Sage 6.9.rc0 released
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Volker Braun
Sep 25, 2015, 6:54:16 AM9/25/15
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As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html
This release now supports Xcode 7 but not OSX 10.11. The letter doesn't look encouraging, so I probably won't upgrade the OSX buildbot anytime soon.
Please do something about the outstanding blocker tickets!
2f7c727 Updated Sage version to 6.9.rc0
accc100 Trac #19233: ecm doesn't build with Xcode 7.0
973504c Trac #19222: RIF: fix min/max when one of the arguments is a NaN
fd52571 Trac #19277: Cremona-Richmond configuration
2c41984 Trac #19178: Make Coxeter3 a new-style spkg
c1fec0f Trac #18838: GLPK backend does not detect unboundedness in simplex-only mode
d14eabb Trac #18675: Add 'connected' as a class for graded Hopf algebras with basis.
fbcd898 Trac #17435: Cythonise path algebra elements
26c2243 Trac #14107: Expose quantum Littlewood-Richardson coefficients from lrcalc
991eca9 Trac #19267: Update documentation about Sage packages
7c13250 Trac #19234: gsl doesn't build with Xcode 7.0
ec83784 Trac #19266: configure: create directories using AC_CONFIG_COMMANDS
04dd11c Trac #19043: Move configuration part of build/make/install to configure
b53e36d Trac #19263: Coproduct by coercion
e342c18 Trac #19253: Complete and Random Semi-Complete digraph generators
3029ac5 Trac #19241: fixing hidden doc errors in sage/combinat
dd3fe49 Trac #19118: Suggested improvement to computing Ihara zeta functions
b35f56a Trac #19260: documentation fix in tilings.py
a7bfce3 Trac #19247: Two SRG on 243 and 276 vertices
159de7b Trac #19227: Graphs: DFS and broken distance-parameter
7ca4917 Trac #19191: LatticePoset: add is_planar()
d83db35 Trac #17715: AsymptoticTerm
7aec32d Trac #19244: Broken doctest in src/sage/categories/fields.py
019923e Trac #19243: Do not test SageKernelSpec.update()
3558883 Trac #19255: remove adams_operation
a1cbbfc Trac #19248: Add declarations for gmp/mpir C++ classes
6d84386 Trac #19252: Faster GridGraph generator
af6a0a8 Trac #19242: Improve register_unpickle_override() doc
f55ee04 Trac #19187: Add rules for installing packages with pip
1b32539 Trac #19240: Rename matrix_mod2e_dense to matrix_gf2e_dense
4cc6f80 Trac #19208: Replace remaining instances of has_coerce_map_from_[c_]impl by _coerce_map_from_
aaaa782 Trac #12162: simplify_full for matrix
f183133 Trac #19221: Some new (n,2^k,1)-BIBD
12c8dd0 Trac #19210: rename automata.word to automata.Word
2dca304 Trac #19237: Fix ReSt errors in reference/rings
ec5b364 Trac #19238: Remove the "SPKG Maintainers" section in packages and doc
14c0eca Trac #19236: Lock mirror_list file in MirrorList.__init__
5b4c634 Trac #19200: various typoes in doc
3e152bf Trac #19197: LatticePoset: add breadth()
a9354cf Trac #19193: is_planar() fails with an immutable graph
49350d6 Trac #18885: ecm fail to build with "no such instruction: vfmadd312sd"
4158b77 Trac #18227: Finite state machines: some cleanup and code rewriting
1faa57d Trac #6337: Implement jordan_form over symbolic ring
4be9b1e Trac #19239: Race conditions building LiE
af210ee Trac #19207: Automata: Add documentation illustrating the use of automata operations
de474e0 Trac #18123: let Transducer(word) output a word
f0bd56d Trac #15267: automaton: iterator over words of language
505041f Trac #14164: Error in NumberField.composite_fields()
47cc49a Trac #18594: Add additional mutation options for clusters
58db58e Trac #18305: Element comparison for Python classes
aeeddeb Updated Sage version to 6.9.beta7
strogdon
Sep 25, 2015, 5:09:58 PM9/25/15
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The current rc0 builds here on my gentoo box. However, I'm having difficulty merging tickets with rc0. Yesterday, with 6.9.beta7 I was testing a branch with trac #19272 merged and everything was fine. Today, after pulling 6.9.rc0 and building it I created a new branch for trac #19272 and merged that ticket. Things seemed to build fine, after typing "make", with the exception that the networkx-1.10 package for trac #19272 was not built! This has happened here on another newly created branch for trac #18497 where after merging the ticket and and typing "make" the sphinx-1.3.1 package is not built. It is as if the "make" is insensitive to time-stamp changes (or something) in the build folder.
strogdon
Sep 25, 2015, 5:16:27 PM9/25/15
to sage-release
Nevermind! I missed the new ".configure" before "make".
