#6391 closed enhancement (duplicate)
libGAP! -- create a Cython library interface to gap
Reported by: | was | Owned by: | was |
---|---|---|---|
Priority: | major | Milestone: | sage-duplicate/invalid/wontfix |
Component: | group theory | Keywords: | |
Cc: | burcin, nborie, robertwb, jeremywest, iandrus, davidm, kini, kcrisman, nthiery, jpflori, SimonKing | Merged in: | |
Authors: | Reviewers: | Dmitrii Pasechnik, Ivan Andrus, Volker Braun, William Stein | |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #13415, #13123, #13211 | Stopgaps: |
Description (last modified by )
There's libSingular, there's libPari, and next we need to create libGAP.
To try it out,
- Install http://boxen.math.washington.edu/home/dima/packages/gap-4.5.6.spkg from #13211
- Install http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.6.spkg
- Apply trac_6391_libGAP.patch to the Sage library
- Apply trac_6391_libGAP_root.patch to the root repository
Code in sage/libs/gap/test/
demonstrates an interface to libgap
from C.
Attachments (12)
Change History (180)
comment:1 Changed 12 years ago by
comment:2 Changed 12 years ago by
Before the above, be sure to do
import sage.libs.gap.gap
Changed 12 years ago by
comment:3 Changed 12 years ago by
- Description modified (diff)
Make sure to use the latest spkg, which I'll keep in the ticket description.
Changed 12 years ago by
comment:4 Changed 12 years ago by
- Description modified (diff)
comment:5 Changed 12 years ago by
- Description modified (diff)
comment:6 Changed 12 years ago by
- Type changed from defect to enhancement
Changed 12 years ago by
comment:7 Changed 12 years ago by
- Description modified (diff)
Changed 11 years ago by
comment:8 Changed 11 years ago by
- Description modified (diff)
comment:9 follow-up: ↓ 37 Changed 11 years ago by
This log pretty much explains what/why/what next:
sage: import sage.libs.gap.gap as g sage: a = g.libgap('10') sage: a 10 sage: type(a) <type 'sage.libs.gap.gap.GapElement'> sage: a*a 100 sage: timeit('a*a') 625 loops, best of 3: 209 ns per loop sage: b = gap('10') sage: b 10 sage: b*b 100 sage: type(b) <class 'sage.interfaces.gap.GapElement'> sage: !ps ax |grep gap 5497 pts/110 Ss+ 0:00 /home/bober/sage-4.1/local/lib/gap-4.4.10/bin/x86_64-unknown-linux-gnu-gcc/gap -m 24m -l /home/bober/sage-4. 19751 pts/84 SNs+ 0:00 /home/SimonKing/SAGE/sage-4.1.alpha1/local/lib/gap-4.4.10/bin/x86_64-unknown-linux-gnu-gcc/gap -m 24m -l /ho 27563 pts/109 Ss+ 0:00 /scratch/steinz/sage/local/lib/gap-4.4.10/bin/x86_64-unknown-linux-gnu-gcc/gap -m 24m -l /scratch/steinz/sag 27572 pts/98 S+ 0:00 sh -c ps ax |grep gap 27574 pts/98 S+ 0:00 grep gap sage: b.name() '$sage1' sage: timeit('b*b') 625 loops, best of 3: 292 µs per loop sage: a = g.libgap('0') sage: a 0 sage: b = g.libgap('10') sage: b/a hit stderr
comment:10 Changed 11 years ago by
Overview:
- Modified version of GAP, which is built by doing
sage -f -m http://sage.math.washington.edu/home/wstein/patches/gap/gap-4.4.10.p17.spkg wait... cd sage/spkg/build/gap-4.4.10.p17
To rebuild:
steinz@sage:~/scratch/sage/spkg/build/gap-4.4.10.p17/src$ make steinz@sage:~/scratch/sage/spkg/build/gap-4.4.10.p17/src/bin/x86_64-unknown-linux-gnu-gcc$ gcc -shared *.o -o libgap.so
- Cython code to use the Gap library:
In here: sage/devel/sage/sage/libs/gap/gap.pyx
If you change gap.pyx, do sage -br
to build the changed version and start Sage.
comment:11 Changed 11 years ago by
- Cc burcin added
comment:12 Changed 11 years ago by
- Cc nborie added
- Report Upstream set to N/A
comment:13 Changed 11 years ago by
- Cc robertwb added
comment:14 follow-up: ↓ 19 Changed 11 years ago by
I get an error when importing libgap on sage 4.3.5 on OSX 10.6.3:
sage: import sage.libs.gap.gap --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /Users/ayeq/sage-devel/<ipython console> in <module>() /Users/ayeq/sage-devel/gap.pyx in init sage.libs.gap.gap (sage/libs/gap/gap.c:6286)() /Users/ayeq/sage-devel/local/lib/python2.6/site-packages/sage/misc/cachefunc.pyc in __init__(self, f, classmethod) 54 55 """ ---> 56 self._common_init(f, ArgumentFixer(f,classmethod=classmethod)) 57 self.cache = {} 58 /Users/ayeq/sage-devel/local/lib/python2.6/site-packages/sage/misc/function_mangling.pyc in __init__(self, f, classmethod) 107 """ 108 --> 109 defaults = f.func_defaults 110 if defaults is None: 111 defaults = [] AttributeError: 'builtin_function_or_method' object has no attribute 'func_defaults'
The cached_function decorator works at the interpreter level so I really do not see what is happening. When the line is removed the import works fine and from what I understand about cache_function this should be okay.
--- a/sage/libs/gap/gap.pyx Sat Jun 27 05:49:14 2009 +0200 +++ b/sage/libs/gap/gap.pyx Sat Apr 10 16:30:27 2010 -0700 @@ -71,8 +71,8 @@ from sage.structure.element cimport ModuleElement, RingElement -from sage.misc.cachefunc import cached_function -@cached_function +#from sage.misc.cachefunc import cached_function +#@cached_function def gap_root(): """ Find the location of the GAP root install which is stored in the gap
comment:15 Changed 10 years ago by
- Cc jeremywest added
comment:16 Changed 10 years ago by
- Cc iandrus added
comment:17 Changed 10 years ago by
- Cc davidm added
comment:18 Changed 10 years ago by
- Description modified (diff)
comment:19 in reply to: ↑ 14 ; follow-up: ↓ 20 Changed 10 years ago by
Replying to davidm:
I get an error when importing libgap on sage 4.3.5 on OSX 10.6.3:
sage: import sage.libs.gap.gap --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /Users/ayeq/sage-devel/<ipython console> in <module>() /Users/ayeq/sage-devel/gap.pyx in init sage.libs.gap.gap (sage/libs/gap/gap.c:6286)() /Users/ayeq/sage-devel/local/lib/python2.6/site-packages/sage/misc/cachefunc.pyc in __init__(self, f, classmethod) 54 55 """ ---> 56 self._common_init(f, ArgumentFixer(f,classmethod=classmethod)) 57 self.cache = {} 58 /Users/ayeq/sage-devel/local/lib/python2.6/site-packages/sage/misc/function_mangling.pyc in __init__(self, f, classmethod) 107 """ 108 --> 109 defaults = f.func_defaults 110 if defaults is None: 111 defaults = [] AttributeError: 'builtin_function_or_method' object has no attribute 'func_defaults'
I see exactly the same with the new spkg on OSX 10.6. And the patch to gap.pyx you suggest works for me too.
comment:20 in reply to: ↑ 19 ; follow-up: ↓ 21 Changed 10 years ago by
Replying to dimpase:
Replying to davidm:
I get an error when importing libgap on sage 4.3.5 on OSX 10.6.3:
I see exactly the same with the new spkg on OSX 10.6. And the patch to gap.pyx you suggest works for me too.
moreover, I get the same problem (and solition(?)) on Linux (on boxen). So this is certainly not OSX-specific.
comment:21 in reply to: ↑ 20 Changed 10 years ago by
Replying to dimpase:
Replying to dimpase:
Replying to davidm:
I get an error when importing libgap on sage 4.3.5 on OSX 10.6.3:
I see exactly the same with the new spkg on OSX 10.6. And the patch to gap.pyx you suggest works for me too.
moreover, I get the same problem (and solition(?)) on Linux (on boxen). So this is certainly not OSX-specific.
it turns out that cached_function won't work in Cython at all, so indeed this needs to be changed. The cumulative patch 6391.6.patch fixed this, as well, as it supersedes the previous 4 patches.
To install for Sage 4.6.1, install the updated spkg, and this patch.
Dima
comment:22 follow-up: ↓ 23 Changed 10 years ago by
Perhaps someone who understands libs/gap/gap.pyx better than me can comment on few sticking points I encounter:
class Gap(ParentWithBase?) is instantiated only once, for base=ZZ. Is it meant that it should be instantiated for other bases, too? And if so, which ones? (I must say it's very puzzling to me piece of code...)
in the class GapElement?, _div_ and other member functions can potentially fail (as demonstrated in the comment "This log pretty much explains what/why/what next:..." above), e.g. due to division by 0. It is meant that the corresponding checks are to be implemented in these member functions? I guess not, it's rather a matter of properly catching the corresponding GAP interrupts, right?
What _dealloc_ in this class meant to do?
comment:23 in reply to: ↑ 22 ; follow-up: ↓ 24 Changed 10 years ago by
Replying to dimpase:
class Gap(ParentWithBase?) is instantiated only once, for base=ZZ. Is it meant that it should be instantiated for other bases, too? And if so, which ones? (I must say it's very puzzling to me piece of code...)
No, only once for base=ZZ.
in the class GapElement?, _div_ and other member functions can potentially fail (as demonstrated in the comment "This log pretty much explains what/why/what next:..." above), e.g. due to division by 0. It is meant that the corresponding checks are to be implemented in these member functions? I guess not, it's rather a matter of properly catching the corresponding GAP interrupts, right?
Yes. I don't know if GAP uses "interrupts" though. You are basically above asking: "Here is a problem nobody has solved yet, which is why libgap hasn't moved forward. What is the solution?"
What _dealloc_ in this class meant to do?
See {{dealloc}} at http://docs.cython.org/src/reference/extension_types.html for the definition of dealloc. It is like del in python.
comment:24 in reply to: ↑ 23 Changed 10 years ago by
Replying to was:
Replying to dimpase:
in the class GapElement?, _div_ and other member functions can potentially fail (as demonstrated in the comment "This log pretty much explains what/why/what next:..." above), e.g. due to division by 0. It is meant that the corresponding checks are to be implemented in these member functions? I guess not, it's rather a matter of properly catching the corresponding GAP interrupts, right?
Yes. I don't know if GAP uses "interrupts" though. You are basically above asking: "Here is a problem nobody has solved yet, which is why libgap hasn't moved forward. What is the solution?"
From printing contents of the GAP interpreter output_buffer (introduced in the patch of GAP's scanner.c), I see that during the fatal a._div_(g.libgap('0'))_ it starts getting the contents of the usual GAP error message, like Entering break read-eval-print loop (i.e. it does a "GAP interrupt"). And then the crash happens in the Python interpreter. So I suppose more reverse engineering/understanding of the GAP interpreter is needed here, in order to avoid replicating it in Python...
comment:25 follow-up: ↓ 26 Changed 10 years ago by
- Status changed from new to needs_work
I updated the patch to work with Sage-4.7.alpha1. I also added a bunch of doctests while trying to understand what is going on and replaced the deprecated ParentWithBase
with Parent
.
I'll be doing some more work on libgap during Sage Days 29, so let me know if you have any suggestions.
comment:26 in reply to: ↑ 25 Changed 10 years ago by
Replying to vbraun:
I updated the patch to work with Sage-4.7.alpha1. I also added a bunch of doctests while trying to understand what is going on and replaced the deprecated
ParentWithBase
withParent
.I'll be doing some more work on libgap during Sage Days 29, so let me know if you have any suggestions.
I am not so sure that we should invest a lot of time in libGAP based on the current GAP 4.4.12, as GAP 4.5 is almost ready, (as a GAP package developer, I'm expecting to get it pretty soon) and has a lot of internals reworked. I understand that the GC is replaced by the Bohm's GC, and the arbitrary precision arithmetic is done by GMP, not by the internal GAP code (I suggested that they should try MPIR instead of GMP).
comment:27 follow-up: ↓ 32 Changed 10 years ago by
From my memory of libGAP the GC and the large integer arithmetic are totally orthogonal/irrelevant. I think working on libGAP whenever somebody has the interest (!) is a good idea, since it really will be a major, major plus for Sage when it starts working.
comment:28 follow-up: ↓ 29 Changed 10 years ago by
I think the big issues right now are
- being able to get out of the break/debug loop after a gap error
- use libtool to build the library
If upstream manages to rid themselves of their memory manager and arbitrary precision arithmetic then thats awesome!
comment:29 in reply to: ↑ 28 Changed 10 years ago by
Replying to vbraun:
I think the big issues right now are
- being able to get out of the break/debug loop after a gap error
- use libtool to build the library
If upstream manages to rid themselves of their memory manager and arbitrary precision arithmetic then thats awesome!
