Port changes in PARI 2.3.5.p4 (#9722) to current 2.4.3

[leif]

Some fixes to PARI 2.3.5.p2 from #9722 had to be ported to the current ​NewPARI spkg. The new PARI 2.4.3.p5 spkg here contains some further changes (including some on Sage's side, mostly clean-up), while other issues have meanwhile been fixed upstream.

This package is intended to be tested with Sage 4.6.prealpha3. If you want to test it with Sage 4.5.3.*, apart from installing this spkg here, you also need to apply the sagelib and extcode patches from #9343. See ​the wiki page for detailed instructions. You can also download ​Sage 4.6.prealpha4, which includes the new package with all changes made here.

New (complete) spkg up at ​http://sage.math.washington.edu/home/jdemeyer/spkg/pari-2.4.3.svn-12577.p5.spkg

---

pari-2.4.3.svn-12577.p5 (Leif Leonhardy, Jeroen Demeyer, September 5th, 2010)

• Added patches to:
  • config/get_config_options:
    • Make invalid arguments to "--graphic" a "Configure" error (rather than potentially running into *compilation* errors later).
  • config/get_fltk: (see also/ported from #9722)
    • Add libstdc++ to the libraries (to support Fedora 13 et al.).
    • Also check the presence of the FLTK include directory to prevent compilation errors on broken installations.
  • config/get_X11: (see also/ported from #9722)
    • Also search */lib64/* directories when doing a 64-bit build.
    • Give more specific messages.
• Slightly extended existing patch to src/kernel/gmp/mp.c:
  • Allow disabling PARI's use of "GMP internals" by preprocessor directive (i.e. by adding "-DPARI_DONT_USE_GMP_INTERNALS" to CFLAGS). Brief explanation added.
• spkg-install:
  • Don't override user-specified CFLAGS (w.r.t. optimization, unless SAGE_DEBUG=yes).
  • Handle PARI_EXTRA_OPTS properly, and print informative messages (regarding graphics support for plotting).
  • Recognize SAGE_TUNE_PARI in addition to SAGE_TUNE_pari, and add "--tune" to PARI_EXTRA_OPTS if self-tuning was requested.
  • Clear/unset lots of (environment) variables used by PARI that might unintentionally get their values from user settings.
  • Quote *all* occurrences of SAGE_LOCAL (and some other expressions).
  • Use $UNAME instead of uname everywhere, use "elif ...".
  • *Always* use $MAKE (changed for "install-data").
  • Begin all error messages with "Error".
  • Removed useless tests of $? at end.
  • Some clean-up (typos, formatting); some comments, some messages added.
• spkg-check:
  • Use $MAKE instead of "make".
  • Don't override user-specified CFLAGS (w.r.t. optimization, unless SAGE_DEBUG=yes).
  • Begin error message with "Error".
  • Some clean-up.
• Slight corrections to SPKG.txt.
• Updated patches/README.txt, some cosmetic changes.
• Remove patch for config/Makefile.SH and add upstream fix instead in spkg-make.
• Add upstream fix for src/tune/tune.c which should fix tuning.
• Add -O0 to CFLAGS in spkg-make to speed up compiling (the output of the compiling is not used anyway).

[leif]

Apply to pari-2.4.3.svn-12577.p4.spkg. Note that added/changed files in patches/files are not included here!

[leif]

Diff of files in patches/files. Apply with patch -p1 inside spkg directory.

[leif]

I've only tested this with a couple of variations on parameters and installed libraries / graphics packages on Ubuntu 10.04 x86_64 and Fedora 13 x86.

Should work on other systems as well... ;-)

[drkirkby]

What do I need to do to test this - just download the package - do I need to patch anything else?

I've done:

• Downloaded and installed ​http://spkg-upload.googlecode.com/files/pari-2.4.3.svn-12577.p5.spkg
• Nothing else changed from 4.5.3.alpha2
• No attempt to tune code

drkirkby@hawk:~/5/sage-4.5.3.alpha2$ ./sage -b

----------------------------------------------------------
sage: Building and installing modified Sage library files.


Installing c_lib
gcc -o src/convert.pic.o -c -fPIC -I/export/home/drkirkby/5/sage-4.5.3.alpha2/local/include -I/export/home/drkirkby/5/sage-4.5.3.alpha2/local/include/python2.6 -I/export/home/drkirkby/5/sage-4.5.3.alpha2/local/include/NTL -Iinclude src/convert.c
g++ -o libcsage.so -shared src/convert.pic.o src/interrupt.pic.o src/mpn_pylong.pic.o src/mpz_pylong.pic.o src/mpz_longlong.pic.o src/stdsage.pic.o src/gmp_globals.pic.o src/ZZ_pylong.pic.o src/ntl_wrap.pic.o -L/export/home/drkirkby/5/sage-4.5.3.alpha2/local/lib -L/export/home/drkirkby/5/sage-4.5.3.alpha2/local/lib/python/config -lntl -lgmp -lpari -lpython2.6
Updating Cython code....
Execute 0 commands (using 0 threads)
Time to execute 0 commands: 0.0976297855377 seconds
Finished compiling Cython code (time = 3.07916307449 seconds)
running install
running build
running build_py
running build_ext
Total time spent compiling C/C++ extensions:  0.913223028183 seconds.
running install_lib
running install_egg_info
Removing /export/home/drkirkby/5/sage-4.5.3.alpha2/local/lib/python2.6/site-packages/sage-0.0.0-py2.6.egg-info
Writing /export/home/drkirkby/5/sage-4.5.3.alpha2/local/lib/python2.6/site-packages/sage-0.0.0-py2.6.egg-info