Clemens Heuberger
Sep 26, 2015, 3:58:38 AM9/26/15
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ubuntu 14.04, 64 bit, 4 GB RAM: make -j4 ran out of memory while building
documentation, last line in logfile:
[tutorial ] reading sources... [ 43%] sagetex
I then killed 4 processes using 2.7 GB each.
On the same machine, there haven't been any problems with make -j4 for any beta
or rc releases since this February.
Regards, Clemens
documentation, last line in logfile:
[tutorial ] reading sources... [ 43%] sagetex
I then killed 4 processes using 2.7 GB each.
On the same machine, there haven't been any problems with make -j4 for any beta
or rc releases since this February.
Regards, Clemens
Jeroen Demeyer
Sep 26, 2015, 7:03:49 AM9/26/15
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I can confirm that there is indeed a problem with docbuilding. When
looking at the patchbot, I saw a similar problem.
looking at the patchbot, I saw a similar problem.
Volker Braun
Sep 26, 2015, 8:48:36 AM9/26/15
to sage-release
Though afaik our docs say that you need 2gb per process, so you were quite a bit below that. It could just be slightly different order of execution that blows things up now even though memory consumption didn't increase.
Volker Braun
Sep 26, 2015, 9:16:16 AM9/26/15
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Graph of CPU + RAM usage of
export MAKE='make -j4' make doc
Jeroen Demeyer
Sep 26, 2015, 2:49:43 PM9/26/15
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On 2015-09-26 14:48, Volker Braun wrote:
> Though afaik our docs say that you need 2gb per process, so you were
> quite a bit below that. It could just be slightly different order of
> execution that blows things up now even though memory consumption didn't
> increase.
The question is: did it really not increase? You should compare 6.8 with
> Though afaik our docs say that you need 2gb per process, so you were
> quite a bit below that. It could just be slightly different order of
> execution that blows things up now even though memory consumption didn't
> increase.
6.9.rc0 for example.
Justin C. Walker
Sep 27, 2015, 12:30:08 AM9/27/15
to sage-r...@googlegroups.com
> On Sep 25, 2015, at 03:54, Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html
>
> This release now supports Xcode 7 but not OSX 10.11. The letter doesn't look encouraging, so I probably won't upgrade the OSX buildbot anytime soon.
Now updating command-line tools to Xcode 7 and rebuilding. End result: same as with the Xcode 6 tools (no problems, all tests passed)!
--
Justin C. Walker
Curmudgeon-at-large
--
Network, n., Difference between work
charged for and work done
Rob Beezer
Sep 27, 2015, 12:47:49 AM9/27/15
to sage-r...@googlegroups.com
On SageMathCloud, built from source, passes long tests ("ptestlong").
https://cloud.sagemath.com/projects/53b77207-8614-4086-a032-432af4b4cdbd/files/sage-dev-images/
https://cloud.sagemath.com/projects/53b77207-8614-4086-a032-432af4b4cdbd/files/sage-dev-images/
Volker Braun
Sep 27, 2015, 8:25:16 AM9/27/15
to sage-release
With Sage-6.8 is pretty much the same, maybe ~< 10% less memory usage; In any case no drastic change.
leif
Sep 27, 2015, 9:00:33 AM9/27/15
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Volker Braun wrote:
> With Sage-6.8 is pretty much the same, maybe ~< 10% less memory usage;
> In any case no drastic change.
Just about 50+% increase in build time...? ;-)
> With Sage-6.8 is pretty much the same, maybe ~< 10% less memory usage;
> In any case no drastic change.
-leif
For reference: The figures for 6.9.rc0:
https://lh3.googleusercontent.com/-fvz6bvxGrVo/Vgaae7pRfgI/AAAAAAAAXkE/c4eAUFjADgE/s1600/make-j4.png
> <https://lh3.googleusercontent.com/--2ehZ4UbeAA/VgffV2dBKcI/AAAAAAAAXlE/WKaIWN0FxBE/s1600/make-doc-2.png>
Volker Braun
Sep 27, 2015, 9:36:18 AM9/27/15
to sage-release
The wall time isn't comparable, different system load.