Hi Volker, please see my current (Sage-4.6.1) snapshot, catching zero division etc.
http://sage.math.washington.edu/home/dima/packages/gap-4.4.12.p6.spkg
It gets rid of the zero division problem. I.e. I can divide by 0 in GAP and still retain Sage/GAP session. Here is an example (sorry for extra print statements producing noise below)
sage: import sage.libs.gap.gap as g ######### ###### ########### ### ############# ###### ############ #### ############## ######## ############# ##### ############### ######## ##### ###### ##### ###### # ######### ##### ##### ###### ###### ########## ##### ##### ####### ##### ##### #### ##### ###### ######## #### ##### ##### ############# ### #### ##### ####### #### #### ########### #### #### ##### ####### ##### ##### ###### #### #### ##### ####### ##### ##### ##### ############# ##### ##### ################ ##### ############# ###### ##### ################ ##### ############# ################ ################## ##### #### ############### ##### ##### ##### #### ############# ##### ##### ##### #### ######### ##### ##### ##### #### Information at: http://www.gap-system.org Try '?help' for help. See also '?copyright' and '?authors' Loading the library. Please be patient, this may take a while. GAP4, Version: 4.4.12 of 17-Dec-2008, i686-apple-darwin10.6.0-gcc sage: a = g.libgap('0') > status in GapElement()= 0 sage: b = g.libgap('10') > status in GapElement()= 0 sage: a calling READ_ERR at ViewObjVar0 output_buffer=0 0 sage: b calling READ_ERR at ViewObjVar10 output_buffer=10 10 sage: a*b calling READ_ERR at ViewObjVar0 output_buffer=0 0 sage: b/a Rational operations: <divisor> must not be zero not in any function Entering break read-eval-print loop ... you can 'quit;' to quit to outer loop, or you can replace <divisor> via 'return <divisor>;' to continue --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) /usr/local/src/sage/sage-4.6.1.rc0/spkg/standard/<ipython console> in <module>() /usr/local/src/sage/current/local/lib/python2.6/site-packages/sage/structure/element.so in sage.structure.element.RingElement.__div__ (sage/structure/element.c:11931)() RuntimeError: ReadEvalDebug called! sage: a*b calling READ_ERR at ViewObjVar0 output_buffer=0 0 sage: b+b calling READ_ERR at ViewObjVar20 output_buffer=20 20 sage:
Dima
comment:30 Changed 10 years ago by
- Cc kini added
comment:31 Changed 10 years ago by
- Description modified (diff)
comment:32 in reply to: ↑ 27 Changed 10 years ago by
- Description modified (diff)
Replying to was:
From my memory of libGAP the GC and the large integer arithmetic are totally orthogonal/irrelevant. I think working on libGAP whenever somebody has the interest (!) is a good idea, since it really will be a major, major plus for Sage when it starts working.
I'll try to get access to GAP 4.5 for Sage as soon as possible. As I understood from GAP people, their current GC is a major headache making it hard to write a "usual" library interface, which might be much nicer to have... AFAIK, Bohm's GC is more manageable in this respect.
Well, perhaps indeed the changes in 4.5 aren't that big to warrant putting this on old.
comment:33 follow-up: ↓ 35 Changed 10 years ago by
- Description modified (diff)
Changes to the newest spkg:
- removed dist directory
- removed unsetting CC/CXX since "sage -sh" sets these to sane values
- converted all copied files from patches/ into patches
- using libtool to build libGAP
- Code cleanups
Basic functionality now works including trapping errors:
sage: import sage.libs.gap.gap as g sage: g.libgap('1/0') ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (1312, 0)) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/vbraun/opt/sage-4.7.alpha1/devel/sage-main/sage/libs/gap/<ipython console> in <module>() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__call__ (sage/structure/parent.c:6816)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3254)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3157)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.Gap._element_constructor_ (sage/libs/gap/gap.c:4963)() 684 """ 685 initialize_libgap() --> 686 return self.element_class(self, x) 687 688 /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.GapElement.__init__ (sage/libs/gap/gap.c:3047)() 366 except RuntimeError, msg: 367 ClearError() --> 368 raise ValueError, 'Gap: '+str(msg) 369 370 assert Symbol == S_SEMICOLON, 'Did not end with semicolon?' ValueError: Gap: Rational operations: <divisor> must not be zero
comment:34 Changed 10 years ago by
comment:35 in reply to: ↑ 33 Changed 10 years ago by
Replying to vbraun:
Changes to the newest spkg:
Volker,
the spkg does not buid on MacOSX. When building the library, I get
... checking host system type... (cached) i686-apple-darwin10.6.0 configure: creating ./config.status config.status: creating gac config.status: creating Makefile config.status: creating config.h ( cd bin/i686-apple-darwin10.6.0-gcc ; make CC='gcc' ) libtool --mode=compile gcc -I. -I../.. -DCONFIG_H -Wall -g -O2 -o ariths.o -c ../../src/ariths.c libtool: unknown option character `-' in: --mode=compile Usage: libtool -static [-] file [...] [-filelist listfile[,dirname]] [-arch_only arch] [-sacLT] Usage: libtool -dynamic [-] file [...] [-filelist listfile[,dirname]] [-arch_only arch] [-o output] [-install_name name] [-compatibility_version #] [-current_version #] [-seg1addr 0x#] [-segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table <filename>] [-seg_addr_table_filename <file_system_path>] [-all_load] [-noall_load] make[1]: *** [ariths.o] Error 1 make: *** [compile] Error 2 Error building GAP.
comment:36 Changed 10 years ago by
Hi Dima, Ivan Andrus already told me about the OSX issue and I'm pretty sure he'll fix it tomorrow. The problem is that OSX calls libtool glibtool
.
comment:37 in reply to: ↑ 9 Changed 10 years ago by
Replying to was:
This log pretty much explains what/why/what next:
sage: import sage.libs.gap.gap as g sage: a = g.libgap('10') sage: a 10 sage: type(a) <type 'sage.libs.gap.gap.GapElement'> sage: a*a 100 sage: timeit('a*a') 625 loops, best of 3: 898 ns per loop sage: b = gap('10') sage: timeit('b*b') 125 loops, best of 3: 2.05 ms per loop sage: a = g.libgap('0') sage: a 0 sage: b = g.libgap('10') sage: b/a --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/vbraun/opt/sage-4.7.alpha1/devel/sage-main/sage/libs/gap/<ipython console> in <module>() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/element.so in sage.structure.element.RingElement.__div__ (sage/structure/element.c:12696)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.GapElement._div_ (sage/libs/gap/gap.c:4443)() 613 except RuntimeError, msg: 614 ClearError() --> 615 raise ValueError, 'Gap: '+str(msg) 616 617 ValueError: Gap: Rational operations: <divisor> must not be zero
I'm currently adding code to access Gap containers, e.g.
sage: S4 = g.libgap('SymmetricGroup(4)') sage: S4.List() [ (), (1,4), (1,2,4), (1,3,4), (2,4), (1,4,2), (1,2), (1,3,4,2), (2,3,4), (1,4,2,3), (1,2,3), (1,3)(2,4), (3,4), (1,4,3), (1,2,4,3), (1,3), (2,4,3), (1,4,3,2), (1,2)(3,4), (1,3,2), (2,3), (1,4)(2,3), (1,2,3,4), (1,3,2,4) ] sage: S4_elements = _ sage: type(S4_elements) <type 'sage.libs.gap.gap.GapElement_List'> sage: S4_elements[3] (1,3,4) sage: prod( g for g in S4_elements ) (1,3)(2,4)
comment:38 follow-up: ↓ 39 Changed 10 years ago by
I got it into a bad state:
sage: import sage.libs.gap.gap as g sage: g.libgap('0') 0 sage: g.libgap('if 4>3 then\nPrint("hi");\nfi') NULL sage: g.libgap('if 4>3 thenPrint("hi");\nfi') --------------------------------------------------------------------------- AssertionError Traceback (most recent call last) /Users/gvol/<ipython console> in <module>() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__call__ (sage/structure/parent.c:6816)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3254)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3157)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.Gap._element_constructor_ (sage/libs/gap/gap.c:6866)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.libgap_eval (sage/libs/gap/gap.c:2976)() AssertionError: The return status of ReadEvalCommand must be zero. sage: g.libgap('0') --------------------------------------------------------------------------- AssertionError Traceback (most recent call last) /Users/gvol/<ipython console> in <module>() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__call__ (sage/structure/parent.c:6816)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3254)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3157)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.Gap._element_constructor_ (sage/libs/gap/gap.c:6866)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.libgap_eval (sage/libs/gap/gap.c:2976)() AssertionError: The return status of ReadEvalCommand must be zero. sage:
comment:39 in reply to: ↑ 38 ; follow-up: ↓ 40 Changed 10 years ago by
Replying to iandrus:
well, it works as it should in p6, so that's something that got in p7. Indeed, with p6 I get
sage: gap('if 4>3 thenPrint("hi");\nfi') --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /private/tmp/<ipython console> in <module>() /usr/local/src/sage/current/local/lib/python2.6/site-packages/sage/interfaces/expect.pyc in __call__(self, x, name) 1093 1094 if isinstance(x, basestring): -> 1095 return cls(self, x, name=name) 1096 try: 1097 return self._coerce_from_special_method(x) /usr/local/src/sage/current/local/lib/python2.6/site-packages/sage/interfaces/expect.pyc in __init__(self, parent, value, is_name, name) 1520 except (TypeError, KeyboardInterrupt, RuntimeError, ValueError), x: 1521 self._session_number = -1 -> 1522 raise TypeError, x 1523 self._session_number = parent._session_number 1524 TypeError: Gap produced error output Syntax error: expression expected $sage3:=if 4>3 thenPrint("hi");fi;; ^ executing $sage3:=if 4>3 thenPrint("hi");fi;;
which is basically how it should be: cf. sage: gap('if 4>3 then\nPrint("hi");\nfi')
comment:40 in reply to: ↑ 39 Changed 10 years ago by
Replying to dimpase:
oops, no, sorry, please disregard my last comment; with p6 I also get something strange...
comment:41 Changed 10 years ago by
- Cc kcrisman added
comment:42 Changed 10 years ago by
Updated version (both spkg and library patch) fixes this issue:
sage: import sage.libs.gap.gap as g sage: g.libgap('0') 0 sage: g.libgap('if 4>3 then\nPrint("hi");\nfi') NULL sage: g.libgap('if 4>3 thenPrint("hi");\nfi') ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (1312, 0)) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/vbraun/opt/sage-4.7.alpha1/devel/sage-main/sage/libs/gap/<ipython console> in <module>() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__call__ (sage/structure/parent.c:6816)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3254)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3157)() /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.Gap._element_constructor_ (sage/libs/gap/gap.c:6995)() 1125 if not isinstance(x, str): 1126 x = x._gap_init_() -> 1127 return make_GapElement(self, libgap_eval(x)) 1128 1129 /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.libgap_eval (sage/libs/gap/gap.c:3034)() 424 if status != STATUS_END: 425 ClearError() --> 426 raise ValueError, 'Not a normal statement.' 427 return NULL 428 ValueError: Not a normal statement. sage: g.libgap('0') 0
Also, I changed the libGAP memory allocation to not use sbrk()
, now it runs under valgrind ;-)
comment:43 Changed 10 years ago by
The latest version of the libGAP patch now properly holds references to the GAP memory objects and releases them during GapElement.__deref__
. No more random crashes because the GAP memory manager (GASMAN) recycles the Gap objects that Sage still references!
