Move interrupt.pyx to package cysignals #20002

malb · 2016-02-02T09:14:45Z

Move Sage’s interrupt handling to a separate package: https://github.com/sagemath/cysignals

See also https://groups.google.com/d/topic/sage-devel/oA9NsF26eOA/discussion for a discussion. We need one trivial Cython patch, see cython/cython#483

Tarball: https://github.com/sagemath/cysignals/releases/download/1.0rc2/cysignals-1.0rc2.tar.bz2

Upstream: Reported upstream. No feedback yet.

CC: @jdemeyer @videlec @kiwifb @vbraun

Component: packages: standard

Author: Jeroen Demeyer

Branch/Commit: 4677a93

Reviewer: Martin Albrecht

Issue created by migration from https://trac.sagemath.org/ticket/20002

The text was updated successfully, but these errors were encountered:

videlec · 2016-02-02T18:41:00Z

comment:1

I am interested, partly because of pplpy.

jdemeyer · 2016-02-04T11:19:25Z

comment:2

This is certainly something that I would like to work on, I think it fits very well with OpenDreamKit/OpenDreamKit#52.

jdemeyer · 2016-02-06T20:23:38Z

comment:4

Cool! I guess the next step is to figure out how to actually make this signals.pyx available to external packages (you need to install the .pxd, .pxi and .h files).

I think it would be very useful to have an example package using signals.pyx. Both as documentation, but also as an additional test.

malb · 2016-02-07T15:52:46Z

comment:5

I created a cysignals branch for fpylll which uses the new cysignals.

jdemeyer · 2016-02-10T11:26:38Z

Author: Jeroen Demeyer

jdemeyer · 2016-02-11T09:14:54Z

Dependencies: #20021

jdemeyer · 2016-02-11T09:17:17Z

Upstream: Reported upstream. No feedback yet.

jdemeyer · 2016-02-11T11:37:11Z

Branch: u/jdemeyer/move_interrupt_pyx_to_package_cysignals

sagetrac-git · 2016-02-11T12:33:25Z

Commit: 434b272

sagetrac-git · 2016-02-11T12:33:25Z

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

`aee6a5f`	`Check that sig_on()/sig_off() works in .spyx files`
`434b272`	`cysignals depends on PARI`

jdemeyer · 2016-02-11T13:00:30Z

comment:15

@vbraun: please test on buildbots.

malb · 2016-02-11T14:07:53Z

comment:16

Couldn't we use the include_path=sys.path trick to avoid patching Cython, just in case they don't accept the pull request?

jdemeyer · 2016-02-11T15:39:33Z

comment:17

Replying to @malb:

Couldn't we use the include_path=sys.path trick to avoid patching Cython, just in case they don't accept the pull request?

The problem is that we have to support:

the Sage library
the cython(...) command
the %cython notebook magic
./sage somefile.spyx
external spkgs using cysignals

Instead of patching all these, I think it is much cleaner to apply just the Cython patch.

malb · 2016-02-11T16:46:53Z

comment:18

Makes sense to me.

jdemeyer · 2016-02-15T07:03:07Z

Changed dependencies from #20021 to none

malb · 2016-02-15T13:24:25Z

comment:20

Building a fresh Sage installation and running make ptestlong works on 64-bit Debian/GNU Linux.

malb · 2016-02-15T13:47:51Z

comment:21

What is our convention for dependencies in SPKG.txt, shall we mention Pari?
I'm no fan of "init_interrupts -> init_cysignals". Why not fix up cysignals if that's needed?

sagetrac-git · 2016-02-18T10:22:43Z

Changed commit from 741db03 to c6fdc05

sagetrac-git · 2016-02-18T10:22:43Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`c6fdc05`	`cysignals version 1.0rc1`

vbraun · 2016-02-18T23:40:15Z

comment:35

The test is now hanging for half an hour on my desktop:

