Closed vbraun closed 11 years ago
Author: Volker Braun
Miguel, you said that you had some mysterious error. Can you try this patch? It depends on the recently-updated patches on #6391, #13211.
Dependencies: #6391, #13211
I have been checking the different updates of libgap, and the error seemed to go away several versions ago. Anyways, i will keep testing it.
I don't know if it is an issue related with this patch or if it comes from libgap itself, but i have experienced some problems when i use tab completion in a session in the command line (i haven't checked it in the notebook).
An example:
sage: F=libgap.eval('FreeGroup(2)')
sage: (a,b)=F.GeneratorsOfGroup()
sage: H=F/libgap([a^2,b^2,a*b*a*b])
sage: H
<fp group on the generators [ f1, f2 ]>
sage: H.IsomorphismSimplifiedFpGroup()
[ f1, f2 ] -> [ f1, f2 ]
sage: H=F/libgap([a^2,b^2,a*b])
sage: c=H.Gene
H.GeneralLinearGroup H.GeneralisedEigenspaces H.GeneralizedEigenvalues H.GeneratorsOfIdeal
H.GeneralOrthogonalGroup H.GeneralisedEigenvalues H.GeneratorsOfField
H.GeneralUnitaryGroup H.GeneralizedEigenspaces H.GeneratorsOfGroup
sage: c=H.GeneratorsOfGroup()[0]
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/mmarco/sage-5.4/<ipython console> in <module>()
/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()
AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: c=H.GeneratorsOfGroup()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/mmarco/sage-5.4/<ipython console> in <module>()
/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()
AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: H
Exception RuntimeError: 'Entered a critical block twice' in 'sage.libs.gap.util.error_handler' ignored
<fp group on the generators [ f1, f2 ]>
sage: H.GeneratorsOfGroup()
[ f1, f2 ]
sage: c=H.GeneratorsOfGroup()[0]
sage: c
f1
sage: c=H.Generat
H.GeneratorsOfField H.GeneratorsOfGroup H.GeneratorsOfIdeal
sage: c=H.GeneratorsOfGroup()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/mmarco/sage-5.4/<ipython console> in <module>()
/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()
AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: c=H.GeneratorsOfGroup()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/mmarco/sage-5.4/<ipython console> in <module>()
/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()
AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: H
Exception RuntimeError: 'Entered a critical block twice' in 'sage.libs.gap.util.error_handler' ignored
<fp group on the generators [ f1, f2 ]>
sage: c=H.GeneratorsOfGroup()
This same behaviour appears when i don't use this patch, so reported in the libgap ticket.
Description changed:
---
+++
@@ -1 +1,5 @@
Currently, libGAP doesn't give useful errors if something goes wrong during initialization.
+
+Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
+
+Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg)
Updated patch fixes the issue with the command line completion
Updated spkg fixes long input lines (>32k characters):
sage: S = SymmetricGroup(10000)
sage: s = S.random_element()
sage: len(str(s._gap_()))
61673
sage: libgap(s)
(1,5243,8582,5012,6862,7477,1681,7423,8405,3101,...,5257,9362,2495,8500)( [...] )
Description changed:
---
+++
@@ -2,4 +2,4 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg)
+Install [http://sagepad.org/spkg/libgap-4.5.6.p1.spkg](http://sagepad.org/spkg/libgap-4.5.6.p1.spkg)
I've added the same workaround for the gap command line option issue as just discussed in #13211
I've added __nonzero__
for wrapped GAP booleans for easier use.
Updated patch
Attachment: trac_13588_improve_libGAP.patch.gz
The new patch allows to change the comparison method for libgap objects since not all GAP objects can be compared. This is important if you want use them as cache keys.
Also, the comparison was not properly wrapped in sig_on/sig_off
I forgot to package aclocal.m4
, updated spkg adds that file.
Description changed:
---
+++
@@ -2,4 +2,4 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-Install [http://sagepad.org/spkg/libgap-4.5.6.p1.spkg](http://sagepad.org/spkg/libgap-4.5.6.p1.spkg)
+Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg)
Description changed:
---
+++
@@ -2,4 +2,4 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.p1.spkg)
+Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
Updated to libGap-4.5.7
Description changed:
---
+++
@@ -2,4 +2,9 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
+* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg) from #13211
+* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
+* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
+* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
+
+The patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
Changed dependencies from #6391, #13211 to #13211
patch from #6391
Description changed:
---
+++
@@ -4,7 +4,8 @@
* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg) from #13211
* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
+* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
-* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
+* Apply [attachment: trac_13588_improve_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656442/trac_13588_improve_libGAP.patch.gz) to the Sage library
The patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
Description changed:
---
+++
@@ -8,4 +8,4 @@
* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
* Apply [attachment: trac_13588_improve_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656442/trac_13588_improve_libGAP.patch.gz) to the Sage library
-The patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
+The `trac_6391_*` patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
I still see the segfault when trying to execute "Exec" trough libgap. This seems to make it impossible to load gap packages that make use of external programs.