Clemens Heuberger
Sep 28, 2015, 10:23:01 AM9/28/15
to sage-r...@googlegroups.com
I recompiled 6.9.beta7 and 6.9.rc0 last night one after the other on the same
machine with negligible other load.
6.9.beta7: 81 minutes
6.9.rc0: 173 minutes
(make -j4 with 8 GB RAM, linux 64 bit).
I currently do not have a breakdown as "time" would give it (because I did not
know that this does not go into the logfile), but can rerun the experiment this
night, but based on the file times (checking out and logfiles), the
approximation should be good enough.
In 6.9.rc0, the compilation of gcc-4.9.2.p1 seems to have taken quite some time,
in the logfiles, here is are 4 consecutive lines of ls -ltr.
-rw-r--r-- 1 cheuberg domain users 905244 Sep 27 22:43 scipy-0.14.0.log
-rw-r--r-- 1 cheuberg domain users 1611 Sep 27 22:52
conway_polynomials-0.4.p0.log
-rw-r--r-- 1 cheuberg domain users 9490 Sep 27 23:26 ccache-3.2.2.log
-rw-r--r-- 1 cheuberg domain users 29830155 Sep 27 23:55 gcc-4.9.2.p1.log
Regards,
Clemens
Am 2015-09-27 um 15:36 schrieb Volker Braun:
> The wall time isn't comparable, different system load.
>
>
> On Sunday, September 27, 2015 at 3:00:33 PM UTC+2, leif wrote:
>
> Volker Braun wrote:
> > With Sage-6.8 is pretty much the same, maybe ~< 10% less memory usage;
> > In any case no drastic change.
>
> Just about 50+% increase in build time...? ;-)
>
>
> -leif
>
> For reference: The figures for 6.9.rc0:
> https://lh3.googleusercontent.com/-fvz6bvxGrVo/Vgaae7pRfgI/AAAAAAAAXkE/c4eAUFjADgE/s1600/make-j4.png
>
>
>
> >
> <https://lh3.googleusercontent.com/--2ehZ4UbeAA/VgffV2dBKcI/AAAAAAAAXlE/WKaIWN0FxBE/s1600/make-doc-2.png
> <https://lh3.googleusercontent.com/--2ehZ4UbeAA/VgffV2dBKcI/AAAAAAAAXlE/WKaIWN0FxBE/s1600/make-doc-2.png>>
>
> >
> >
> >
> >
> >
> > On Saturday, September 26, 2015 at 8:49:43 PM UTC+2, Jeroen Demeyer wrote:
> >
> > On 2015-09-26 14:48, Volker Braun wrote:
> > > Though afaik our docs say that you need 2gb per process, so you were
> > > quite a bit below that. It could just be slightly different order of
> > > execution that blows things up now even though memory consumption
> > didn't
> > > increase.
> >
> > The question is: did it really not increase? You should compare 6.8
> > with
> > 6.9.rc0 for example.
>
> --
>
> >
> >
> >
> >
> >
> > On Saturday, September 26, 2015 at 8:49:43 PM UTC+2, Jeroen Demeyer wrote:
> >
> > On 2015-09-26 14:48, Volker Braun wrote:
> > > Though afaik our docs say that you need 2gb per process, so you were
> > > quite a bit below that. It could just be slightly different order of
> > > execution that blows things up now even though memory consumption
> > didn't
> > > increase.
> >
> > The question is: did it really not increase? You should compare 6.8
> > with
> > 6.9.rc0 for example.
