Opened 6 years ago

Closed 6 years ago

#15198 closed enhancement (fixed)

Upgrade Pynac to 0.3.1

Reported by: eviatarbach Owned by:
Priority: major Milestone: sage-6.2
Component: packages: standard Keywords:
Cc: burcin Merged in:
Authors: Jean-Pierre Flori Reviewers: Volker Braun
Report Upstream: N/A Work issues:
Branch: 9bcfc04 (Commits) Commit: 9bcfc042078b3a35767b2fc69dbd59db4b3063a1
Dependencies: #12289, #14778, #13356 Stopgaps:

Description (last modified by jpflori)

Let's update to Pynac 0.3.1.

Use upstream tarball at:

To be merged with #14778

Attachments (2)

pynac-0.3.1.tar.bz2 (495.0 KB) - added by eviatarbach 6 years ago.
pynac-0.3.1.spkg (598.6 KB) - added by eviatarbach 6 years ago.

Download all attachments as: .zip

Change History (22)

comment:1 Changed 6 years ago by eviatarbach

  • Dependencies set to #12289, #14778

Changed 6 years ago by eviatarbach

comment:2 Changed 6 years ago by eviatarbach

Attached is a proposed Pynac release, which should be approved by Burcin beforehand. This release is a dependency for #13356, #14800, #12289, and #14778, while #12289, #14778, #13356 are a dependency for this patch (of course circular dependencies don't make sense, but they need to be merged in the same release) since they modify Sage code and doctests which this release will break.

Last edited 6 years ago by eviatarbach (previous) (diff)

comment:3 Changed 6 years ago by eviatarbach

  • Dependencies changed from #12289, #14778 to #12289, #14778, #13356

comment:4 Changed 6 years ago by novoselt

Is it supposed to be an spkg?

comment:5 Changed 6 years ago by eviatarbach

The tarball here is old. Use the one at https://bitbucket.org/pynac/www/src/2f581d33ea462ac3573dffb84acf0985eb911706/download/pynac-0.3.1.tar.bz2?at=default

I think you can just rename it to pynac-0.3.1.spkg and put it in spkg/standard.

Last edited 6 years ago by eviatarbach (previous) (diff)

comment:6 Changed 6 years ago by novoselt

But I am not going to rebuild Sage to test this: the usual way is to run sage -i hyperlink-to-new-spkg - why isn't it made by Sage packaging command?

comment:7 Changed 6 years ago by eviatarbach

Sorry, you're right, it's not a proper spkg. I'll make one.

Changed 6 years ago by eviatarbach

comment:8 Changed 6 years ago by eviatarbach

Okay, here's an spkg.

comment:9 Changed 6 years ago by novoselt

Does not work:

┌────────────────────────────────────────────────────────────────────┐
│ Sage Version 5.12.beta5, Release Date: 2013-09-06                  │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
Forcing sage-location, probably because a new package was installed.
Updating various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done updating paths.
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
------------------------------------------------------------------------
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/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(+0x10bcee)[0x7f7677d16cee]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(+0x10cdcc)[0x7f7677d17dcc]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(+0x10d023)[0x7f7677d18023]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x199)[0x7f7677d18619]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(+0xed08f)[0x7f7677cf808f]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5af2)[0x7f7677cffbd2]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5de9)[0x7f7677cffec9]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5de9)[0x7f7677cffec9]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x822)[0x7f7677d00a02]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(+0x77ce7)[0x7f7677c82ce7]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyObject_Call+0x4e)[0x7f7677c5775e]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1289)[0x7f7677cfb369]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x822)[0x7f7677d00a02]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x45ed)[0x7f7677cfe6cd]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x822)[0x7f7677d00a02]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x45ed)[0x7f7677cfe6cd]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x822)[0x7f7677d00a02]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f7677d00b32]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xaa)[0x7f7677d224fa]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xed)[0x7f7677d22f3d]
/home/novoselt/sage.git/local/lib/libpython2.7.so.1.0(Py_Main+0xc22)[0x7f7677d38a72]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7676f5f995]
python[0x4006ee]
------------------------------------------------------------------------
Attaching gdb to process id 8592.
Unable to start gdb (not installed?)

GDB is not installed.
Install the gdb spkg (sage -f gdb) for enhanced tracebacks.
------------------------------------------------------------------------
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(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
/home/novoselt/bin/sage: line 134:  8592 Aborted                 "$SAGE_ROOT/src/bin/sage" "$@"

comment:10 Changed 6 years ago by eviatarbach

I got that error too, but after running sage -br it worked. Maybe it's necessary?

comment:11 Changed 6 years ago by vbraun

You definitely need to rebuild cython files whenever you change the pynac ABI...

comment:12 Changed 6 years ago by vbraun_spam

  • Milestone changed from sage-6.1 to sage-6.2

comment:13 Changed 6 years ago by jpflori

  • Description modified (diff)

comment:14 Changed 6 years ago by jpflori

  • Authors set to Jean-Pierre Flori
  • Branch set to u/jpflori/ticket/15198
  • Commit set to 9bcfc042078b3a35767b2fc69dbd59db4b3063a1
  • Description modified (diff)

With all the dependencies and this ticket, I just have one problem with "make ptest": it seems that

ascii_art(integral(exp(x + x^2)/(x+1), x))

takes ages.


New commits:

9bcfc04Update pynac to 0.3.1.

comment:15 Changed 6 years ago by jpflori

With new pynac:

sage: %time ascii_art(integral(exp(x + x^2)/(x+1), x))
CPU times: user 158.72 s, sys: 0.46 s, total: 159.17 s
Wall time: 158.98 s
  /          
 |           
 |   2       
 |  x  + x   
 | e         
 | ------- dx
 |  x + 1    
 |           
/            

In fact it is already as slow with the develop branch so is a "no-issue" here. Without new pynac:

sage: %time ascii_art(integral(exp(x + x^2)/(x+1), x))
CPU times: user 164.25 s, sys: 0.35 s, total: 164.61 s
Wall time: 167.80 s
  /          
 |           
 |   2       
 |  x  + x   
 | e         
 | ------- dx
 |  x + 1    
 |           
/  

That's a ppc64 machine, who knows, maybe that's the problem.

Last edited 6 years ago by jpflori (previous) (diff)

comment:16 Changed 6 years ago by jpflori

  • Status changed from new to needs_review

comment:17 Changed 6 years ago by vbraun

The slow ascii art is #15636. The reason is that sympy tries to solve the integral...

comment:18 Changed 6 years ago by jpflori

All dependencies are now positively reviewed.

comment:19 Changed 6 years ago by vbraun

  • Reviewers set to Volker Braun

comment:20 Changed 6 years ago by vbraun

  • Branch changed from u/jpflori/ticket/15198 to 9bcfc042078b3a35767b2fc69dbd59db4b3063a1
  • Resolution set to fixed
  • Status changed from needs_review to closed
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