Thanks for reminding me, I completely forgot about the Exec thing.
In the meantime, can we get this reviewed and included into Sage before the next GAP version comes out?
I've replaced the spkg with a new version that fixes the GAP Exec command.
Description changed:
---
+++
@@ -7,5 +7,6 @@
* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
* Apply [attachment: trac_13588_improve_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656442/trac_13588_improve_libGAP.patch.gz) to the Sage library
+* Apply [attachment: trac_13588_exec_fix.patch](https://github.com/sagemath/sage-prod/files/10656445/trac_13588_exec_fix.patch.gz) to the Sage library
The `trac_6391_*` patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
Attachment: trac_13588_exec_fix.patch.gz
Updated patch
Thanks. Still i can't load the kbmag package :(
I've updated the spkg, now loading kbmag works for me. I had to install it by hand since your spkg at #13673 is offline.
I get a slew of errors in ptestlong after following the instructions of the ticket with Sage 5.5; e.g.:
sage -t --long -force_lib devel/sage/sage/libs/gap/libgap.pyx
**********************************************************************
File "/usr/local/src/sage/sage-5.5/devel/sage-main/sage/libs/gap/libgap.pyx", line 11:
sage: a = libgap(10)
Exception raised:
Traceback (most recent call last):
File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/usr/local/src/sage/sage-5.5/local/bin/sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_0[2]>", line 1, in <module>
a = libgap(Integer(10))###line 11:
sage: a = libgap(10)
File "lazy_import.pyx", line 244, in sage.misc.lazy_import.LazyImport.__call__ (sage/misc/lazy_import.c:2012)
File "lazy_import.pyx", line 148, in sage.misc.lazy_import.LazyImport._get_object (sage/misc/lazy_import.c:1291)
File "libgap.pyx", line 574, in init sage.libs.gap.libgap (sage/libs/gap/libgap.c:4157)
libgap = Gap()
File "libgap.pyx", line 395, in sage.libs.gap.libgap.Gap.__init__ (sage/libs/gap/libgap.c:2716)
initialize()
File "util.pyx", line 193, in sage.libs.gap.util.initialize (sage/libs/gap/util.c:3312)
from sage.interfaces.gap import get_gap_memory_pool_size
ImportError: cannot import name get_gap_memory_pool_size
**********************************************************************
File "/usr/local/src/sage/sage-5.5/devel/sage-main/sage/libs/gap/libgap.pyx", line 12:
sage: a
Exception raised:
Traceback (most recent call last):
File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/usr/local/src/sage/sage-5.5/local/bin/sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_0[3]>", line 1, in <module>
a###line 12:
sage: a
NameError: name 'a' is not defined
are some patches missing or not up date?
Did you apply the patches from #13211? The get_gap_memory_pool_size()
function was added in trac_13211_fix_gap_doctests_vb.patch
.
Replying to @vbraun:
Did you apply the patches from #13211? The
get_gap_memory_pool_size()
function was added intrac_13211_fix_gap_doctests_vb.patch
.
indeed, I overlooked that #13211 isn't merged in 5.5. Sorry for noise.
Does sig_on() need a matching sig_off() in case sig_on() is issued in a try block, which throws an exception?
Comparison functions returning -1, 0, +1... So FORTRAN |V... :-)
sig_on
and sig_off
must be paired, though ideally they enclose only C/Cython code which cannot raise Python exceptions. A C signal will jump back to sig_on
and raise there.
http://www.sagemath.org/doc/developer/coding_in_cython.html#using-sig-on-and-sig-off
patches from #13880 are needed for doctests to (eventually) pass here.
Changed dependencies from #13211 to #13211, #13880
Description changed:
---
+++
@@ -2,7 +2,7 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/gap-4.5.7.p1.spkg) from #13211
+* Start with sage-5.6.beta1 or later.
* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
Description changed:
---
+++
@@ -2,7 +2,7 @@
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
-* Start with sage-5.6.beta1 or later.
+* Start with sage-5.6.beta3 or later.