>
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Sébastien Labbé
Sep 28, 2015, 10:48:21 AM9/28/15
to sage-release
On Ubuntu 14.04 64 bit,
Using --optional=arb,benzene,bliss,buckygen,cbc,coxeter3,cryptominisat,database_cremona_ellcurve,database_gap,database_odlyzko_zeta,database_pari,database_stein_watkins,database_symbolic_data,dot2tex,gambit,gap_packages,gcc,gdb,mcqd,modular_decomposition,mpir,nauty,plantri,python2,sage,scons,tides
make ptestlong finishes with
----------------------------------------------------------------------
sage -t --long --warn-long 2.3 src/sage/combinat/kazhdan_lusztig.py # 1 doctest failed
sage -t --long --warn-long 2.3 src/sage/schemes/product_projective/wehlerK3.py # Timed out
----------------------------------------------------------------------
The problem with wehlerK3.py is not reproducible (all test passed). But I get the following reproducible failing doctest involving optional coxeter3 package:
sage -t --long --warn-long 2.3 src/sage/combinat/kazhdan_lusztig.py
**********************************************************************
File "src/sage/combinat/kazhdan_lusztig.py", line 68, in sage.combinat.kazhdan_lusztig.KazhdanLusztigPolynomial
Failed example:
W.kazhdan_lusztig_polynomial([2], [3,2,3,1,2]) # optional - coxeter3
Expected:
1 + q
Got:
q + 1
**********************************************************************
Sébastien
Using --optional=arb,benzene,bliss,buckygen,cbc,coxeter3,cryptominisat,database_cremona_ellcurve,database_gap,database_odlyzko_zeta,database_pari,database_stein_watkins,database_symbolic_data,dot2tex,gambit,gap_packages,gcc,gdb,mcqd,modular_decomposition,mpir,nauty,plantri,python2,sage,scons,tides
make ptestlong finishes with
----------------------------------------------------------------------
sage -t --long --warn-long 2.3 src/sage/combinat/kazhdan_lusztig.py # 1 doctest failed
sage -t --long --warn-long 2.3 src/sage/schemes/product_projective/wehlerK3.py # Timed out
----------------------------------------------------------------------
The problem with wehlerK3.py is not reproducible (all test passed). But I get the following reproducible failing doctest involving optional coxeter3 package:
sage -t --long --warn-long 2.3 src/sage/combinat/kazhdan_lusztig.py
**********************************************************************
File "src/sage/combinat/kazhdan_lusztig.py", line 68, in sage.combinat.kazhdan_lusztig.KazhdanLusztigPolynomial
Failed example:
W.kazhdan_lusztig_polynomial([2], [3,2,3,1,2]) # optional - coxeter3
Expected:
1 + q
Got:
q + 1
**********************************************************************
Sébastien
Volker Braun
Sep 28, 2015, 12:07:29 PM9/28/15
to sage-release
Fixed in #19294
William Stein
Sep 28, 2015, 2:00:54 PM9/28/15
to sage-release
In Sage-6.7 this library (which is *pure python*) works well:
https://github.com/datasift
In Sage-6.9.beta6 (for me) this library crashes with the following
weird traceback. Any ideas?
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ which
[Kpython
Python 2.7.9 (default, Sep 22 2015, 12:04:36)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import datasift
sig_retry() without sig_on()
------------------------------------------------------------------------
/projects/sage/sage-6.9/local/lib/python2.7/site-packages/sage/ext/interrupt/interrupt.so(+0x3c18)[0x7f5093148c18]
/projects/sage/sage-6.9/local/lib/python2.7/site-packages/sage/ext/interrupt/interrupt.so(+0x3c87)[0x7f5093148c87]
/projects/sage/sage-6.9/local/lib/python2.7/site-packages/sage/ext/interrupt/interrupt.so(+0x635c)[0x7f509314b35c]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10d10)[0x7f5099764d10]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f50993bf267]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f50993c0eca]
/projects/sage/sage-6.9/local/lib/python2.7/site-packages/sage/libs/pari/handle_error.so(+0x37d0)[0x7f5088cb67d0]
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0(pari_err+0x185)[0x7f5092d381f5]
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0(new_chunk_resize+0x40)[0x7f5092d39230]
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0(gcopy+0x2a0)[0x7f5092d3cb30]
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0(concat+0x830)[0x7f5092b00680]
/usr/lib/libkpathsea.so.6(kpathsea_selfdir+0x2af)[0x7f504b6d0c2f]
/usr/lib/libkpathsea.so.6(kpathsea_set_program_name+0x6b)[0x7f504b6d0d1b]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x97)[0x7f5099a97cc7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x123721)[0x7f5099a95721]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1dd)[0x7f5099a9641d]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x105888)[0x7f5099a77888]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f50999c5913]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f5099a794b7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x155f)[0x7f5099a7b02f]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f5099a80940]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x7f5099a80a69]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x99)[0x7f5099a94559]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x1228de)[0x7f5099a948de]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x123721)[0x7f5099a95721]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1dd)[0x7f5099a9641d]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x105888)[0x7f5099a77888]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f50999c5913]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f5099a794b7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x155f)[0x7f5099a7b02f]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f5099a80940]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x7f5099a80a69]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x99)[0x7f5099a94559]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x1228de)[0x7f5099a948de]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x123721)[0x7f5099a95721]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1dd)[0x7f5099a9641d]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x105888)[0x7f5099a77888]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f50999c5913]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f5099a794b7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x155f)[0x7f5099a7b02f]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f5099a80940]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x7f5099a80a69]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x99)[0x7f5099a94559]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x1228de)[0x7f5099a948de]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x123721)[0x7f5099a95721]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1dd)[0x7f5099a9641d]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(+0x105888)[0x7f5099a77888]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f50999c5913]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f5099a794b7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x155f)[0x7f5099a7b02f]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f5099a80940]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x7f5099a80a69]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x99)[0x7f5099a94559]
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Attaching gdb to process id 14653.
