Sage FreeBSD 7.x/amd64 and 8-current/amd64 build notes for Sage 4.1
Note that this page is under construction and currently incomplete
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 - 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.
Building Sage
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.
On FreeBSD 7.x
- Unpack sage-4.1.rc1.tar
cd sage-4.1.rc1
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_LIB=/usr/local/lib/gcc-43/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
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
- numpy on FreeBSD expects atlas to build threaded libraries (eg libatlas_r) [and possibly static, this isn't clear]. The current atlas build is not creating the expected libraries. This is still under investigation.
- Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific)
numpy error from last point above:
atlas_blas_info:
libraries f77blas,cblas,atlas_r not found in /home/pjeremy/sage-3.4/local/lib
NOT AVAILABLE
/home/pjeremy/sage-3.4/spkg/build/numpy-1.2.0.p0/src/numpy/distutils/system_info.py:1340: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
...
atlas_info:
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
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/home/pjeremy/sage-3.4/spkg/build/numpy-1.2.0.p0/src/numpy/distutils/system_info.py:1247: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
...
/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'
...
sage_scripts-4.1.rc1
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.
On FreeBSD 8.x
cd sage-3.4
mkdir -p local/bin spkg/patches
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 # specifying SAGE_FORTRAN isn't sufficient
Unpack the attached shar archive: sage-3.4.shar
patch < spkg/patches/base.patch
CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib gmake