port Sage to FreeBSD 11

[dimpase]

Please see #26249 for the followup (for FreeBSD 12).

FreeBSD as of version 10 uses clang by default, and is closer to OSX in other ways too, so it would be a good free testing ground for the use of clang with Sage.

preparing tools:

• install gcc6 and create fake gfortran by making a link to gfortran6
• make sure as is new enough: pkg install binutils will install as version 2.28, and you need it to come first in PATH (i.e. make sure that /usr/local/bin comes before /usr/bin).
• remove stale /lib/libgcc_s.so.1 and point it to the right one in /usr/local/lib/gcc6/ (perhaps there is a better way...)
• install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
• make sure /bin/sh is actually bash
• install pkgconf (FreeBSD's replacement of pkg-config)
• install wget (needed for AtlasRep GAP package).
• install icu (needed for R)

building Sage itself

starting from a clean git repo:

export CFLAGS="-fPIC"
export CXXFLAGS="-fPIC"
export LDFLAGS="-L/usr/local/lib -Wl,--add-needed -lm"
./configure CC=cc CXX=c++  #(this is clang 3.8.0 a.t.m.)
MAKE="make -j7" make build
MAKE="make -j4" make # building docs is very memory-hungry

HISTORICAL: Sage itself:

• hack configure.ac to make freebsd allowed platform
• deal with cephes' complex.h conflicting with numpy - cephes' complex.h conflicts with a numpy header on FreeBSD #22786
• gf2x: only builds with SAGE_FAT_BINARY on
• upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline (see update sqlite to version 3.17 #22687)
• flint: remove "-ascii -pedantic" flags from CFLAGS in configure
• libraries (libgap, cddlib, etc) need -fPIC for CFLAGS (so we build with CC="cc -fPIC -pipe" ; (-pipe is probably not really needed)) - see on clang libgap needs -fPIC #22784
• but gap cannot be built with CC="cc -fPIC -pipe", as it does something weird in ./configure, setting BASECC to be cc, and generating broken Makefile (with -fPIC and -pipe on two separate lines); so build gap with CC=cc
• giac needs CFLAGS="-I/usr/local/include" to find libintl.h and LDFLAGS="-L/usr/local/lib -lintl" to link.
• either provide /bin/bash or fix this properly (get rid of /bin/bash #22689)
• Sage builds and runs, modulo linking issues with flint and arb, which can be fixed ad hoc by hand.
• deal with cephes' libm not pulling system's libm, unless some arcane linker flags are used (see comments below)
• old freebsd workaround for libgd removed in remove obsolete FreeBSD workaround in libgd #22785
• ...

Depends on #12426
Depends on #23700

CC: @sagetrac-stephen @kiwifb @jdemeyer @jpflori

Component: porting: BSD

Author: Dima Pasechnik

Branch/Commit: u/dimpase/fbsd-support @ 4aaeeb4

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/22679

[dimpase]

comment:6

cf my comments at
numpy/numpy#8530

for the need for /lib/libgcc_s.so.1 to be replaced.

Basically, gcc/gfortran and clang's toolchains are slightly incompatible; while workarounds are in place for OSX,
linking on freebsd makes it more or less mandatory.

[dimpase]

comment:9

one of internal giac tests fail (harmlessly, I hope):

< -sqrt(6)*I*sqrt(sqrt(13)+3),sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*sqrt(sqrt(13)-3),sqrt(6)*sqrt(sqrt(13)-3),0,
---
> sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*sqrt(sqrt(13)-3),sqrt(6)*sqrt(sqrt(13)-3),0,
FAIL: chk_fhan16

[dimpase]

Author: Dima Pasechnik

[dimpase]

Dependencies: #22687

[dimpase]

New commits:

a44a934	updating sqlite to version 3.17
a32b0c7	let Sage accept freebsd
3178fbc	remove -ascii -pedantic flags from configure
4691d92	allow clang++ and libc++ combo on freebsd
90234a3	using libintl from /usr/local/

[dimpase]

Commit: 90234a3

[dimpase]

Branch: u/dimpase/freebsd_experimental

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

df76ac2

temporary fix to mke building on freebsd work

[sagetrac-git]