Saved trace to /projects/4a5f0542-5873-4eed-a85c-a18c706e8bcd/.sage/crash_logs/sage_crash_5c6whR.log
------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Sage will now terminate.
------------------------------------------------------------------------
Aborted (core dumped)
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ q [Kexit
Exited Sage subshell.
> To post to this group, send email to sage-r...@googlegroups.com.
William (http://wstein.org)
https://github.com/datasift
In Sage-6.9.beta6 (for me) this library crashes with the following
weird traceback. Any ideas?
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ which
[Kpython
Python 2.7.9 (default, Sep 22 2015, 12:04:36)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import datasift
sig_retry() without sig_on()
------------------------------------------------------------------------
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/lib/x86_64-linux-gnu/libpthread.so.0(+0x10d10)[0x7f5099764d10]
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/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f5099a794b7]
/projects/sage/sage-6.9/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x155f)[0x7f5099a7b02f]
Attaching gdb to process id 14653.
Saved trace to /projects/4a5f0542-5873-4eed-a85c-a18c706e8bcd/.sage/crash_logs/sage_crash_5c6whR.log
------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Sage will now terminate.
------------------------------------------------------------------------
Aborted (core dumped)
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$
(sage-sh) [m 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ q [Kexit
Exited Sage subshell.
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William (http://wstein.org)
William Stein
Sep 28, 2015, 2:04:24 PM9/28/15
to sage-release
On Mon, Sep 28, 2015 at 11:00 AM, William Stein <wst...@gmail.com> wrote:
> In Sage-6.7 this library (which is *pure python*) works well:
>
> https://github.com/datasift
>
> In Sage-6.9.beta6 (for me) this library crashes with the following
> weird traceback. Any ideas?
Two additional points:
> In Sage-6.7 this library (which is *pure python*) works well:
>
> https://github.com/datasift
>
> In Sage-6.9.beta6 (for me) this library crashes with the following
> weird traceback. Any ideas?
(1) If I just run sage, rather than "sage -sh" then python then this
problem does not happen.
(2) If I run "sage -python" or "sage -ipython", then things blow up.
Anybody can replicate this in any SageMathCloud project by the way by
typing "sage -python", then "import datasift".
Datasift imports various serious libraries like multiprocessing, etc.
https://github.com/datasift/datasift-python/blob/master/datasift/client.py
William
William (http://wstein.org)
Volker Braun
Sep 28, 2015, 2:28:22 PM9/28/15
to sage-release
Symbol collision. Unless TeX's libkpathsea really intends to use concat() from Pari...
William Stein
Sep 28, 2015, 3:17:26 PM9/28/15
to sage-release
On Mon, Sep 28, 2015 at 11:28 AM, Volker Braun <vbrau...@gmail.com> wrote:
> Symbol collision. Unless TeX's libkpathsea really intends to use concat()
> from Pari...
That makes sense. Basically you're noticing this part of the traceback:
> Symbol collision. Unless TeX's libkpathsea really intends to use concat()
> from Pari...
...
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0(concat+0x830)[0x7f5092b00680]
/usr/lib/libkpathsea.so.6(kpathsea_selfdir+0x2af)[0x7f504b6d0c2f]
/usr/lib/libkpathsea.so.6(kpathsea_set_program_name+0x6b)
...