buildsl+ 11539  0.0  0.0 117516  3068 ?        SN   Feb18   0:00 bash ./install start
buildsl+ 11568  0.0  0.0 115080  2948 ?        SN   Feb18   0:00 make -j8 start
buildsl+ 11576  0.0  0.0 116776  4588 ?        SN   Feb18   0:00 make -j8 all-sage
vbraun   13964  0.0  0.0 117000  2256 pts/4    S+   00:30   0:00 grep --color=auto buildsl
buildsl+ 24718  0.0  0.0 117512  3144 ?        SN   Feb18   0:00 bash /mnt/disk/home/buildslave-sage/slave/sage_git/build/build/bin/sage-logger sage-spkg cysignals-1.0rc1 /mnt/disk/home/buildslave-sage/slave/sage_git/build/logs/pkgs/cysignals-1.0rc1.log
buildsl+ 24735  0.0  0.0 117512  1828 ?        SN   Feb18   0:00 bash /mnt/disk/home/buildslave-sage/slave/sage_git/build/build/bin/sage-logger sage-spkg cysignals-1.0rc1 /mnt/disk/home/buildslave-sage/slave/sage_git/build/logs/pkgs/cysignals-1.0rc1.log
buildsl+ 24737  0.0  0.0 117512   220 ?        SN   Feb18   0:00 bash /mnt/disk/home/buildslave-sage/slave/sage_git/build/build/bin/sage-logger sage-spkg cysignals-1.0rc1 /mnt/disk/home/buildslave-sage/slave/sage_git/build/logs/pkgs/cysignals-1.0rc1.log
buildsl+ 24739  0.0  0.0 112180  1856 ?        SN   Feb18   0:00 tee -a /mnt/disk/home/buildslave-sage/slave/sage_git/build/logs/pkgs/cysignals-1.0rc1.log
buildsl+ 24740  0.0  0.0 117648  3120 ?        SN   Feb18   0:00 bash /mnt/disk/home/buildslave-sage/slave/sage_git/build/build/bin/sage-spkg cysignals-1.0rc1
buildsl+ 25822  0.0  0.0   9636  2456 ?        SN   Feb18   0:00 bash ./spkg-check
buildsl+ 25823  0.0  0.0   6720  1980 ?        SN   Feb18   0:00 make check
buildsl+ 25828  0.1  0.0 116652 18112 ?        SN   Feb18   0:08 python -m doctest src/cysignals/alarm.pyx src/cysignals/signals.pyx src/cysignals/tests.pyx

After killing it

cd example && python setup.py build
Compiling cysignals_example.pyx because it changed.
[1/1] Cythonizing cysignals_example.pyx
running build
running build_ext
building 'cysignals_example' extension
creating build
creating build/temp.linux-x86_64-2.7-pydebug
gcc -fno-strict-aliasing -g -O2 -g -O0 -Wall -Wno-unused -fPIC -I/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/python2.7/site-packages/cysignals -I/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/include/python2.7 -c cysignals_example.c -o build/temp.linux-x86_64-2.7-pydebug/cysignals_example.o
creating build/lib.linux-x86_64-2.7-pydebug
gcc -pthread -shared -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -Wl,-rpath,/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -Wl,-rpath,/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib build/temp.linux-x86_64-2.7-pydebug/cysignals_example.o -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -lpython2.7 -o build/lib.linux-x86_64-2.7-pydebug/cysignals_example.so -lpari -Ddummy
Makefile:40: recipe for target 'check-doctest' failed
make[3]: *** [check-doctest] Terminated
make[3]: Target 'check' not remade because of errors.
make[3]: Leaving directory '/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/cysignals-1.0rc1/src'