I feel this is now stable enough for wider testing. I can't crash it any more :-) Please give it a whirl and let me know if you manage to segfault it!
comment:44 follow-up: ↓ 45 Changed 10 years ago by
Newest version can convert various GAP datatypes back to Sage, for example cyclotomic numbers
sage: libgap('5/3 + 7*E(3)').sage() 7*zeta3 + 5/3
and permutations:
sage: generators = libgap.AlternatingGroup(4).GeneratorsOfGroup().sage() sage: generators # a Sage list of Sage permutations! [(1,2,3), (2,3,4)] sage: PermutationGroup(generators).cardinality() # computed in Sage 12 sage: libgap.AlternatingGroup(4).Size() # computed in GAP 12
comment:45 in reply to: ↑ 44 ; follow-up: ↓ 47 Changed 10 years ago by
Replying to vbraun:
Newest version can convert various GAP datatypes back to Sage, for example cyclotomic numbers
sage: libgap('5/3 + 7*E(3)').sage() 7*zeta3 + 5/3and permutations:
sage: generators = libgap.AlternatingGroup(4).GeneratorsOfGroup().sage() sage: generators # a Sage list of Sage permutations! [(1,2,3), (2,3,4)] sage: PermutationGroup(generators).cardinality() # computed in Sage 12 sage: libgap.AlternatingGroup(4).Size() # computed in GAP 12
This sounds great! What about matrices? (it would be even better if there was a well-explained in docs implementation example of such a conversion). E.g. for my work I need to convert GAP matrices (or non-standard sparse GAP matrices) into CVXOPT matrices.
comment:46 Changed 10 years ago by
Hi -- vbraun, this is amazing! You are a genius. W00t.
comment:47 in reply to: ↑ 45 Changed 10 years ago by
Replying to dimpase:
This sounds great! What about matrices?
If a dense matrix is good enough for you then you can just convert it to a List of Lists in Gap and then use the .sage()
method which recurses through the lists and can convert numbers:
sage: from sage.libs.gap.libgap import libgap sage: M = libgap('BlockMatrix([[1,1,[[1, 2],[ 3, 4]]], [1,2,[[9,10],[11,12]]], [2,2,[[5, 6],[ 7, 8]]]],2,2)') sage: M <block matrix of dimensions (2*2)x(2*2)> sage: M.List().sage() [[1, 2, 9, 10], [3, 4, 11, 12], [0, 0, 5, 6], [0, 0, 7, 8]] sage: matrix(ZZ,_) [ 1 2 9 10] [ 3 4 11 12] [ 0 0 5 6] [ 0 0 7 8]
comment:48 follow-up: ↓ 49 Changed 10 years ago by
When testing the sage/libs/gap/ directory, I get a number of errors in libgap.pyx only. Most stuff passes, but it seems to handle errors differently. See below for an example; every error is something analogous to this, though of course they look different depending on what error is raised instead of what is expected.
This is on Mac OS X 10.4 PPC.
File "/Users/student/Desktop/sage-4.6.2/devel/sage/sage/libs/gap/libgap.pyx", line 670: sage: libgap(1) / libgap('0') Expected: Traceback (most recent call last): ... ValueError: Gap: Rational operations: <divisor> must not be zero Got: Traceback (most recent call last): File "/Users/student/Desktop/sage-4.6.2/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/Users/student/Desktop/sage-4.6.2/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/Users/student/Desktop/sage-4.6.2/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_17[7]>", line 1, in <module> libgap(Integer(1)) / libgap('0')###line 670: sage: libgap(1) / libgap('0') File "element.pyx", line 1549, in sage.structure.element.RingElement.__div__ (sage/structure/element.c:11981) RuntimeError: Rational operations: <divisor> must not be zero
By the way, this needs some authors and reviewers in the list :)
comment:49 in reply to: ↑ 48 Changed 10 years ago by
Replying to kcrisman:
When testing the sage/libs/gap/ directory, I get a number of errors in libgap.pyx only. Most stuff passes, but it seems to handle errors differently. See below for an example; every error is something analogous to this, though of course they look different depending on what error is raised instead of what is expected.
This is on Mac OS X 10.4 PPC.
File "/Users/student/Desktop/sage-4.6.2/devel/sage/sage/libs/gap/libgap.pyx", line 670: sage: libgap(1) / libgap('0')
I expect that this is caught by Sage itself rather than by GAP (Sage recognizes that an illegal division is going to happen).
[...]
By the way, this needs some authors and reviewers in the list :)
I added some authors, in alphabetical order--–don't know if this is a complete list.
comment:50 follow-up: ↓ 52 Changed 10 years ago by
No, libgap(1) / libgap('0')
is evaluated in GAP and raises an error in GAP. We injected an abort()
in the GAP code, so the sig_on()
/sig_off()
block catches it as RuntimeError
. The GapElement._div_
method should catch the RuntimeError
and re-raise it as ValueError
. This works for me (all doctests pass on Fedora 14 x86_64). Are you using the newest version of trac_6391_libGAP.patch
?
comment:51 Changed 10 years ago by
Assuming you do not have the GAP small group database installed, then running
sage: import sage.libs.gap.gap as g sage: g.libgap('SmallGroup(12,3)') --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /Users/gvol/SageStuff/gap-4.4.12.p7/src/<ipython console> in <module>() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__call__ (sage/structure/parent.c:6816)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3254)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/structure/coerce_maps.so in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (sage/structure/coerce_maps.c:3157)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.Gap._element_constructor_ (sage/libs/gap/gap.c:7237)() /Users/gvol/vcs/cur-sage/local/lib/python2.6/site-packages/sage/libs/gap/gap.so in sage.libs.gap.gap.libgap_eval (sage/libs/gap/gap.c:3005)() ValueError: Gap: Aborted
The error message could be a bit more helpful, but when runnning under sage --valgrind
it leads to a segfault.
comment:52 in reply to: ↑ 50 ; follow-up: ↓ 53 Changed 10 years ago by
- Reviewers set to Dima Pasechnik, Ivan Andrus, Volker Braun, William Stein
Replying to vbraun:
No,
libgap(1) / libgap('0')
is evaluated in GAP and raises an error in GAP. We injected anabort()
in the GAP code, so thesig_on()
/sig_off()
block catches it asRuntimeError
. TheGapElement._div_
method should catch theRuntimeError
and re-raise it asValueError
. This works for me (all doctests pass on Fedora 14 x86_64). Are you using the newest version oftrac_6391_libGAP.patch
?
I think so.
sage: hg_sage.import_patch('http://trac.sagemath.org/sage_trac/raw-attachment/ticket/6391/trac_6391_libGAP.patch')
is how I imported it, then ./sage -br
. Like I said, it passes everything else in that directory. (I haven't done other tests because it takes a loooong time.)
That part seems to have first shown in in the .2.patch. It didn't get cancelled in the going back to just .patch, did it?
comment:53 in reply to: ↑ 52 ; follow-up: ↓ 54 Changed 10 years ago by
Replying to kcrisman:
That part seems to have first shown in in the .2.patch. It didn't get cancelled in the going back to just .patch, did it?
The patches are not cummulative. You need to back out old versions before applying the newest one.
comment:54 in reply to: ↑ 53 Changed 10 years ago by
Replying to vbraun:
Replying to kcrisman:
That part seems to have first shown in in the .2.patch. It didn't get cancelled in the going back to just .patch, did it?
The patches are not cummulative. You need to back out old versions before applying the newest one.
I only applied this most recent one. I was just wondering whether somehow I should have applied the .2.patch. But I don't think this is the issue.
Interestingly, I get long hangs, so I think you may be right that I'm somehow missing the !sig_on stuff. But
try: sig_on() result = make_GapElement(self.parent(), DIFF(self.value, (<GapElement>right).value)) sig_off() return result except RuntimeError, msg: ClearError() raise ValueError, 'Gap: '+str(msg)
is what I get for the code of g1._sub_??
.
But I did get this scary thing:
sage: libgap(1) /Users/student/Desktop/sage-4.6.2/local/bin/sage-sage: line 308: 14591 Abort trap sage-ipython "$@" -i
Could this is another example of using the wrong !MAC_OSX_DEPLOYMENT_TARGET or something, like it was for the initial problems with 10.6 not working... ? Maybe that's impossible.
comment:55 Changed 10 years ago by
This also seems to be a strangely formed spkg. All that is in it is a folder called gap-4.4.12.p7, which is not the usual practice. Where is src/, spkg-install, etc?
comment:56 follow-up: ↓ 57 Changed 10 years ago by
The libGAP requires Sage-4.7.alpha1 or later because it uses the new signal handling stuff that Jeroen just merged. I saw you use 4.6.2, so that explains why the exceptions are not caught correctly. The spkg has the normal layout, not sure what you are doing wrong. It is not bzip2-compressed since that is faster to test, seems like you are not unpacking it correctly.
comment:57 in reply to: ↑ 56 Changed 10 years ago by
Replying to vbraun:
The libGAP requires Sage-4.7.alpha1 or later because it uses the new signal handling stuff that Jeroen just merged. I saw you use 4.6.2, so that explains why the exceptions are not caught correctly.
Great, that clarifies that.
The spkg has the normal layout, not sure what you are doing wrong. It is not bzip2-compressed since that is faster to test, seems like you are not unpacking it correctly.
This is hilarious - my Macs interpret the file ending .p7
as a cryptographic file. Removing that makes all well.
Sounds like you are all well on the way to solving this - another nice addition!
comment:58 Changed 10 years ago by
- Description modified (diff)
comment:59 follow-up: ↓ 60 Changed 10 years ago by
- Status changed from needs_work to needs_review
The updated gap-4.4.12.p8 now contains a separate libgap/
directory with a copy of the gap kernel sources and new autoconf scripts that can actually build a shared library on Solaris.
While this layout is probably not the final word in how to build libgap, I think its good enough to test it on a wider audience. Once we are confident that it works well we should contact upstream and find out in how far they are willing to add shared library support. Ready for review!
comment:60 in reply to: ↑ 59 Changed 10 years ago by
Replying to vbraun:
The updated gap-4.4.12.p8 now contains a separate
libgap/
directory with a copy of the gap kernel sources and new autoconf scripts that can actually build a shared library on Solaris.While this layout is probably not the final word in how to build libgap, I think its good enough to test it on a wider audience. Once we are confident that it works well we should contact upstream and find out in how far they are willing to add shared library support. Ready for review!
Hi Volker, you mentioned adding doctests etc. Do you mean for the low-level stuff in gap.pyx ?
Did you try completely replacing gap interface with libgap interface? IMHO it's about time to start doing this --- this would uncover more things to do, I imagine.
It would be great is libgap/ contained at least one C example on building a C application that links against libGAP and does something, like computing the order of a permutation group. Would be good for stress-testing, and just understanding the interface better. Anyone out there who has time for this now? (not me :-( ) I imagine it's more work on a makefile than on the C side.
Regarding Sage-libGAP interface, I would like to understand what happens in a scenario when a Python object P holds a reference to a GAP object G, and then P gets GC'ed. This should result in G getting freed (eventually) by GAP's GC. It would be good to see an evidence that this actually does happen.
Did you check that things work with GAP workspaces (Saving/Loading? workspaces, that is)?
comment:61 follow-up: ↓ 62 Changed 10 years ago by
Hi Dima,
Yes everything in libgap.pyx
is doctested. I have't tried to replace gap by libgap in the Sage library, first I want to see if the new spkg compiles on all supported platforms. But p8 uses the standard autotools to build the shared library, so I'm pretty confident.
There is a subdirectory sage/libs/gap/test
that contains a small C program for testing purposes just like what you want.
Getting garbage collection in Gap work to work correctly was one of the major issues that I worked on over the week. For starters, Gasman has no explicit reference counts. It is also compacting, so we must never hold direct pointers into the memory. The way it works is that
libgap.pyx
first creates a new Gap global variablelibgap_owned_objects
and assigns an emptyrec()
to it.- Every Python
GapElement
adds is wrapped Gap object tolibgap_owned_objects
. - The
GapElement.__dealloc__
removes the Gap object fromlibgap_owned_objects
. It is then no longer referenced inside Gap and Gasman eventually recycles the object.
This is doctested in the __dealloc__
documentation.
I haven't tried saving/loading Gap workspaces. But it doesn't make much sense in libGAP since it would break the Python<->Gap object relations. If you need to load a huge pre-evaluated Gap script then you probably don't need libGAP, which is all about fast interaction with Gap.
comment:62 in reply to: ↑ 61 Changed 10 years ago by
Replying to vbraun:
I haven't tried saving/loading Gap workspaces. But it doesn't make much sense in libGAP since it would break the Python<->Gap object relations. If you need to load a huge pre-evaluated Gap script then you probably don't need libGAP, which is all about fast interaction with Gap.
At least the initialization of libGAP should probably use a prebuilt workspace, as is done by the current interface. The reason is to speed it up.
Even with Python<-> GAP relations lost, saving workspace might still make sense (if you know the GAP names of objects
created, you can get them, right?).
And I don't see why it is really lost, as is it recorded in Gap global variable libgap_owned_objects.