Changed commit from 90234a3 to df76ac2

[sagetrac-git]

Changed commit from df76ac2 to f5a9b80

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

f5a9b80

disable cephes installation on freebsd version >= 10

[sagetrac-git]

Changed commit from f5a9b80 to 9b622a8

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

516f029	Upgraded to R 3.3.3
cbe9134	Merge branch 'public/r311' of git://trac.sagemath.org/sage into finalr
f029f66	This simple patch removes an overkill check in R's configure.
c8a0b1b	Merge branch 'public/r311' of trac.sagemath.org:sage into sqliteupdate
d0d5ca7	update fplll/fpylll to 5.1.0/0.2.4dev
9f702f3	Merge branch 'u/malb/22643-fplll-upgrade' of trac.sagemath.org:sage into sqliteupdate
1201132	LONG_LONG_MAX is an obsolete gnu-ism
276e658	R on freebsd needs this for libcurl
0c0c603	Write custom create_extension() for Cython
9b622a8	Merge branch 'u/jdemeyer/use_create_extension___from_cython' of trac.sagemath.org:sage into sqliteupdate

[dimpase]

comment:89

ticket description should be edited on an updated ticket page, duh...

[dimpase]

Changed dependencies from #12426, #23565 to #12426, #23565, #23700

[dimpase]

comment:90

The segfault in the bottom part of comment 87 remains the same if gc and libatomic_ops are rebuilt with threads disabled.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

eacd3d6	Merge branch 'develop' of trac.sagemath.org:sage into fbsdon81
6f17c02	Merge branch 'compiler' into clang-progress
ceb3bf5	conform to new packaging in place since 8.1.beta1
07bfc5a	Merge branch 'compiler' into clang-progress
d8cb828	Merge branch 'compiler' into clang-progress
0ec453b	Merge branch 'develop' into clang-progress
a7bf51f	Merge branch 'u/fbissey/clang-progress' of trac.sagemath.org:sage into fbsdon81

[sagetrac-git]

Changed commit from d04c9f7 to a7bf51f

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

f9ca589	Merge branch 'u/dimpase/gcupdate' of trac.sagemath.org:sage into gc76
e365c32	backported patch for FreeBSD support
c98c98c	Merge branch 'u/dimpase/gcupdate' of trac.sagemath.org:sage into fbsdon81
83815b2	Merge branch 'develop' into clang-progress
40d3214	Merge branch 'develop' into clang-progress
6902166	Simplify gfortran spkg-install a bit. Thanks to Jeroen Demeyer for the feedback on this.
afca2b6	no need to be so verbose about gfortran.
235c09e	Including upstream PR 29 to compile with xcode 9 until we have a new release.
48462ea	Merge branch 'eclib-xcode9' into clang-progress
4aaeeb4	Merge branch 'u/fbissey/clang-progress' of trac.sagemath.org:sage into fbsdon81

[sagetrac-git]

Changed commit from a7bf51f to 4aaeeb4

[dimpase]

comment:93

New code for RiemannSurface uses Voronoi from scipy. But the latter is broken on FreeBSD:

$ ./sage --python
Python 2.7.13 (default, Oct 11 2017, 17:41:18) 
[GCC 4.2.1 Compatible Clang 6.0.0 ] on freebsd11
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> points = np.array([[0, 0], [0, 1], [0, 2], [1, 0], [1, 1], [1, 2],[2, 0], [2, 1], [2, 2]])
>>> from scipy.spatial import Voronoi
>>> Voronoi(points)
Segmentation fault (core dumped)

(might be due to careless use of threading...)

Note that the previously used in Sage version of scipy 0.17.1, still works.

[dimpase]

comment:94

it turns out that scipy's Voronoi works with the system's Python 2.7.14, but not with Sage's one (there are BSD-only Python patches; trying them now).

[dimpase]

Changed dependencies from #12426, #23565, #23700 to #12426, #23700

[dimpase]

comment:96

Please see #26249 for a followup, for FreeBSD version 12, where things are considerably simpler.

[dimpase]

Reviewer: Dima Pasechnik