GDB

(gdb) bt
#0  0x00007fb1ed0f24ec in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x00007fb1ed05f863 in ptmalloc_lock_all () from /lib64/libc.so.6
#2  0x00007fb1ed0aa832 in fork () from /lib64/libc.so.6
#3  0x00007fb1e786b957 in signal_pid_after_delay (signum=2, killpid=16455, ms=200, 
    interval=0, n=1) at src/cysignals/tests_helper.c:66
#4  0x00007fb1e7875934 in __pyx_pf_9cysignals_5tests_70test_signal_during_malloc (
    __pyx_self=0x0, __pyx_v_delay=200) at build/src/cysignals/tests.c:7948
#5  0x00007fb1e78758a1 in __pyx_pw_9cysignals_5tests_71test_signal_during_malloc (
    __pyx_self=0x0, __pyx_args=0x7fb1ee2eb060, __pyx_kwds=0x0)
    at build/src/cysignals/tests.c:7894
#6  0x00007fb1edd7d798 in PyCFunction_Call (func=0x7fb1e7828678, arg=0x7fb1ee2eb060, kw=0x0)
    at Objects/methodobject.c:85
#7  0x00007fb1ede23bf6 in call_function (pp_stack=0x7ffc6fbe3110, oparg=0)
    at Python/ceval.c:4035
#8  0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x7fb1e90727e0, throwflag=0)
    at Python/ceval.c:2681
#9  0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1e7844460, globals=0x7fb1e783fe78, 
    locals=0x7fb1e783fe78, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, 
    closure=0x0) at Python/ceval.c:3267
#10 0x00007fb1ede16998 in PyEval_EvalCode (co=0x7fb1e7844460, globals=0x7fb1e783fe78, 
    locals=0x7fb1e783fe78) at Python/ceval.c:669
#11 0x00007fb1ede2671b in exec_statement (f=0x2054750, prog=0x7fb1e7844460, 
    globals=0x7fb1e783fe78, locals=0x7fb1e783fe78) at Python/ceval.c:4732
#12 0x00007fb1ede1acea in PyEval_EvalFrameEx (f=0x2054750, throwflag=0) at Python/ceval.c:1883
#13 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ecd59b40, globals=0x7fb1ee2df958, 
    locals=0x0, args=0x2050a28, argcount=4, kws=0x2050a48, kwcount=0, defs=0x0, defcount=0, 
    closure=0x0) at Python/ceval.c:3267
#14 0x00007fb1ede24233 in fast_function (func=0x7fb1e9076ae0, pp_stack=0x7ffc6fbe3a20, n=4, 
    na=4, nk=0) at Python/ceval.c:4131
#15 0x00007fb1ede23e00 in call_function (pp_stack=0x7ffc6fbe3a20, oparg=3)
    at Python/ceval.c:4056
---Type <return> to continue, or q <return> to quit---
#16 0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x2050860, throwflag=0) at Python/ceval.c:2681
#17 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ecd59d50, globals=0x7fb1ee2df958, 
    locals=0x0, args=0x203fe20, argcount=2, kws=0x203fe30, kwcount=0, defs=0x7fb1e9075c88, 
    defcount=3, closure=0x0) at Python/ceval.c:3267
#18 0x00007fb1ede24233 in fast_function (func=0x7fb1e9076cd8, pp_stack=0x7ffc6fbe3ee0, n=2, 
    na=2, nk=0) at Python/ceval.c:4131
#19 0x00007fb1ede23e00 in call_function (pp_stack=0x7ffc6fbe3ee0, oparg=1)
    at Python/ceval.c:4056
#20 0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x203fc20, throwflag=0) at Python/ceval.c:2681
#21 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ec8eda90, globals=0x7fb1ee2df958, 
    locals=0x0, args=0x1fa72a8, argcount=1, kws=0x1fa72b0, kwcount=1, defs=0x7fb1eba93988, 
    defcount=11, closure=0x0) at Python/ceval.c:3267
#22 0x00007fb1ede24233 in fast_function (func=0x7fb1e90795a0, pp_stack=0x7ffc6fbe43a0, n=3, 
    na=1, nk=1) at Python/ceval.c:4131
#23 0x00007fb1ede23e00 in call_function (pp_stack=0x7ffc6fbe43a0, oparg=257)
    at Python/ceval.c:4056
#24 0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x1fa70d0, throwflag=0) at Python/ceval.c:2681
#25 0x00007fb1ede24119 in fast_function (func=0x7fb1e907be28, pp_stack=0x7ffc6fbe46d0, n=0, 
    na=0, nk=0) at Python/ceval.c:4121
#26 0x00007fb1ede23e00 in call_function (pp_stack=0x7ffc6fbe46d0, oparg=0)
    at Python/ceval.c:4056
#27 0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x1e551a0, throwflag=0) at Python/ceval.c:2681
#28 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ec8f7d50, globals=0x7fb1ee2df958, 
    locals=0x7fb1ee2df958, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, 
    closure=0x0) at Python/ceval.c:3267
#29 0x00007fb1ede16998 in PyEval_EvalCode (co=0x7fb1ec8f7d50, globals=0x7fb1ee2df958, 
    locals=0x7fb1ee2df958) at Python/ceval.c:669
#30 0x00007fb1ede2671b in exec_statement (f=0x1f8cb20, prog=0x7fb1ec8f7d50, 
    globals=0x7fb1ee2df958, locals=0x7fb1ee2df958) at Python/ceval.c:4732
#31 0x00007fb1ede1acea in PyEval_EvalFrameEx (f=0x1f8cb20, throwflag=0) at Python/ceval.c:1883
#32 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ecd62930, globals=0x7fb1ecd806c8, 
---Type <return> to continue, or q <return> to quit---
    locals=0x0, args=0x1ede0c8, argcount=7, kws=0x1ede100, kwcount=0, defs=0x7fb1ecd65aa8, 
    defcount=5, closure=0x0) at Python/ceval.c:3267
#33 0x00007fb1ede24233 in fast_function (func=0x7fb1ecd8d300, pp_stack=0x7ffc6fbe4fe0, n=7, 
    na=7, nk=0) at Python/ceval.c:4131
#34 0x00007fb1ede23e00 in call_function (pp_stack=0x7ffc6fbe4fe0, oparg=7)
    at Python/ceval.c:4056
#35 0x00007fb1ede1e642 in PyEval_EvalFrameEx (f=0x1eddef0, throwflag=0) at Python/ceval.c:2681
#36 0x00007fb1ede2110b in PyEval_EvalCodeEx (co=0x7fb1ecd7e1a0, globals=0x7fb1ecd806c8, 
    locals=0x0, args=0x7fb1ecda4da8, argcount=2, kws=0x0, kwcount=0, defs=0x7fb1ecd85e18, 
    defcount=1, closure=0x0) at Python/ceval.c:3267
#37 0x00007fb1edd5996f in function_call (func=0x7fb1ecd90b88, arg=0x7fb1ecda4d80, kw=0x0)
    at Objects/funcobject.c:526
#38 0x00007fb1edd19a7c in PyObject_Call (func=0x7fb1ecd90b88, arg=0x7fb1ecda4d80, kw=0x0)
    at Objects/abstract.c:2529
#39 0x00007fb1ede6e49c in RunModule (module=0x1e55010 "doctest", set_argv0=1)
    at Modules/main.c:192
#40 0x00007fb1ede6f42b in Py_Main (argc=6, argv=0x7ffc6fbe55c8) at Modules/main.c:587
#41 0x0000000000400846 in main (argc=6, argv=0x7ffc6fbe55c8) at ./Modules/python.c:23