Which would make it possible to re-create the corresponding Python's GapElement
data.
comment:63 follow-up: ↓ 64 Changed 10 years ago by
During the libgGAP initialization you can pass any command line arguments to GAP, so we can easily load a workspace. Note that Gap initialization happens the first time you use libGAP, so it does not add to the Sage startup time.
Its true that one could recreate the GapElement
s from a saved/loaded workspace (though you lose the Python variable names), but it still doesn't seem to be the most pressing issue right now.
comment:64 in reply to: ↑ 63 Changed 10 years ago by
Replying to vbraun:
During the libgGAP initialization you can pass any command line arguments to GAP, so we can easily load a workspace. Note that Gap initialization happens the first time you use libGAP, so it does not add to the Sage startup time.
OK, but it does add to libGAP startup time.
Its true that one could recreate the
GapElement
s from a saved/loaded workspace (though you lose the Python variable names), but it still doesn't seem to be the most pressing issue right now.
I certainly agree with this.
comment:65 Changed 10 years ago by
- Cc nthiery added
comment:66 Changed 10 years ago by
A relevant status update and overview from Volker:
Hi Stephen,
I wanted to contact you for a while about whether and how to integrate the C GAP library interface that we wrote. I think it would be great to have a well-defined shared library interface, and it sounds like you are interested in that as well. We have a working prototype at http://trac.sagemath.org/sage_trac/ticket/6391 that just needs review as far as I am concerned. It doesn't have a nicely abstracted interface, but it works for Sage purposes. Let me comment on the points in your pdf:
1) IO: we want to inject input and catch output, so we can evaluate input strings and parse output strings. For this, we just patched SyFgets?() / PutChrTo?().
2) For errors, just send a signal from the shared library. We patched ReadEvalError?() to call abort(). The user of the shared library can then install their own signal handler if they want to catch that. I don't think entering the break/eval loop is particularly useful in a shared library, we just set BreakOnError? = 0.
3) similarly, if the user of the library wants to interrupt a GAP computation she can just signal SIGINT etc.
4) To keep objects alive, the Sage library interface just creates a global GAP record (which aren't garbage collected)
libgap_owned_objects = GVarName( "libgap_owned_objects" ); AssGVar(libgap_owned_objects, NEW_PREC(0))
and then references any objects that are wrapped by libGAP:
libgap_owned_objects_counter += 1 self.libgap_owned_objects_rnam = RNamIntg(libgap_owned_objects_counter) AssPRec(VAL_GVAR(libgap_owned_objects),
self.libgap_owned_objects_rnam, self.value)
For simplicity we implemented this in Cython, but that should probably be moved in the C library interface.
5) Memory management: I replaced the sbrk with a malloc'ed workspace. Added advantage: you can then use valgrind. I think valgrind disallows large sbrk() calls to force the libc malloc implementation to avoid it. For now, the libGAP workspace size has to be fixed at initialization. This isn't ideal but Dima thought that you have some long-term plans for switching to a different garbage collector. Maybe you can tell us more about that.
6) We didn't hit any name collisions in Sage, so its not an urgent issue. I agree that eventually only the relevant symbols should be exported by the shared library but GAP generally uses less common names. Most C code doesn't use CamelCase, for starters.
7) I haven't tried loading modules from within libGAP.
8) I didn't encounter any problems with GMP. Sage uses MPIR.
In any case, I'm very interested in getting a library implementation upstream and can help with that. I'm currently travelling around for conferences and will be back in DIAS in Dublin for more than a couple of days starting in August.
Best wishes, Volker
comment:67 Changed 10 years ago by
- Status changed from needs_review to needs_work
Needs work?
---------------------------------------------------------------------- | Sage Version 4.7, Release Date: 2011-05-17 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- sage: import sage.libs.gap.all sage: a = sage.libs.gap.all.libgap(2) sage: a + a 4 sage: timeit('a+a', number=10^6) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (27, 0)) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /tmp/wstein/sage-4.7/devel/sage-main/<ipython console> in <module>() /tmp/wstein/sage-4.7/local/lib/python2.6/site-packages/sage/misc/sage_timeit_class.so in sage.misc.sage_timeit_class.SageTimeit.__call__ (sage/misc/sage_timeit_class.c:744)() /tmp/wstein/sage-4.7/local/lib/python2.6/site-packages/sage/misc/sage_timeit_class.so in sage.misc.sage_timeit_class.SageTimeit.eval (sage/misc/sage_timeit_class.c:605)() /tmp/wstein/sage-4.7/local/lib/python2.6/site-packages/sage/misc/sage_timeit.pyc in sage_timeit(stmt, globals, preparse, number, repeat, precision) 182 break 183 --> 184 best = min(timer.repeat(repeat, number)) / number 185 186 finally: /tmp/wstein/sage-4.7/local/lib/python/timeit.pyc in repeat(self, repeat, number) 218 r = [] 219 for i in range(repeat): --> 220 t = self.timeit(number) 221 r.append(t) 222 return r /tmp/wstein/sage-4.7/local/lib/python/timeit.pyc in timeit(self, number) 191 gcold = gc.isenabled() 192 gc.disable() --> 193 timing = self.inner(it, self.timer) 194 if gcold: 195 gc.enable() /tmp/wstein/sage-4.7/devel/sage-main/<magic-timeit> in inner(_it, _timer) /tmp/wstein/sage-4.7/local/lib/python2.6/site-packages/sage/structure/element.so in sage.structure.element.RingElement.__add__ (sage/structure/element.c:11367)() /tmp/wstein/sage-4.7/local/lib/python2.6/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement._add_ (sage/libs/gap/libgap.c:4381)() ValueError: Gap: Exhausted the GAP memory pool.
comment:68 Changed 10 years ago by
- Cc jpflori added
comment:69 Changed 10 years ago by
PING: Should we try to get a very experimental version of libGAP in that has memory leaks? Seems worrisome...?
comment:70 Changed 9 years ago by
I have been trying to make my free groups/finitely presented groups (see #12339) wraper with libgap, and in general it works fine (and an impressive speed, i must say). There are some random segfauls though. And i have run into a problem that can be traced down to:
sage: from sage.libs.gap.all import libgap sage: F=libgap('FreeGroup(2)') sage: lis=libgap('[]') sage: (a,b)=F.GeneratorsOfGroup() sage: lis.Add(a^2) sage: lis.Add(b^2) sage: lis.Add(a*b*a*b) sage: lis [ f1^2, f2^2, f1*f2*f1*f2 ] sage: H=F/lis sage: H <fp group on the generators [ f1, f2 ]> sage: H.IsomorphismSimplifiedFpGroup() --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/mmarco/sage-4.7.2/<ipython console> in <module>() /home/mmarco/sage-4.7.2/local/lib/python2.6/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_MethodProxy.__call__ (sage/libs/gap/libgap.c:7643)() /home/mmarco/sage-4.7.2/local/lib/python2.6/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_Function.__call__ (sage/libs/gap/libgap.c:7259)() ValueError: Gap: Aborted
comment:71 Changed 9 years ago by
- Dependencies set to #13211
- Description modified (diff)
The libgap doctests pass now. Also, mmarco's example works:
sage: F = libgap.FreeGroup(2) sage: a,b = F.GeneratorsOfGroup() sage: lis = libgap('[]') sage: lis.Add(a^2) sage: lis.Add(b^2) sage: lis.Add(a*b*a*b) sage: lis [ f1^2, f2^2, f1*f2*f1*f2 ] sage: H=F/lis sage: H <fp group on the generators [ f1, f2 ]> sage: H.IsomorphismSimplifiedFpGroup() [ f1, f2 ] -> [ f1, f2 ]
William's timeit('a+a', number=10^6)
also works. If you have any interest in libGAP please try it out this week and let me know if you find any bugs, then I can investigate them during the rest of this week...
comment:72 Changed 9 years ago by
I am running some tests with it. It seems to work fine, except for a few random segfaults (much less than before) I cannot reproduce them.
I will run some more tests, but so far, it looks great.
Is it possible to fix the memory limit for the gap session?
comment:73 Changed 9 years ago by
What do you mean by "fix memory limit"? The absolute limit is fixed. But we can increase the memory limit to be very large on 64-bit, it will only be virtual and not actually used. On 32-bit it will hurt that it counts against the 4GB process limit.
comment:74 Changed 9 years ago by
What i mean is the amount of memory that the gap session can use (which is determined by the -o option). I have noticed that libgap handles this question in a different way than the classical pexpect interface.
Before, if i run a computaqtion that took too much memory in gap, the gap session would eventually be killed (because it is run with the option -o 9999G) by the system, leaving orphaned all the sage objects that interfaced objects in that session.
I have noticed that with this interface it just returns an error, but the objects are not orphaned. This error is returned before all the system memory is exhausted. So i wonder how much memory is used before the error is issued, and how is all this handled.
comment:75 Changed 9 years ago by
The gap command line options that are used for setting up libgap can easily be changed. Right now its pretty small, I know.
If you have any random segfaults can you post your code? I can still debug it even if it is not reproducable.
comment:76 Changed 9 years ago by
I think it would be best if the memory limit would be set automatically deppending on the available RAM in the system.
I just got a segfault playing with a modified version of my patch for finitely presented groups:
F=FreeGroup(3) F.inject_variables() Defining x0, x1, x2 G=F.quotient([x0^2,x1^2,x2^2,(x0*x1)^3,(x1*x2)^3,(x0*x2)^2]) G.inject_variables() Defining x0, x1, x2 sage: g=G.gap() sage: g <fp group of size 24 on the generators [ x0, x1, x2 ]> sage: x=x0.gap() sage: x.Order() --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/mmarco/sage-5.2/<ipython console> in <module>() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_MethodProxy.__call__ (sage/libs/gap/libgap.c:8449)() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_Function.__call__ (sage/libs/gap/libgap.c:8037)() ValueError: libGAP: Segmentation fault
I can send you the whole file with the definition of the classes for G and x0, but i don't think it would give any useful information here: g is just a finitely presented group object of the ligbap interface, and x is one of its generators.
I couldn't reproduce the error.
comment:77 Changed 9 years ago by
Another comment (i am not sure if itshould be fixed or if it is my fault): the testuite of my classes fails because comparison bewteen objects of this interface is not implemented. It works for the old interface though.
comment:78 Changed 9 years ago by
Comparison isn't implemented yet.
If the error is not reproducible try to run it ~100 times to see if it crashes occasionally. And/or run it on another architecture.
comment:79 Changed 9 years ago by
Ok, i have tried to isolate the issue and run it in a loop to reproduce it. It is not easy to catch, but every few thousand iterations it fails:
sage: g=libgap('FreeGroup(2)') sage: (a,b)=g.GeneratorsOfGroup() sage: lis=libgap('[]') sage: lis.Add(a^2) sage: lis.Add(b^2) sage: lis.Add(b*a) sage: h=g/lis sage: c=h.GeneratorsOfGroup()[0] sage: for i in range(3000):^J n=c.Order() ....: sage: for i in range(3000):^J n=c.Order() ....: sage: for i in range(3000):^J n=c.Order() ....: sage: for i in range(3000):^J n=c.Order() ....: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/mmarco/sage-5.2/<ipython console> in <module>() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_MethodProxy.__call__ (sage/libs/gap/libgap.c:8449)() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/libgap.so in sage.libs.gap.libgap.GapElement_Function.__call__ (sage/libs/gap/libgap.c:8037)() ValueError: libGAP: Error, no method found! For debugging hints type ?Recovery from NoMethodFound Error, no 1st choice method found for `CallFuncList' on 2 arguments
I am not sure if it is the same problem though. The error message is different.
comment:80 Changed 9 years ago by
problem persists with the new patch.
comment:81 Changed 9 years ago by
- Cc SimonKing added
- Component changed from interfaces to group theory
- Status changed from needs_work to needs_review
I've fixed Miguel's bug and tested that libGAP remains running through hundreds of GAP garbage collections. All in all, I have not had any random crashes with the new version at all even in hundreds of repetitions. So I declare the current state to be totally awesome and ready to be released into the wild and exposed to the general Sage community. Please review!
comment:82 Changed 9 years ago by
Problem persists for me. Not in a 3000 iterations loop, but in longer loops:
sage: g=libgap('FreeGroup(2)') sage: (a,b)=g.GeneratorsOfGroup() sage: lis=libgap('[]') sage: lis.Add(a^2) sage: lis.Add(b^2) sage: lis.Add(b*a) sage: h=g/lis sage: c=h.GeneratorsOfGroup()[0] sage: for i in range(300000): ....: n=c.Order() ....: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/mmarco/sage-5.2/<ipython console> in <module>() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_MethodProxy.__call__ (sage/libs/gap/element.c:7860)() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_Function.__call__ (sage/libs/gap/element.c:7433)() ValueError: libGAP: Error, no method found! For debugging hints type ?Recovery from NoMethodFound Error, no 1st choice method found for `CallFuncList' on 2 arguments sage: i 6862
comment:83 Changed 9 years ago by
After considerable despair I finally realized that Python called the libgap initialization from a higher stack frame than where c.Order()
was executing. One peculiarities of the GAP memory manager is that it trawls the stack for pointers into its memory pool and keeps these alive (so you can just work with local stack-allocated GAP objects and not worry). While its easy to figure out the highest stack frame (its you, the currently executing function) we must take care to inform GAP about the lowest stack frame that can hold a pointer to a memory bag!
