGS from the environment into the build process. |
}}} === r-2.6.1.p23 === Pass CFLAGS, CPPFLAGS and LDFLAGS from the environment into the build process. This also corrects a typo in CPPFLAGS. |
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| gcc -shared -o libreadline.so.5 readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so | gcc -shared -o libreadline.so.5 readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so |
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| gcc -shared -o libhistory.so.5 history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so xmalloc.so | gcc -shared -o libhistory.so.5 history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so xmalloc.so |
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=== sage-3.4 === FreeBSD does not include a definition for log2() in libm. Use a simplistic definition of log2(x) = log2(e) * ln(x) === sage_scripts-3.4 === |
}}} === sage-4.1 === [[attachment:sage-4.1.patch]] * 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_scripts-4.1 === |
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Sage FreeBSD 7.x and 8.x build notes for Sage 4.1
Note that this page is under construction and currently incomplete. In particular, it still includes references to sage-3.4 in areas that have not been converted to sage-4.1.
Contents
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 4.0.24)
- Install ports/devel/gmake
- Install ports/lang/gcc43 - 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 7.x
- Unpack sage-4.1.tar
cd sage-4.1
mkdir -p local/bin spkg/patches
- 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/gcc43 local/bin/gcc
ln -s /usr/local/bin/g++43 local/bin/g++
ln -s /usr/local/bin/gfortran43 local/bin/gfortran
Copy the patches listed below into spkg/patches
- Build Sage
SAGE_FORTRAN=/usr/local/bin/gfortran43 SAGE_FORTRAN_LIB=/usr/local/lib/gcc43/libgfortran.so gmake
Current Status
Notes on spkgs and attached patches
A number of the following patches change make to ${MAKE}. This the recommended way to recursively invoke make to ensure that the subordinate make is the same as the parent make (and also ensures that the two make instances will communicate on things like '-jX').
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.p5
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/?func=detail&atid=379483&aid=2728930&group_id=23725
- Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific)
matplotlib-0.98.5.3rc0-svn6910.p4
Add hooks to ensure that the local Sage versions of dependencies are used by FreeBSD. Otherwise you get:
BUILDING MATPLOTLIB
matplotlib: 0.98.6svn
python: 2.5.2 (r252:60911, Apr 1 2009, 08:50:05) [GCC
4.3.4 20090326 (prerelease)]
platform: freebsd7
REQUIRED DEPENDENCIES
numpy: no
* You must install numpy 1.1 or later to build
* matplotlib.
Error building matplotlib package.Add support for FreeBSD later than 6.x. Otherwise you get :
REQUIRED DEPENDENCIES
Traceback (most recent call last):
File "setup.py", line 119, in <module>
if not check_for_numpy():
File "/home/pjeremy/sage-3.4/spkg/build/matplotlib-0.98.5.3rc0-svn6910.p3/src/setupext.py", line 499, in check_for_numpy
add_base_flags(module)
File "/home/pjeremy/sage-3.4/spkg/build/matplotlib-0.98.5.3rc0-svn6910.p3/src/setupext.py", line 320, in add_base_flags
[os.path.join(p, 'include') for p in basedir[sys.platform] ])
KeyError: 'freebsd7'
Error building matplotlib package.gcc4.3 (though not gcc4.2) appears to define putchar() in a way that breaks the putchar() definitions inside ttconv. I couldn't quickly identify what the underlying cause was so I took the easy way out and undef'd the offending putchar() macro.
Individual character bounding boxes in AFM files do not have to be integral so convert each bounding box to a list of floats, rather than a list of ints. This corrects a problem where most of the tests would fail with ValueError: invalid literal for int() with base 10: '539.621'.
All three sub-patches are in #5873
numpy-1.2.0.p0
__init__.py needs a sage-specific patch to prefer sage_fortran on FreeBSD.
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.
r-2.6.1.p23
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.
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.
sage-4.1
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_scripts-4.1
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.