Retried and hangs again at same spot.

This is a debug Python build (SAGE_DEBUG=yes)

kiwifb · 2016-02-19T00:00:21Z

comment:36

Considering the change between rc0 and rc1 it is very strange if it didn't happen before.

jdemeyer · 2016-02-19T09:35:52Z

comment:37

It's also surprising that it doesn't happen with the interrupt code currently in Sage... it's the same code as in cysignals.

jdemeyer · 2016-02-19T10:30:02Z

comment:38

The malloc() problem is genuine. I will update cysignals.

sagetrac-git · 2016-02-19T17:38:51Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`4677a93`	`cysignals version 1.0rc2`

sagetrac-git · 2016-02-19T17:38:51Z

Changed commit from c6fdc05 to 4677a93

jdemeyer · 2016-02-19T17:40:21Z

comment:42

I disabled the failing malloc() test. Eventually we should move sage_malloc() and friends to cysignals too and re-enable the test.

jdemeyer · 2016-02-22T08:35:59Z

comment:43

needs review...

kiwifb · 2016-02-22T08:41:06Z

comment:44

There, let's put it on one more time.

vbraun · 2016-02-23T08:26:19Z

Changed branch from u/jdemeyer/move_interrupt_pyx_to_package_cysignals to 4677a93

malb added this to the sage-7.1 milestone Feb 2, 2016

malb added c: packages: standard labels Feb 2, 2016

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jdemeyer changed the title ~~stand-alone interrupt.pyx~~ Move interrupt.pyx to package cysignals Feb 10, 2016

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vbraun closed this as completed in dbee691 Feb 23, 2016

dkrenn mentioned this issue Feb 24, 2016

broken spyx support concerning imports #20093

Closed

This was referenced Apr 29, 2017

Move the Sage <-> PARI interface to a stand-alone package CyPari #20238

Closed

Remove deprecated code #22738

Closed

Move interrupt.pyx to package cysignals #20002

Move interrupt.pyx to package cysignals #20002

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