Now Miguel's example runs perfectly! For the record, you can use the following syntactic sugar to make the code look nicer:
sage: G =libgap.FreeGroup(2) sage: a,b = G.GeneratorsOfGroup() sage: rel = libgap([a^2, b^2, a*b*a*b]) sage: H = G / rel sage: c = H.GeneratorsOfGroup()[0] sage: for i in range(300000): ... n = c.Order()
comment:84 Changed 9 years ago by
x86 means x86_64 also?
comment:85 Changed 9 years ago by
Yes, anything with an esp/ebp register (I'll add support for the rest later).
comment:86 Changed 9 years ago by
I guess i am missing something, but that's what i get with the new patch:
sage: g=libgap('FreeGroup(2)') gap: halfing pool size. sage: (a,b)=g.GeneratorsOfGroup() sage: h=g/libgap([a^2,b^2,a*b]) sage: h <fp group on the generators [ f1, f2 ]> sage: x=h.GeneratorsOfGroup()[0] sage: x f1 sage: x^2 f1^2 sage: x^3 f1^3 sage: x.Order() --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/mmarco/sage-5.2/<ipython console> in <module>() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_MethodProxy.__call__ (sage/libs/gap/element.c:8003)() /home/mmarco/sage-5.2/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_Function.__call__ (sage/libs/gap/element.c:7576)() ValueError: libGAP: Segmentation fault
comment:87 Changed 9 years ago by
Great work! I noticed one thing in keeping references in owned_objects
. The way I read the code, it's a list that any new object gets appended to (and index is stored). Upon deletion of the sage wrapper of the object, the particular location in the owned_objects
list is unbound. Doesn't that mean that the owned_object list can grow in an unbounded way even when only a bounded number of references to gap_objects is held? i.e., wouldn't something like
i = 0 a = GapElement(i) while True: i+=1 b = a a = GapElement(i)
let memory balloon? For ecllib I ended up keeping a doubly linked list, since insertions and deletions are O(1), at the cost of a largish constant in memory overhead.
Alternatives include inserting in the first unbound spot of the list, which has the wrong complexity for object creation unless you keep a free list. You could keep a stack or a deque of free spots. I don't know if a FIFO or LIFO strategy would lead to better opportunities to shorten the reference list.
comment:88 Changed 9 years ago by
Miguel: the "halfing pool size" means that GAP can't allocate its 4gb pool (or so). I suppose thats the issue here, will try to investigate.
Nils: I know, though it is only a pointer... Originally I was using GAP records (dictionaries/hashes), but back then I didn't understand some of the subtle points of how GAP works with them so I replaced it with the simplest possibility. I'm actually thinking that the best solution would be to add a hook to the garbage collector so we can directly force objects alive.
comment:89 Changed 9 years ago by
It's strange, since i have plenty of RAM available.
comment:90 Changed 9 years ago by
I can manually force the "halfing pool size" message by limiting the virtual mem size (in the followng example to 5gb which is a bit more than half of what GAP wants to take on x86 --- note that this is purely virtual and not used unless you actually do a huge computation)
[vbraun@volker-desktop ~]$ ulimit -v 5000000 [vbraun@volker-desktop ~]$ sage -c 'print libgap(1)' gap: halfing pool size. 1
Though still all doctests pass and I don't see Miguel's segfault. Can you post a backtrace? (sage -gdb
and type 'bt' at the gdb prompt after the segfault)
comment:91 Changed 9 years ago by
mmarco@neumann ~/sage-5.2 $ ./sage -gdb ---------------------------------------------------------------------- | Sage Version 5.2, Release Date: 2012-07-25 | | Type "notebook()" for the browser-based notebook interface. | | Type "help()" for help. | ---------------------------------------------------------------------- /home/mmarco/sage-5.2/local/bin/sage-ipython GNU gdb (Gentoo 7.3.1 p2) 7.3.1 Copyright (C) 2011 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-pc-linux-gnu". For bug reporting instructions, please see: <http://bugs.gentoo.org/>... Reading symbols from /home/mmarco/sage-5.2/local/bin/python...done. [Thread debugging using libthread_db enabled] Python 2.7.3 (default, Aug 30 2012, 14:13:06) [GCC 4.5.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. Loading Sage library. Current Mercurial branch is: libgap4 sage: sage: g=libgap('FreeGroup(2)') sage: (a,b)=g.GeneratorsOfGroup() sage: h=g/libgap([a^2,b^2,a*b]) sage: x=h.GeneratorsOfGroup()[0] sage: x.Order() Program received signal SIGSEGV, Segmentation fault. 0x00007fffcb4d15c5 in libGAP_GenStackFuncBags () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 (gdb) bt #0 0x00007fffcb4d15c5 in libGAP_GenStackFuncBags () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #1 0x00007fffcb4d1c2f in libGAP_CollectBags () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #2 0x00007fffcb4d0fda in libGAP_NewBag () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #3 0x00007fffcb4412df in libGAP_SwitchToNewLvars () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #4 0x00007fffcb447ea9 in libGAP_DoExecFunc2args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #5 0x00007fffcb445555 in libGAP_EvalFunccall2args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #6 0x00007fffcb34c9c4 in libGAP_ExecAssLVar () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #7 0x00007fffcb45f8b1 in libGAP_ExecSeqStat4 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #8 0x00007fffcb460a61 in libGAP_ExecFor () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #9 0x00007fffcb46366d in libGAP_ExecRepeat2 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #10 0x00007fffcb45f56a in libGAP_ExecSeqStat () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #11 0x00007fffcb460151 in libGAP_ExecIf () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #12 0x00007fffcb460a61 in libGAP_ExecFor () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #13 0x00007fffcb45f56a in libGAP_ExecSeqStat () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #14 0x00007fffcb4634e8 in libGAP_ExecRepeat () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #15 0x00007fffcb45fd27 in libGAP_ExecSeqStat6 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #16 0x00007fffcb460151 in libGAP_ExecIf () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #17 0x00007fffcb45f56a in libGAP_ExecSeqStat () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #18 0x00007fffcb46006d in libGAP_ExecSeqStat7 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #19 0x00007fffcb447e08 in libGAP_DoExecFunc1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #20 0x00007fffcb359b16 in libGAP_DoWrap1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #21 0x00007fffcb445067 in libGAP_EvalFunccall1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #22 0x00007fffcb34ccf8 in libGAP_ExecAssLVar02 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #23 0x00007fffcb460567 in libGAP_ExecIfElifElse () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #24 0x00007fffcb45fcbb in libGAP_ExecSeqStat6 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #25 0x00007fffcb447e08 in libGAP_DoExecFunc1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #26 0x00007fffcb41ac00 in libGAP_DoOperation1Args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #27 0x00007fffcb422ad4 in libGAP_DoAttribute () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #28 0x00007fffcb445067 in libGAP_EvalFunccall1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #29 0x00007fffcb3ec5cb in libGAP_EvalNe () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #30 0x00007fffcb46049d in libGAP_ExecIfElifElse () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #31 0x00007fffcb45f5eb in libGAP_ExecSeqStat2 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #32 0x00007fffcb447e08 in libGAP_DoExecFunc1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #33 0x00007fffcb41ac00 in libGAP_DoOperation1Args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #34 0x00007fffcb422ad4 in libGAP_DoAttribute () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #35 0x00007fffcb445067 in libGAP_EvalFunccall1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #36 0x00007fffcb4451e3 in libGAP_EvalFunccall2args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #37 0x00007fffcb464adf in libGAP_ExecReturnObj () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #38 0x00007fffcb45f654 in libGAP_ExecSeqStat2 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #39 0x00007fffcb447f0b in libGAP_DoExecFunc2args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #40 0x00007fffcb41afe0 in libGAP_DoOperation2Args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #41 0x00007fffcb2e792c in libGAP_EqObject () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #42 0x00007fffcb3ec77b in libGAP_EvalNe () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #43 0x00007fffcb463257 in libGAP_ExecWhile2 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #44 0x00007fffcb460004 in libGAP_ExecSeqStat7 () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #45 0x00007fffcb447e08 in libGAP_DoExecFunc1args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #46 0x00007fffcb41ac00 in libGAP_DoOperation1Args () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #47 0x00007fffcb422ad4 in libGAP_DoAttribute () from /home/mmarco/sage-5.2/local/lib/libgap.so.0 #48 0x00007fffcb074e7d in __pyx_pf_4sage_4libs_3gap_7element_19GapElement_Function_2__call__ (__pyx_v_self=0x49651b0, __pyx_v_args=0x7ffff7ed4f50) at sage/libs/gap/element.c:7201 #49 0x00007fffcb0763a8 in __pyx_pw_4sage_4libs_3gap_7element_19GapElement_Function_3__call__ (__pyx_v_self=0x49651b0, __pyx_args=0x7ffff7ed4f50, __pyx_kwds=<optimized out>) at sage/libs/gap/element.c:6998 #50 0x00007ffff7a41913 in PyObject_Call (func=0x494de90, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529 #51 0x00007ffff7ae7c57 in PyEval_CallObjectWithKeywords (func=0x494de90, arg=0x7ffff7ed4f50, kw=<optimized out>) at Python/ceval.c:3890 #52 0x00007ffff7a5ce2b in wrapperdescr_call (descr=<optimized out>, args=0x7ffff7ed4f50, kwds=0x0) at Objects/descrobject.c:306 #53 0x00007ffff7a41913 in PyObject_Call (func=0x3287b40, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529 #54 0x00007fffcb06af0d in __pyx_pf_4sage_4libs_3gap_7element_22GapElement_MethodProxy___call__ (__pyx_v_args=0x7ffff7f78050, __pyx_v_self=0x49651b0) at sage/libs/gap/element.c:8003 #55 __pyx_pw_4sage_4libs_3gap_7element_22GapElement_MethodProxy_1__call__ (__pyx_v_self=0x49651b0, __pyx_args=0x7ffff7f78050, __pyx_kwds=<optimized out>) at sage/libs/gap/element.c:7895 #56 0x00007ffff7a41913 in PyObject_Call (func=0x49651b0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529 #57 0x00007ffff7aed0ee in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fffffffbff0, func=0x49651b0) at Python/ceval.c:4239 #58 call_function (oparg=<optimized out>, pp_stack=0x7fffffffbff0) at Python/ceval.c:4044 #59 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #60 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0x4953830, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3253 #61 0x00007ffff7aef762 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:667 #62 0x00007ffff7aeeb83 in exec_statement (locals=0xbc3c80, globals=0xbc3c80, prog=<optimized out>, f=0x4438bd0) at Python/ceval.c:4718 #63 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:1880 #64 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0xaed9b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0x4998780, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3253 #65 0x00007ffff7aed777 in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffc460, func=0xb7d7d0) at Python/ceval.c:4117 #66 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc460) at Python/ceval.c:4042 #67 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #68 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0xaed930, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=3, kws=0x49a6560, kwcount=0, defs=0xb7b1d0, defcount=2, closure=0x0) at Python/ceval.c:3253 #69 0x00007ffff7aed777 in fast_function (nk=<optimized out>, na=3, n=<optimized out>, pp_stack=0x7fffffffc680, func=0xb7d758) at Python/ceval.c:4117 #70 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc680) at Python/ceval.c:4042 #71 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #72 0x00007ffff7aeed6a in fast_function (nk=<optimized out>, na=<optimized out>, n=<optimized out>, pp_stack=0x7fffffffc7f0, func=0xb7d848) at Python/ceval.c:4107 #73 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc7f0) at Python/ceval.c:4042 #74 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #75 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0xaed4b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0xbe59e8, kwcount=0, defs=0xb72c28, defcount=1, closure=0x0) at Python/ceval.c:3253 #76 0x00007ffff7aed777 in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffca10, func=0xb7d398) at Python/ceval.c:4117 #77 call_function (oparg=<optimized out>, pp_stack=0x7fffffffca10) at Python/ceval.c:4042 #78 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #79 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0xaed030, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0xbef170, kwcount=0, defs=0xb72be8, defcount=1, closure=0x0) at Python/ceval.c:3253 #80 0x00007ffff7aed777 in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffcc30, func=0xb7d0c8) at Python/ceval.c:4117 #81 call_function (oparg=<optimized out>, pp_stack=0x7fffffffcc30) at Python/ceval.c:4042 #82 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #83 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0x7ffff7eeac30, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=1, kws=0x6f2200, kwcount=2, defs=0xa30578, defcount=2, closure=0x0) at Python/ceval.c:3253 #84 0x00007ffff7aed777 in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffce50, func=0xb85a28) at Python/ceval.c:4117 #85 call_function (oparg=<optimized out>, pp_stack=0x7fffffffce50) at Python/ceval.c:4042 #86 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #87 0x00007ffff7aef63d in PyEval_EvalCodeEx (co=0x7ffff7f2ab30, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3253 #88 0x00007ffff7aef762 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:667 #89 0x00007ffff7b11750 in run_mod (arena=0x623430, flags=0x7fffffffd170, locals=0x641160, globals=0x641160, filename=<optimized out>, mod=0x6f1ba0) at Python/pythonrun.c:1353 #90 PyRun_FileExFlags (fp=0x6d70a0, filename=<optimized out>, start=<optimized out>, globals=0x641160, locals=0x641160, closeit=0, flags=0x7fffffffd170) at Python/pythonrun.c:1339 #91 0x00007ffff7b1225f in PyRun_SimpleFileExFlags (fp=0x6d70a0, filename=0x7fffffffe919 "/home/mmarco/sage-5.2/local/bin/sage-ipython", closeit=0, flags=0x7fffffffd170) at Python/pythonrun.c:943 #92 0x00007ffff7b27976 in RunStartupFile (cf=0x7fffffffd170) at Modules/main.c:153 #93 Py_Main (argc=<optimized out>, argv=0x7fffffffd298) at Modules/main.c:593 #94 0x00007ffff6de222d in __libc_start_main () from /lib64/libc.so.6 #95 0x00000000004006e9 in _start ()
comment:92 Changed 8 years ago by
Can you try the new spkg + patch? I think I tracked down the bug ;-)
comment:93 Changed 8 years ago by
- Milestone changed from sage-5.4 to sage-5.3
I am attending a conference this week, so i will have little time. On top of that, i don't have my computer with me. I will try to find time to work remotelly on that, but i cannot ensure when that will happen.