real	0m8.727s
user	0m1.339s
sys	0m0.727s
drkirkby@hawk:~/5/sage-4.5.3.alpha2$ make ptestlong
cd spkg && ./install all 2>&1 | tee -a ../install.log
make[1]: Entering directory `/export/home/drkirkby/5/sage-4.5.3.alpha2/spkg'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/export/home/drkirkby/5/sage-4.5.3.alpha2/spkg'

real	0m0.018s
user	0m0.003s
sys	0m0.003s
To install gap, gp, singular, etc., scripts
in a standard bin directory, start sage and
type something like
   sage: install_scripts('/usr/local/bin')
at the Sage command prompt.

To build the documentation, run
   make doc

Sage build/upgrade complete!
./sage -docbuild all html  2>&1 | tee -a dochtml.log
sphinx-build -b html -d /export/home/drkirkby/5/sage-4.5.3.alpha2/devel/sage/doc/output/doctrees/en/website    /export/home/drkirkby/5/sage-4.5.3.alpha2/devel/sage/doc/en/website /export/home/drkirkby/5/sage-4.5.3.alpha2/devel/sage/doc/output/html/en/website
  ***   bug in PARI/GP (Segmentation Fault), please report
^Cmake: *** [doc-html] Interrupt

IIRC, the changes from sage-4.5.3.alpha2 to sage-4.5.3.rc0 were just a few Solaris-specific changes which would not all all doc tests to pass, but were not need to actually get things working.

This is on an OpenSolaris (Xeon processor) machine. I've not tried on anything else.

I'm rather hoping I've forgot something - in which case you have time to review #9603 !

Dave

[jdemeyer]

Replying to drkirkby:

What do I need to do to test this - just download the package - do I need to patch anything else?

You also need to apply the sagelib and extcode patches from #9343. Or easier: download ​http://sage.math.washington.edu/home/jdemeyer/dist/sage-4.6.prealpha3.tar, install that and then install the new pari spkg.

[jdemeyer]

I have made a few small changes to the pari spkg and put the result at ​http://sage.math.washington.edu/home/jdemeyer/spkg/pari-2.4.3.svn-12577.p5.spkg (I kept the p5 version number).

[drkirkby]

Replying to jdemeyer:

Replying to drkirkby:

What do I need to do to test this - just download the package - do I need to patch anything else?

You also need to apply the sagelib and extcode patches from #9343. Or easier: download ​http://sage.math.washington.edu/home/jdemeyer/dist/sage-4.6.prealpha3.tar, install that and then install the new pari spkg.

It would be good if you could make a new tar file with all the changes in place - i.e. make a sage-4.6.prealpha4.tar

Dave

[jdemeyer]

Replying to drkirkby:

It would be good if you could make a new tar file with all the changes in place - i.e. make a sage-4.6.prealpha4.tar

I will now make a new 4.6-prealpha4 based on 4.5.3-rc0 with the new spkgs (I will also update genus2reduction, see #9591 and lcalc, see #9845).

[jdemeyer]

Additional spkg patches by me

[leif]

Replying to jdemeyer:

I have made a few small changes to the pari spkg and put the result at ​http://sage.math.washington.edu/home/jdemeyer/spkg/pari-2.4.3.svn-12577.p5.spkg (I kept the p5 version number).

I'm ok with your changes ("positive review"). Not very surprisingly Sage 4.6.prealpha4 also passed all tests. Tuning on a Core2 worked, too, at least did pass without errors. ;-)

The way we handle the patches now (without the patched replacement files being under revision control) is a bit dangerous though. Perhaps we should also add some script to generate the patches from patches/files/* and one to just make sure they're in sync.

[jdemeyer]

Leif: your patch looks good on visual inspection. Since it fixes all known build issues, I give it positive review.

[leif]

Otherwise looks a bit funny. Thanks though. ;-)

I think we should report some of the changes upstream when our PARI has successfully reached some Sage 4.6.{alpha,rc}.

[jdemeyer]

Replying to leif:

I think we should report some of the changes upstream when our PARI has successfully reached some Sage 4.6.{alpha,rc}.

Agreed.

[leif]

P.S.: Attempting to build with Qt as the graphics back-end is still broken in some constellations (i.e. may lead to build errors, too), since the code apparently expects Qt <= 3 and some (Qt) tools PARI doesn't look for. I haven't yet worked on config/get_Qt though.