/usr/lib/libkpathsea.so.6(kpathsea_selfdir+0x2af)[0x7f504b6d0c2f]
/usr/lib/libkpathsea.so.6(kpathsea_set_program_name+0x6b)
So some third-party Python library that datasift depends on is
dynamically linking something that depends on tex. Because we put our
own shared libraries at the front of the load path, tex then looks for
various symbols "in the OS" and finds something called "concat" in...
/projects/sage/sage-6.9/local/lib/libpari-gmp-2.8.so.0
which is obviously bad. Very bad. As a result, everything after
that is broken.
Just to clarify diagnosing the problem, we have the following test.
TEST: Figure out where the correct concat symbol is defined and put
that path at the beginning of LD_LIBRARY_PATH. Does it work?
a. Figure out where symbol is defined -- answer: usr/lib/x86_64-linux-gnu/
~/tmp$ scanelf -l -s concat|grep concat
ET_DYN concat /usr/lib/x86_64-linux-gnu/libpari-gmp-tls.so.2.7.2
ET_DYN concat /usr/lib/libbfd-2.25-system.so
ET_DYN concat /usr/lib/libgiac.so.0.0.0
ET_DYN concat /usr/lib/libkpathsea.so.6.2.1
b. Hack Sage so that LD_LIBRARY_PATH starts with /usr/lib/x86_64-linux-gnu/
This does make datasift work without completely breaking importing
sage, in that doing "sage -sh" then
(sage-sh) 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ export
LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH
(sage-sh) 4a5f054258734eeda85ca18c706e8bcd@compute4-us:tmp$ python
Python 2.7.9 (default, Apr 2 2015, 15:37:21)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import datasift
>>> import sage
Type "help", "copyright", "credits" or "license" for more information.
>>> import datasift
>>> import sage.all
But then sage would use the wrong pari library.
TEST2: Sage and the system-wide Python libraries are "compatible"
(same unicode size, etc.), so I have been including the system-wide
python module path in Sage's. Aren't I naively optimistic? This is
very likely *why* importing datasift is picking up something that
depends on kpathsea and a system-wide pari library in Ubuntu. The
right solution should be to (1) not include the system-wide python
path, and (2) install everything that datasift depends on directly
into Sage. Let's try.
... does that.
This works perfectly.
Volker: thanks again for looking carefully at the traceback and
helping me to solve this!
-- William
Volker Braun
Sep 28, 2015, 4:02:03 PM9/28/15
to sage-release
Hmm but /usr/lib/x86_64-linux-gnu/libpari-gmp-tls.so.2.7.2 brings just a slightly different version of Pari's concat. It may very well be that it doesn't trigger libkpathsea crashing but thats just by chance; the symbol conflict is still there.
The correct fix is to not export concat; neither from libpari nor from libkpathsea as its (most likely but haven't checked) not part of the official api but just a convenience function. Or at least link them with -Bsymbolic
William Stein
Sep 28, 2015, 4:05:41 PM9/28/15
to sage-r...@googlegroups.com
On Monday, September 28, 2015, Volker Braun <vbrau...@gmail.com> wrote:
Hmm but /usr/lib/x86_64-linux-gnu/libpari-gmp-tls.so.2.7.2 brings just a slightly different version of Pari's concat. It may very well be that it doesn't trigger libkpathsea crashing but thats just by chance; the symbol conflict is still there.
It's an upstream ununtu bug then though.
The correct fix is to not export concat; neither from libpari nor from libkpathsea as its (most likely but haven't checked) not part of the official api but just a convenience function. Or at least link them with -Bsymbolic
Agreed. Jereon want to do something about this?
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Jeroen Demeyer
Sep 29, 2015, 6:08:09 AM9/29/15
to sage-r...@googlegroups.com
On 2015-09-28 22:05, William Stein wrote:
> Agreed. Jereon want to do something about this?
It's reported upstream to PARI.
> Agreed. Jereon want to do something about this?
Jeroen Demeyer
Sep 30, 2015, 4:46:34 PM9/30/15
to sage-r...@googlegroups.com
On 2015-09-28 20:00, William Stein wrote:
> In Sage-6.7 this library (which is *pure python*) works well:
>
> https://github.com/datasift
>
> In Sage-6.9.beta6 (for me) this library crashes with the following
> weird traceback. Any ideas?