comment:94 Changed 8 years ago by
I finally could test it. It seems to work fine now. Great work!
I don't have the necessary skills to review the code, but i can go on testing it.
comment:95 Changed 8 years ago by
Do you plan to implement comparison of libgap objects? I am trying to port my fpgroups code to libgap, and doctests fail because of this.
comment:96 Changed 8 years ago by
OK I'll try to update everything to gap-4.5.6 today and add comparison.
comment:97 Changed 8 years ago by
- Description modified (diff)
Ok, done. Comparison works now:
sage: libgap('test') == libgap.Concatenation(libgap('te'), libgap('st')) True
I made one incompatible change: since libgap
is the parent to all gap elements, it should do element construction for strings:
sage: libgap('1+1') "1+1" sage: type(_) <type 'sage.libs.gap.element.GapElement_String'>
To evaluate a GAP command in a string, you now have to use
sage: libgap.eval('1+1') 2
Since we aim at wrapping more of GAP one expects that the libgap.eval
method becomes less useful over time.
comment:98 follow-up: ↓ 99 Changed 8 years ago by
PS: I also changed the refcounting system, now its hooking directly into GASMAN to keep objects alive.
I think we should get this into Sage for real, now. Dima, are you up to another reviewing challenge? :-)
comment:99 in reply to: ↑ 98 ; follow-up: ↓ 101 Changed 8 years ago by
Replying to vbraun:
PS: I also changed the refcounting system, now its hooking directly into GASMAN to keep objects alive.
I think we should get this into Sage for real, now. Dima, are you up to another reviewing challenge? :-)
Well, yes 8-/.
What about eliminating a hardcoded path in sage/libs/gap/test/main.c
?
Is it possible to test this, via a Cython wrapper, say? (It's also easier to test this in sage-check script).
comment:100 Changed 8 years ago by
I see several messages halving pool size
if I do sage: libgap?
immediately after starting Sage.
This looks like some debugging printout getting in the way.
comment:101 in reply to: ↑ 99 Changed 8 years ago by
Replying to dimpase:
Replying to vbraun:
PS: I also changed the refcounting system, now its hooking directly into GASMAN to keep objects alive.
I think we should get this into Sage for real, now. Dima, are you up to another reviewing challenge? :-)
Well, yes 8-/.
What about eliminating a hardcoded path in
sage/libs/gap/test/main.c
?
I cannot guess the correct value of this relative to $SAGE_LOCAL
or $SAGE_ROOT
. In fact it should be easy to have this build and run from Sage shell prompt (i.e. sage -sh
), then these hardcoded paths in Makefile and in main.c are not necessary. It would be great to have this fixed.
Then hooking it up on sage-check becomes trivial, too.
comment:102 Changed 8 years ago by
the new libgap spkg needs to be mentioned in SAGE_ROOT/spkg/standard/deps
, as it depends on GAP, but this is not done.
Also, libgap needs to be mentioned in SAGE_ROOT/spkg/install
, AFAIK.
comment:103 Changed 8 years ago by
on the spkg: it has two (!) upstream-gap subdirectories. Does one need them both?
I don't understand whether MPIR is used as the replacement of GMP here, or not. (according to spkg-install it looks as if it uses MPIR, actually). (Last time I checked (well, long ago) GAP didn't run with MPIR; actually, I was too busy to find out how it is now working with the new GAP spkg; does it build its own GMP?)
comment:104 follow-ups: ↓ 109 ↓ 110 Changed 8 years ago by
The sage/libs/gap/test/main.c
is only for instructional purposes, it demonstrates how to build a standalone binary so you can run libGAP under a debugger/valgrind without Sage. It doesn't exercise anything thats not already in doctests.
One could add a spkg-check
to test src/test
in the spkg, but they again don't exercise anything thats not covered by libGAP doctests.
I've removed the upstream-gap-x.y.z directories from the spkg, the make-spkg.sh
script copied them there accidentally.
Gap links against MPIR just fine, the only issue is with a version check that I reported here: https://groups.google.com/d/topic/mpir-devel/X48SfwGkSd8/discussion. This is why the spkg-install
adds -D__GMP_MP_RELEASE=50002
to the CFLAGS
:
(sage-sh) vbraun@volker-desktop:spkg$ ldd ~/Sage/sage/local/lib/libgap.so linux-vdso.so.1 => (0x00007fff8ebff000) libgmp.so.7 => /home/vbraun/opt/sage-5.4.beta1/local/lib/libgmp.so.7 (0x00007f8a82885000) libc.so.6 => /lib64/libc.so.6 (0x00007f8a824a9000) /lib64/ld-linux-x86-64.so.2 (0x00000036c4000000)
comment:105 Changed 8 years ago by
- Description modified (diff)
I've added a patch for the root repo. I guess we need to vote on sage-devel about adding a new spkg? Though its not really new, its just an alternate version of code that we already ship.
comment:106 Changed 8 years ago by
comment:107 Changed 8 years ago by
Can you explain how to set up the amount of memory available for the libgap session?
comment:108 Changed 8 years ago by
Nowadays GAP uses anonymous mmap to reserve a big chunk of addressing space (not physical RAM, mind you) and uses that as needed. This is the origin of the halving pool size
message on stdout. The message is purely cosmetic, but I'll ask upstream to suppress it. It also appears on the GAP command line and has nothing to do with libGAP:
[vbraun@volker-desktop ~]$ sage -gap -o 16384G gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. ┌───────┐ GAP, Version 4.5.6 of 16-Sep-2012 (free software, GPL) │ GAP │ http://www.gap-system.org └───────┘ Architecture: x86_64-unknown-linux-gnu-gcc-default64 Libs used: gmp, readline Loading the library and packages ... Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0 Packages: CTblLib 1.2.1, FactInt 1.5.3, GAPDoc 1.5.1, LAGUNA 3.6.1, TomLib 1.2.2 Try '?help' for help. See also '?copyright' and '?authors'
By default we try to acquire 16TB of addressing space, and then halving that until it succeeds:
Tasks: 352 total, 3 running, 345 sleeping, 1 stopped, 3 zombie Cpu(s): 13.5%us, 0.4%sy, 0.0%ni, 85.9%id, 0.0%wa, 0.2%hi, 0.0%si, 0.0%st Mem: 32835628k total, 32140456k used, 695172k free, 1037012k buffers Swap: 62499996k total, 485252k used, 62014744k free, 13507248k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 11585 vbraun 20 0 78.2g 48m 992 S 0.0 0.2 0:00.72 gap
The memory you can use in the gap session is limited to the pool size, but at least on 64-bit this should always be a lot.
comment:109 in reply to: ↑ 104 Changed 8 years ago by
Replying to vbraun:
Gap links against MPIR just fine, the only issue is with a version check that I reported here: https://groups.google.com/d/topic/mpir-devel/X48SfwGkSd8/discussion. This is why the
spkg-install
adds-D__GMP_MP_RELEASE=50002
to theCFLAGS
:
is there any reason for GAP being linked statically against GMP (i.e. MPIR)?
$sage-5.4.beta1/local/gap/latest$ ldd bin/x86_64-unknown-linux-gnu-gcc-default64/gap linux-vdso.so.1 => (0x00007fff7c4c9000) libm.so.6 => /lib/libm.so.6 (0x00007fa3e0d26000) libreadline.so.6 => /lib/libreadline.so.6 (0x00007fa3e0ae2000) libncurses.so.5 => /usr/lib/libncurses.so.5 (0x00007fa3e089b000) libdl.so.2 => /lib/libdl.so.2 (0x00007fa3e0697000) libutil.so.1 => /lib/libutil.so.1 (0x00007fa3e0494000) libc.so.6 => /lib/libc.so.6 (0x00007fa3e0131000) /lib64/ld-linux-x86-64.so.2 (0x00007fa3e0fc3000) $sage-5.4.beta1/local/gap/latest$ ../../../sage -gap ********* GAP, Version 4.5.6 of 16-Sep-2012 (free software, GPL) * GAP * http://www.gap-system.org ********* Architecture: x86_64-unknown-linux-gnu-gcc-default64 Libs used: gmp, readline Loading the library and packages ... Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0 Packages: CTblLib 1.2.1, FactInt 1.5.3, GAPDoc 1.5.1, LAGUNA 3.6.1, TomLib 1.2.2 Try '?help' for help. See also '?copyright' and '?authors' gap>
comment:110 in reply to: ↑ 104 Changed 8 years ago by
Replying to vbraun:
The
sage/libs/gap/test/main.c
is only for instructional purposes, it demonstrates how to build a standalone binary so you can run libGAP under a debugger/valgrind without Sage. It doesn't exercise anything thats not already in doctests.
I tried it on the system I am testing libgap now, and it doesn't work (I needed to do changes --- see the patch to be attached --- to the source to make it compile, but it seems to need more, as I get suspicious warnings during compilation, and then a segfault)
(sage-sh) dima@spms-banana:test$ make main gcc -std=gnu99 -I/usr/local/src/sage/sage-5.4.beta1/local/include -I/usr/local/src/sage/sage-5.4.beta1/local/include/python2.6 -c -g -DGAPLOCAL=/usr/local/src/sage/sage-5.4.beta1/local/gap/latest main.c In file included from main.c:10: /usr/local/src/sage/sage-5.4.beta1/local/include/gap/vars.h: In function 'libGAP_SwitchToNewLvars': /usr/local/src/sage/sage-5.4.beta1/local/include/gap/vars.h:163: warning: implicit declaration of function 'libGAP_BODY_FUNC' /usr/local/src/sage/sage-5.4.beta1/local/include/gap/vars.h:163: warning: cast to pointer from integer of different size In file included from main.c:10: /usr/local/src/sage/sage-5.4.beta1/local/include/gap/vars.h: In function 'libGAP_SwitchToOldLVars': /usr/local/src/sage/sage-5.4.beta1/local/include/gap/vars.h:205: warning: cast to pointer from integer of different size main.c: In function 'eval': main.c:24: warning: implicit declaration of function 'libgap_set_error' main.c:26: warning: implicit declaration of function 'libGAP_ViewObjHandler' gcc -L/usr/local/src/sage/sage-5.4.beta1/local/lib -o main main.o -lgap -lcsage -lntl -lstdc++ -lpari -lpython2.7 -lm -lgmp (sage-sh) dima@spms-banana:test$ ./main Initialized Input: 1+2+3; Output: 6 Input: g:=FreeGroup(2); Segmentation fault (sage-sh) dima@spms-banana:test$
comment:111 follow-ups: ↓ 112 ↓ 119 Changed 8 years ago by
I don't think there is any reason for statically linking gmp other than their build system predating much of autotools...