* Install [http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg](http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg)
* Apply [attachment: trac_6391_libGAP_root.patch](https://github.com/sagemath/sage-prod/files/10656444/trac_6391_libGAP_root.patch.gz) to the root repository
* Apply [attachment: trac_6391_libGAP.patch](https://github.com/sagemath/sage-prod/files/10656443/trac_6391_libGAP.patch.gz) to the Sage library
Is the test program sage/libs/gap/test/main.c
used anywhere in the Sage library? I don't mind having such a program, but I'd say it belongs in the libgap spkg and not in the Sage library. It could be run when installing libGAP.
Reviewer: Dmitrii Pasechnik
sage/libs/gap/test/main.c
is not used anywhere. As the readme file explains, it is there if you need an example for how to link with libGAP without Sage. This can be useful for debugging. LibGAP has its own testsuite.
libgap tries to run various autotools, which should be avoided (as it can lead to build errors). Probably this is simply timestamps were clobbered during the packaging.
libgap-4.5.7.log:WARNING: 'aclocal-1.12' is missing on your system. You should only need it if
libgap-4.5.7.log:WARNING: 'automake-1.12' is missing on your system. You should only need it if
libgap-4.5.7.log:WARNING: 'autoconf' is missing on your system. You should only need it if
libgap-4.5.7.log:WARNING: 'autoheader' is missing on your system. You should only need it if
Ok I've regenerated the files and checked that it builds without the WARNING on an older machine. Spkg at the same place.
While building the documentation with this patch included, twice something went wrong.
reading sources... [ 86%] sage/schemes/elliptic_curves/cm
reading sources... [ 87%] sage/schemes/elliptic_curves/constructor
reading sources... [ 87%] sage/schemes/elliptic_curves/ec_database
reading sources... [ 87%] sage/schemes/elliptic_curves/ell_curve_isogeny
reading sources... [ 87%] sage/schemes/elliptic_curves/ell_field
reading sources... [ 87%] sage/schemes/elliptic_curves/ell_finite_field
reading sources... [ 87%] sage/schemes/elliptic_curves/ell_generic
Exception occurred:
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 831, in read_doc
pickle.dump(doctree, f, pickle.HIGHEST_PROTOCOL)
MemoryError
The full traceback has been saved in /tmp/release/sphinx-err-QDcECu.log, if you want to report the issue to the developers.
Full traceback:
# Sphinx version: 1.1.2
# Python version: 2.7.3
# Docutils version: 0.7 release
# Jinja2 version: 2.5.5
Traceback (most recent call last):
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/cmdline.py", line 189, in main
app.build(force_all, filenames)
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/application.py", line 204, in build
self.builder.build_update()
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 196, in build_update
'out of date' % len(to_build))
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 216, in build
purple, length):
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 120, in status_iterator
for item in iterable:
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 616, in update_generator
self.read_doc(docname, app=app)
File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 831, in read_doc
pickle.dump(doctree, f, pickle.HIGHEST_PROTOCOL)
MemoryError
I cannot say for sure that this ticket is to blame, but the MemoryError
certainly made me suspect GAP. And I also saw some "halving pool size" messages appear during the docbuilding.
Replying to @jdemeyer:
While building the documentation with this patch included, twice something went wrong.
- First time, I got an "unhandled SIGSEGV" in Sage while reading the sources of some elliptic curve file (sorry, forgot which one) for the PDF documentation. I didn't store the exact logs since I thought it was a cosmic ray or something...
- Next attempt, building from scratch again during the build of the HTML documentation:
if this happens on one host only, I'd blame the RAM there.
Replying to @dimpase:
if this happens on one host only, I'd blame the RAM there.
If this happens only with the libGAP patches, I'd blame libGAP. Besides, why would faulty RAM lead to a MemoryError
exception?
All GAP/libGAP processes should be terminated by the time we are building the manual, so I don't see how we could possibly impact that.
Is this a 32-bit machine? There you might run into warts caused by the limited address space, and the halving pool size would support that. Sphinx uses quite a lot of memory and might fail to load its pickles if there is no memory left or no contiguous address space block available.
Replying to @vbraun:
All GAP/libGAP processes should be terminated by the time we are building the manual
Not really, as building the manual runs Sage code (as witnessed for example that Segmentation Faults run the Sage signal handler and display "Unhandled SIGSEGV...")
Currently, libGAP doesn't give useful errors if something goes wrong during initialization.
Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.
The
trac_6391_*
patch has already been reviewed at #6391.Depends on #13211 Depends on #13880
CC: @miguelmarco @sagetrac-tfeulner @gvol @simon-king-jena
Component: group theory
Author: Volker Braun
Reviewer: Dmitrii Pasechnik
Merged: sage-5.7.beta1
Issue created by migration from https://trac.sagemath.org/ticket/13588