Should be fixed upstream and in Sage at
> In Sage-6.7 this library (which is *pure python*) works well:
>
> https://github.com/datasift
>
> In Sage-6.9.beta6 (for me) this library crashes with the following
> weird traceback. Any ideas?
http://trac.sagemath.org/ticket/19273
William Stein
Sep 30, 2015, 4:58:27 PM9/30/15
to sage-r...@googlegroups.com
Awesome - thanks!!
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Andrey Novoseltsev
Oct 1, 2015, 1:42:28 PM10/1/15
to sage-release
Not sure if has surfaced already, but after make distclean the build with tests fails at
...
Running the test suite for gf2x-1.1.p1...
make[3]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Making check in .
make[4]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
make[4]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Making check in tests
make[4]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
make check-mul check-addmul
make[5]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../gf2x -I.. -I.. -O2 -g -Wall -W -mpclmul -MT check-mul.o -MD -MP -MF .deps/check-mul.Tpo -c -o check-mul.o check-mul.c
mv -f .deps/check-mul.Tpo .deps/check-mul.Po
gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../gf2x -I.. -I.. -O2 -g -Wall -W -mpclmul -MT check-addmul.o -MD -MP -MF .deps/check-addmul.Tpo -c -o check-addmul.o check-addmul.c
mv -f .deps/check-addmul.Tpo .deps/check-addmul.Po
/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o check-mul check-mul.o ../libgf2x.la
libtool: link: gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o .libs/check-mul check-mul.o ../.libs/libgf2x.so -Wl,-rpath -Wl,/home/novoselt/sage/local/lib
/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o check-addmul check-addmul.o ../libgf2x.la
libtool: link: gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o .libs/check-addmul check-addmul.o ../.libs/libgf2x.so -Wl,-rpath -Wl,/home/novoselt/sage/local/lib
make[5]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
make check-TESTS
make[5]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
1x1 2x2 3x3 4x4 5x5 6x6 7x7 8x8 9x9 20x20 100x20 100x100 1000x20 1000x100 1000x1000 failed : '1000 1000 e084de5a 76540123' != '1000 1000 a12a7e03 76540123'
FAIL: do-check-mul.sh
==================
1 of 1 test failed
==================
Makefile:375: recipe for target 'check-TESTS' failed
make[5]: *** [check-TESTS] Error 1
make[5]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
Makefile:497: recipe for target 'check-am' failed
make[4]: *** [check-am] Error 2
make[4]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
Makefile:530: recipe for target 'check-recursive' failed
make[3]: *** [check-recursive] Error 1
make[3]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Error: gf2x failed to pass its test suite.
real 0m0.776s
user 0m0.352s
sys 0m0.076s
************************************************************************
Error testing package gf2x-1.1.p1
************************************************************************
...
Running the test suite for gf2x-1.1.p1...
make[3]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Making check in .
make[4]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
make[4]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Making check in tests
make[4]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
make check-mul check-addmul
make[5]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../gf2x -I.. -I.. -O2 -g -Wall -W -mpclmul -MT check-mul.o -MD -MP -MF .deps/check-mul.Tpo -c -o check-mul.o check-mul.c
mv -f .deps/check-mul.Tpo .deps/check-mul.Po
gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../gf2x -I.. -I.. -O2 -g -Wall -W -mpclmul -MT check-addmul.o -MD -MP -MF .deps/check-addmul.Tpo -c -o check-addmul.o check-addmul.c
mv -f .deps/check-addmul.Tpo .deps/check-addmul.Po
/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o check-mul check-mul.o ../libgf2x.la
libtool: link: gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o .libs/check-mul check-mul.o ../.libs/libgf2x.so -Wl,-rpath -Wl,/home/novoselt/sage/local/lib
/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o check-addmul check-addmul.o ../libgf2x.la
libtool: link: gcc -std=gnu99 -O2 -g -Wall -W -mpclmul -o .libs/check-addmul check-addmul.o ../.libs/libgf2x.so -Wl,-rpath -Wl,/home/novoselt/sage/local/lib
make[5]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
make check-TESTS
make[5]: Entering directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
1x1 2x2 3x3 4x4 5x5 6x6 7x7 8x8 9x9 20x20 100x20 100x100 1000x20 1000x100 1000x1000 failed : '1000 1000 e084de5a 76540123' != '1000 1000 a12a7e03 76540123'
FAIL: do-check-mul.sh
==================
1 of 1 test failed
==================
Makefile:375: recipe for target 'check-TESTS' failed
make[5]: *** [check-TESTS] Error 1
make[5]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
Makefile:497: recipe for target 'check-am' failed
make[4]: *** [check-am] Error 2
make[4]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src/tests'
Makefile:530: recipe for target 'check-recursive' failed
make[3]: *** [check-recursive] Error 1
make[3]: Leaving directory '/home/novoselt/sage/local/var/tmp/sage/build/gf2x-1.1.p1/src'
Error: gf2x failed to pass its test suite.