The implicit declaration and pointer cast warnings are normal, GAP just predates ansi C :-)
comment:112 in reply to: ↑ 111 Changed 8 years ago by
Replying to vbraun:
The implicit declaration and pointer cast warnings are normal, GAP just predates ansi C :-)
Well, anyhow... Could you confirm that my change of the code was OK, and this is a genuine issue? gdb tells me the following:
g:=FreeGroup(2); Program received signal SIGSEGV, Segmentation fault. 0x00007ffff75a8d0f in libGAP_RNamName () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 (gdb) bt #0 0x00007ffff75a8d0f in libGAP_RNamName () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #1 0x00007ffff76cb0e1 in libGAP_CallErrorInner () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #2 0x00007ffff76cb2f4 in libGAP_ErrorQuit () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #3 0x00007ffff757b8df in libGAP_ErrorMustHaveAssObjHandler () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #4 0x00007ffff75b7b70 in libGAP_DoWrap2args () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #5 0x00007ffff76cb299 in libGAP_CallErrorInner () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #6 0x00007ffff76cb2f4 in libGAP_ErrorQuit () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #7 0x00007ffff757b8df in libGAP_ErrorMustHaveAssObjHandler () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #8 0x00007ffff75b7b70 in libGAP_DoWrap2args () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #9 0x00007ffff76cb299 in libGAP_CallErrorInner () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #10 0x00007ffff76cb2f4 in libGAP_ErrorQuit () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #11 0x00007ffff757b8df in libGAP_ErrorMustHaveAssObjHandler () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #12 0x00007ffff75b7b70 in libGAP_DoWrap2args () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #13 0x00007ffff76cb299 in libGAP_CallErrorInner () from /usr/local/src/sage/sage-5.4.beta1/local/lib/libgap.so.0 #14 0x00007ffff76cb2f4 in libGAP_ErrorQuit () .....
and it keeps repeating, ad nauseum... The x86_64 system runs Debian, here are the compiler specs:
(sage-sh) dima@spms-banana:test$ gcc -v Using built-in specs. Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 4.4.5-8' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.4 --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --with-arch-32=i586 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 4.4.5 (Debian 4.4.5-8)
comment:113 follow-up: ↓ 115 Changed 8 years ago by
Your changes look fine. The test/main.c
example doesn't do proper error handling, so you shouldn't expect a useful error message. For a relevant stack backtrace you need to post what happens before you get into the error loop.
comment:114 follow-up: ↓ 116 Changed 8 years ago by
Upon squinting a bit harder, I noticed that
argv[2] = "GAPLOCAL" ;
in your patch does not use the preprocessor macro, it is just the string "GAPLOCAL"
. I've updated the patch to not hardcode the path and pass through the gap directory correctly.
comment:115 in reply to: ↑ 113 Changed 8 years ago by
Replying to vbraun:
Your changes look fine. The
test/main.c
example doesn't do proper error handling, so you shouldn't expect a useful error message. For a relevant stack backtrace you need to post what happens before you get into the error loop.
Well, I rebuilt libgap with SAGE_DEBUG on, and I can see it starting the interpreter interaction, parsing the input, calling gasman, then something goes wrong, it tries to print the message "Variable: 'FreeGroup' must have a value"
(gdb) libGAP_SPrTo (buffer=0x7fffffffd0d0 "Variable: 'FreeGroup' must have a value", maxlen=120, format=0x7ffff7750098 "Variable: '%s' must have a value", arg1=140733014557528, arg2=0) at scanner.c:3049
then I see
(gdb) libGAP_SyStrncat (dst=0x7fffffffcd20 "justQuit", src=0x7ffff775e32c "justQuit", len=1023) at system.c:682 (gdb) libGAP_RNamName (name=0x7ffff775e32c "justQuit") at records.c:110
and it tries to go further. Eventually I see
(gdb) libGAP_ErrorQuit (msg=0x7ffff77472a0 "Variable: <<unknown>> must have an assigned value", arg1=0, arg2=0) at gap.c:1451 (gdb) libGAP_CallErrorInner (msg=0x7ffff77472a0 "Variable: <<unknown>> must have an assigned value", arg1=0, arg2=0, justQuit=1, mayReturnVoid=0, mayReturnObj=0, lateMessage=0x7ffef510a678, printThisStatement=1) at gap.c:1430
this gets repeated many times (buffer corruption), and eventually a segfault.
Program received signal SIGSEGV, Segmentation fault. 0x00007ffff75a8eef in libGAP_RNamName (name=Cannot access memory at address 0x7fffff7fefa8 ) at records.c:79
the trouble starts of course much earlier, before it fails to recognize FreeGroup
as a valid GAP function...
.
comment:116 in reply to: ↑ 114 Changed 8 years ago by
Replying to vbraun:
Upon squinting a bit harder, I noticed that
argv[2] = "GAPLOCAL" ;in your patch does not use the preprocessor macro, it is just the string
"GAPLOCAL"
. I've updated the patch to not hardcode the path and pass through the gap directory correctly.
/me facepalm...
OK, now, with the updated patch, it works.
comment:117 follow-up: ↓ 118 Changed 8 years ago by
What was the reason that sage.interfaces.interface wasn't used? It seems like we should at least have a GAP Interface that is compatible with the old pexpect one much like was done for the maxima pexpect / ecl interface.
comment:118 in reply to: ↑ 117 Changed 8 years ago by
Replying to mhansen:
What was the reason that sage.interfaces.interface wasn't used? It seems like we should at least have a GAP Interface that is compatible with the old pexpect one much like was done for the maxima pexpect / ecl interface.
My understanding is that at this point it's still very far to compatibility. On the other hand, it seems that replacing the pexpect
interface using libgap's eval
should already be quite possible.
comment:119 in reply to: ↑ 111 Changed 8 years ago by
Replying to vbraun:
I don't think there is any reason for statically linking gmp other than their build system predating much of autotools...
Would it be much work to libtoolize GAP itself, given that, as far as I understand, the work on this ticket can largely be re-used?
comment:120 Changed 8 years ago by
- Description modified (diff)
- Status changed from needs_review to positive_review
comment:121 Changed 8 years ago by
- Dependencies changed from #13211 to #13123, #13211
- Milestone changed from sage-5.3 to sage-5.5
comment:122 Changed 8 years ago by
- Status changed from positive_review to needs_work
- Work issues set to assert usage
As I said on a different ticket, assert
should not be used for control flow. An assert checks something which should always be true, a failed assertion is always a bug. I consider the following to be bad usage of assert
:
try: sig_on() proxy = make_GapElement_MethodProxy(self.parent(), gap_eval(name), self) sig_off() assert proxy.is_function() except RuntimeError, AssertionError: raise AttributeError, 'Name "'+str(name)+'" does not define a GAP function.' return proxy
comment:123 Changed 8 years ago by
- Dependencies changed from #13123, #13211 to #13415, #13123, #13211
The SAGE_ROOT
patch needs to be rebased to #13415.
comment:124 follow-up: ↓ 125 Changed 8 years ago by
sage.interfaces.interface.Interface
doesn't look like the most useful parent, its non-unique and operates on the assumption that one is dealing with a separate process. Here we have a shared library that is full of global variables. I think libGAP should aim at directly translating Sage<->GAP objects, so that the libGAP user does not have to input gap commands as strings at all.
It wouldn't take much to also build a libtoolized standalone interpreter, or even a GAP interpreter that communicates over zeromq. The problem is that 3rd party packages often expect a stand-alone gap tree with upstream's hacked up semi-autotools to install themselves in. From talking with people in St. Andrews I understand that upstream probably would have switched their build system already if it were not for this legacy problem.
I got rid of the assert abuse and added some more tests.
comment:125 in reply to: ↑ 124 ; follow-ups: ↓ 126 ↓ 127 Changed 8 years ago by
Replying to vbraun:
a GAP interpreter that communicates over zeromq
This is a great idea. Would we be able to use IPython as the GAP interpreter if we tied your libGAP to zeromq?
Also based on conversations in St. Andrews, some upstream developers are interested in an autotools based build system. AFAICT, the main problem with compiled GAP packages is that they rely on the object files previously compiled for the GAP executable to find symbols they need from the GAP kernel. libGAP solves this problem. This can be fixed by changing GAP's compiler wrapper which adds the path of these object files to find your libGAP instead. Before trying this approach, a GAP interpreter that uses libGAP is needed. Otherwise we will have the GAP binary and libGAP in memory with the same code.
Volker, many thanks for all the hard work on libGAP.
comment:126 in reply to: ↑ 125 Changed 8 years ago by
Replying to burcin:
Would we be able to use IPython as the GAP interpreter if we tied your libGAP to zeromq?
zeromq is just a transport, you'd have to speak the IPython protocol to do this. Much harder than just tying stdin/stdout/stderr to sockets.
AFAICT, the main problem with compiled GAP packages is that they rely on the object files previously compiled for the GAP executable to find symbols they need from the GAP kernel. libGAP solves this problem. This can be fixed by changing GAP's compiler wrapper which adds the path of these object files to find your libGAP instead.
You also need to prefix the symbol names with libGAP_
if you want to link against libGAP with legacy code. Doable but at least in the short term its much easier to have libGAP and standalone GAP separately. Much like libSingular and Singular.
comment:127 in reply to: ↑ 125 Changed 8 years ago by
Replying to burcin:
Replying to vbraun:
a GAP interpreter that communicates over zeromq
Also based on conversations in St. Andrews, some upstream developers are interested in an autotools based build system. AFAICT, the main problem with compiled GAP packages is that they rely on the object files previously compiled for the GAP executable to find symbols they need from the GAP kernel.
Do you mean GAP extension packages, things which are compiled using gac
?
"Normal" GAP packages do not need any of this, AFAIK.
The extension packages are few and far apart. The only one I know is EDIM.
The main use of gac
seems to be
to create faster loading GAP executables.
comment:128 follow-ups: ↓ 129 ↓ 133 Changed 8 years ago by
OS X 10.4 PPC:
sage -t "devel/sage-main/sage/algebras/group_algebra_new.py" ********************************************************************** File "/Users/student/Desktop/sage-5.4.beta1/devel/sage-main/sage/algebras/group_algebra_new.py", line 592: sage: GroupAlgebra(DihedralGroup(6), QQ).random_element() Expected: -1/95*(2,6)(3,5) - 1/2*(1,3)(4,6) Got: -1/95*(1,3)(4,6) - 1/2*(1,5,3)(2,6,4) ********************************************************************** File "/Users/student/Desktop/sage-5.4.beta1/devel/sage-main/sage/algebras/group_algebra_new.py", line 594: sage: GroupAlgebra(SU(2, 13), QQ).random_element(1) Expected: 1/2*[ 1 9*a + 2] [9*a + 2 12] Got: 1/2*[ 4 9*a + 2] [6*a + 10 1] ********************************************************************** 1 items had failures: 2 of 5 in __main__.example_23 ***Test Failed*** 2 failures.
There were other errors as well, which I'm rerunning.
comment:129 in reply to: ↑ 128 Changed 8 years ago by
comment:130 follow-up: ↓ 131 Changed 8 years ago by
Thanks, I'll comment there (I only ran tests after doing everything just to save time).
Dasher-03:~/Desktop/sage-5.4.beta1/devel/sage student$ ../../sage -hg qseries trac_13211_fix_gap_doctests.patch trac_6391_libGAP.patch
I think that's right?
comment:131 in reply to: ↑ 130 Changed 8 years ago by
Replying to kcrisman:
Thanks, I'll comment there (I only ran tests after doing everything just to save time).