real 0m0.776s
user 0m0.352s
sys 0m0.076s
************************************************************************
Error testing package gf2x-1.1.p1
************************************************************************
Volker Braun
Oct 1, 2015, 1:47:54 PM10/1/15
to sage-release
This is probably http://trac.sagemath.org/ticket/18882
leif
Oct 1, 2015, 2:03:41 PM10/1/15
to sage-r...@googlegroups.com
Andrey Novoseltsev wrote:
> Not sure if has surfaced already, but after make distclean the build
> with tests fails at
>
> ...
> Running the test suite for gf2x-1.1.p1...
Which version of GCC, CPU?
> Not sure if has surfaced already, but after make distclean the build
> with tests fails at
>
> ...
> Running the test suite for gf2x-1.1.p1...
-leif
Andrey Novoseltsev
Oct 1, 2015, 2:16:37 PM10/1/15
to sage-release
On Thursday, 1 October 2015 12:03:41 UTC-6, leif wrote:
Andrey Novoseltsev wrote:
> Not sure if has surfaced already, but after make distclean the build
> with tests fails at
>
> ...
> Running the test suite for gf2x-1.1.p1...
Which version of GCC, CPU?
novoselt@sage:~/sage$ gcc --version
gcc (Debian 4.9.2-10) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
novoselt@sage:~/sage$ cat /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 21
model : 2
model name : AMD FX(tm)-8350 Eight-Core Processor
stepping : 0
microcode : 0x6000822
cpu MHz : 1400.000
cache size : 2048 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 4
apicid : 16
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 popcnt aes xsave avx f16c lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 tce nodeid_msr tbm topoext perfctr_core perfctr_nb arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold vmmcall bmi1
bogomips : 8026.40
TLB size : 1536 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm 100mhzsteps hwpstate cpb eff_freq_ro
...
Will retry and see if it is reproducible.
Andrey Novoseltsev
Oct 1, 2015, 4:36:45 PM10/1/15
to sage-release
On Thursday, 1 October 2015 12:16:37 UTC-6, Andrey Novoseltsev wrote:
Will retry and see if it is reproducible.
It was reproducible (at least once) if I do "make distclean" first. Doing "make" after the failure went fine (stuck on SageTeX).
Jeroen Demeyer
Oct 3, 2015, 5:28:43 AM10/3/15
to sage-r...@googlegroups.com
On 2015-09-28 16:22, Clemens Heuberger wrote:
>
> I recompiled 6.9.beta7 and 6.9.rc0 last night one after the other on the same
> machine with negligible other load.
What does the word "recompiled" mean in the sentence above?
>
> I recompiled 6.9.beta7 and 6.9.rc0 last night one after the other on the same
> machine with negligible other load.
Clemens Heuberger
Oct 3, 2015, 1:00:45 PM10/3/15
to sage-r...@googlegroups.com
rm -rf sage-6.9.beta7
git clone ...
make -j4; ./sage -i ccache; make
(the last line is due to the fact that I use some script which sets everything
up and I forgot the fact that I wrote the last line as it is. This did not have
any consequences until beta7 and leads to much longer total time in rc0.)
Clemens
Clemens Heuberger
Oct 4, 2015, 12:57:49 AM10/4/15
to sage-r...@googlegroups.com
Am 2015-10-03 um 19:00 schrieb Clemens Heuberger:
> rm -rf sage-6.9.beta7
> git clone ...
> make -j4; ./sage -i ccache; make
6.9.beta7:
real 88m39.989s
user 247m40.494s
sys 19m13.816s
6.9.rc0:
real 181m18.663s
user 498m37.352s
sys 38m7.824s
6.9.rc2:
real 87m33.002s
user 248m6.490s
sys 19m28.353s
So for me, the issue has been solved, thank you.
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