Dasher-03:~/Desktop/sage-5.4.beta1/devel/sage student$ ../../sage -hg qseries trac_13211_fix_gap_doctests.patch trac_6391_libGAP.patchI think that's right?
hopefully you also did sage -b
before starting the tests? Just checking...
comment:132 Changed 8 years ago by
Yes, and I just checked that this was the case. But I hear you on that kind of thing - it's so easy to forget.
comment:133 in reply to: ↑ 128 Changed 8 years ago by
Replying to kcrisman:
sage -t "devel/sage-main/sage/algebras/group_algebra_new.py" ********************************************************************** File "/Users/student/Desktop/sage-5.4.beta1/devel/sage-main/sage/algebras/group_algebra_new.py", line 592: sage: GroupAlgebra(DihedralGroup(6), QQ).random_element() File "/Users/student/Desktop/sage-5.4.beta1/devel/sage-main/sage/algebras/group_algebra_new.py", line 594: sage: GroupAlgebra(SU(2, 13), QQ).random_element(1)
these are calls to random stuff, or so it seems! No wonder different hardware gives different (pseudo?)random elements. If it were tests I'd say they'd be marked # random
, like
GroupAlgebra(DihedralGroup(6), QQ).random_element() # random
not sure about examples in this case though. Or else, if these random elements are actually predictable, this could be a bug in the pseudorandom source.
comment:134 Changed 8 years ago by
I couldn't apply the root patch through normal hg_sage.apply(). Is it supposed to be applied in some other way?.
Now i get this message when i start the sage session:
---------------------------------------------------------------------- | Sage Version 5.2, Release Date: 2012-07-25 | | Type "notebook()" for the browser-based notebook interface. | | Type "help()" for help. | ---------------------------------------------------------------------- gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. gap: halving pool size. An error occurred, but libGAP has no handler set. Error message: Loading Sage library. Current Mercurial branch is: libgap6 sage:
But, regardless of the mysterious error, everything seems to work ok (at least my fpgroups code, which is what i am using for testing).
comment:135 Changed 8 years ago by
You'd use hg_root.apply()
. hg_sage
applies things to the Sage library code directories, not the root directory of Sage.
comment:136 Changed 8 years ago by
- Description modified (diff)
comment:137 Changed 8 years ago by
- Status changed from needs_work to needs_review
- Work issues assert usage deleted
I've rebased the root patch just now, and removed the assert that offended Jeroen a while ago.
The startup error handling will be dealt with at #13588, this ticket is already way too long.
This ticket should be easy to review since it contains only minor changes from the previously-reviewed state.
comment:139 Changed 8 years ago by
I get a strange behaviour when i use tab completion with libgap objects:
sage: F=libgap.eval('FreeGroup(2)') sage: F.GeneratorsOfGroup() [ f1, f2 ] sage: F.GeneratorsOf F.GeneratorsOfField F.GeneratorsOfGroup F.GeneratorsOfIdeal sage: F.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: F Exception RuntimeError: 'Entered a critical block twice' in 'sage.libs.gap.util.error_handler' ignored <free group on the generators [ f1, f2 ]> sage: F.GeneratorsOfGroup() [ f1, f2 ]
(i hitted TAB in the line F.GeneratorsOf?, so it showed the possible completions).
comment:140 Changed 8 years ago by
Another question: i can use much less memory in a gap computation through libgap that i can in a standard sage/gap session:
./sage -gap ********* GAP, Version 4.5.6 of 16-Sep-2012 (free software, GPL) * GAP * http://www.gap-system.org ********* Architecture: x86_64-unknown-linux-gnu-gcc-default64 Libs used: gmp, readline Loading the library and packages ... Packages: GAPDoc 1.5.1 Try '?help' for help. See also '?copyright' and '?authors' gap> F:=FreeGroup(2); <free group on the generators [ f1, f2 ]> gap> H:=F/[F.1^2,F.2^3]; <fp group on the generators [ f1, f2 ]> gap> a:=GeneratorsOfGroup(H)[1]; f1 gap> a; f1 gap> Order(a); 2 gap> quit;
But:
sage: G=libgap.FreeGroup(2) sage: (a,b)=G.GeneratorsOfGroup() sage: H=G/libgap([a^2,b^3]) sage: (c,d)=H.GeneratorsOfGroup() sage: c.Order() --------------------------------------------------------------------------- ValueError 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_MethodProxy.__call__ (sage/libs/gap/element.c:8414)() /home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_Function.__call__ (sage/libs/gap/element.c:7947)() ValueError: libGAP: Error, exceeded the permitted memory (`-o' command line option)
It is the same computation, but in the gap session it has enough memory (it doesn't need much: even with -o 256M the computation succeeds), and through libgap it runs out of memory.
I don't know if it is relevant, but i have no swap enabled in my system.
comment:141 Changed 8 years ago by
Gap and libGap now use the same function sage.interfaces.gap.get_gap_memory_pool_size() to determine how much address space to reserve. Without swap you will reserve actual memory, this is why the current patch then reserves a pretty small amount (free ram / 50). I guess we need to fine-tune the actual values a bit. I'll do this and fix the tab completion issue in #13588.
And whoever comes first gets more memory, so this is probably why gap got more than libgap in your case.
comment:142 follow-up: ↓ 143 Changed 8 years ago by
Is it possible to use some memory balooning technique? Or are we forced to choose between having too few memory for gap and leaving too few memory for the rest of the system?
comment:143 in reply to: ↑ 142 Changed 8 years ago by
Replying to mmarco:
Is it possible to use some memory balooning technique?
Gap does that already. I've described some of the details here:
def set_gap_memory_pool_size(size_in_bytes): """ Set the desired gap memory pool size. Subsequently started GAP/libGAP instances will use this as default. Currently running instances are unchanged. GAP will only reserve ``size_in_bytes`` address space. Unless you actually start a big GAP computation, the memory will not be used. However, corresponding swap space will be reserved so that GAP will always be able to use the reserved address space if needed. While nothing is actually written to disc as long as you don't run a big GAP computation, the reserved swap space will not be available for other processes. ...
comment:144 Changed 8 years ago by
So it sounds like a good idea to reserve a big amount of physical RAM, doesn't it?
comment:145 Changed 8 years ago by
- Milestone changed from sage-5.5 to sage-pending
comment:146 Changed 8 years ago by
I am starting to work on some project to allow computing reduced forms in some fp groups, and i found that i can't load gap packages via libgap:
./sage -gap ********* GAP, Version 4.5.6 of 16-Sep-2012 (free software, GPL) * GAP * http://www.gap-system.org ********* Architecture: x86_64-unknown-linux-gnu-gcc-default64 Libs used: gmp, readline Loading the library and packages ... Packages: CTblLib 1.2.1, FactInt 1.5.3, GAPDoc 1.5.1, LAGUNA 3.6.1 Try '?help' for help. See also '?copyright' and '?authors' gap> LoadPackage("kbmag") > ; --------------------------------------------------------------------------------------------------------------------------------------------------------- Loading kbmag 1.5 (Knuth-Bendix on Monoids and Automatic Groups) by Derek Holt (http://www.warwick.ac.uk/~mareg). Homepage: http://www.warwick.ac.uk/~mareg/kbmag --------------------------------------------------------------------------------------------------------------------------------------------------------- true gap> LoadPackage("braid"); --------------------------------------------------------------------------------------------------------------------------------------------------------- Loading braid 1.2 (braid groups package) by Kay Magaard (http://www.math.wayne.edu/~kaym/), Sergey Shpectorov (http://www-math.bgsu.edu/~sergey/), and Helmut Voelklein (http://www.exp-math.uni-essen.de/algebra/people/voelklein.html). Homepage: http://www.math.wayne.edu/~kaym/research/braid/ --------------------------------------------------------------------------------------------------------------------------------------------------------- true gap> quit;
But
./sage ---------------------------------------------------------------------- | Sage Version 5.4.rc1, Release Date: 2012-10-05 | | Type "notebook()" for the browser-based notebook interface. | | Type "help()" for help. | ---------------------------------------------------------------------- ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** Loading Sage library. Current Mercurial branch is: test sage: libgap.LoadPackage('"kbmag"') fail sage: libgap.LoadPackage('"braid"') fail sage: libgap.LoadPackage("braid") true sage: libgap.LoadPackage("kbmag") fail
Also, i don't know if it is because of libgap overwriting something in the usual gap interface, but gap.LoadPackage?() gives an error message.
I installed the kbmag package with this .spkg i just made: https://docs.google.com/open?id=0B_B7eBQ-W5NGOFpIMmxiNXZVaGc
Is there something i should take into account?
comment:147 Changed 8 years ago by
The kbmag
package has a binary compiled component, this won't work with libgap until kbmag learns about shared libraries. Packages that are pure Gap scripts do work, as you saw:
sage: libgap.LoadPackage("braid") true
comment:148 Changed 8 years ago by
So the only hope for my project is to rewrite kbmag to be able to communicate with shared libraries? I am afraid that is way beyond my skills now. Anyways, if you can help me a little bit i can try to learn about it.
comment:149 Changed 8 years ago by
I don't think you need to do anything with shared libraries. As far as I can see, the package communicates with external stand-alone executables via Exec
calls. I'm a little surprised that libgap doesn't support Gap's Exec
when it does support the rest of the interpreted language. Perhaps it's just a matter of initializing the environment of the Gap interpreter more fully?
Anyway, if you can't get the Exec
approach to work, it should be possible to rewrite the kbmag
routines that interface with the executable so that they produce the output that needs to go into a temporary communication file in a way that does work. Then you can call the executable with whatever means are appropriate and you parse its output back. It may not be pleasant to do, but doesn't require particular skills either. You'd better be very sure it really has a benefit over using a separate GAP process, because it'll be quite a bit of work.
Grep for Exec
to see where the interfacing takes place.
comment:150 Changed 8 years ago by
How hard would it be to make Gap's Exec work through libgap?
comment:151 follow-up: ↓ 152 Changed 8 years ago by
If kbmag
only uses stdin/out to communicate with its binary component then it should work. The Exec
GAP function basically works when calling it via libGAP
sage: libgap_exec = libgap.eval("Exec") sage: libgap_exec <Gap function "Exec"> sage: libgap_exec('echo $HOME') /home/vbraun --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/vbraun/<ipython console> in <module>() /home/vbraun/opt/sage-5.4.rc1/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement_Function.__call__ (sage/libs/gap/element.c:7929)() ValueError: libGAP: Segmentation fault
There is a segfault when returning the result, I'll fix that in another ticket (maybe #13588).
How did you install kbmag
, I don't think its one that we ship. Is there a spkg for it?
comment:152 in reply to: ↑ 151 ; follow-up: ↓ 153 Changed 8 years ago by
Replying to vbraun:
How did you install
kbmag
, I don't think its one that we ship. Is there a spkg for it?
the googledocs link above will give you the spkg... That's certainly not the best way to host files. There is http://code.google.com/p/spkg-upload/ which would make much more sense.
Or, perhaps, even easier, a bitbucket or github account.
comment:153 in reply to: ↑ 152 Changed 8 years ago by
And open a ticket to make kbmag an experimental spkg so we have a place to discuss it. This issue is really done so nobody should post to it.
comment:154 Changed 8 years ago by
I have opened #13673.
comment:155 Changed 8 years ago by
Thanks for this great contribution!
I just want to mention a problem with the assertion `strlen(libGAP_stdin_buffer) < length' which leads to an unhandled SIGABRT. Could this be avoided?
sage: S = SymmetricGroup(10000) sage: s = S.random_element() sage: libgap(s)
comment:156 Changed 8 years ago by
Will be done in #13588
comment:157 Changed 8 years ago by
- Milestone changed from sage-pending to sage-5.7
comment:158 Changed 8 years ago by
Now that it seems that gap upgrading has moved to 4.5.7, will this need to change?
comment:159 follow-up: ↓ 160 Changed 8 years ago by
Indeed, the actual version of libgap is incompatible with the gap-4.5.7 spkg:
sage: libgap.FreeGroup(4) An error occurred, but libGAP has no handler set. Error message: --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) /home/mmarco/sage-5.5/<ipython console> in <module>() /home/mmarco/sage-5.5/local/lib/python2.7/site-packages/sage/misc/lazy_import.so in sage.misc.lazy_import.LazyImport.__getattr__ (sage/misc/lazy_import.c:1877)() /home/mmarco/sage-5.5/local/lib/python2.7/site-packages/sage/misc/lazy_import.so in sage.misc.lazy_import.LazyImport._get_object (sage/misc/lazy_import.c:1291)() /home/mmarco/sage-5.5/libgap.pyx in init sage.libs.gap.libgap (sage/libs/gap/libgap.c:4157)() /home/mmarco/sage-5.5/libgap.pyx in sage.libs.gap.libgap.Gap.__init__ (sage/libs/gap/libgap.c:2716)() /home/mmarco/sage-5.5/local/lib/python2.7/site-packages/sage/libs/gap/util.so in sage.libs.gap.util.initialize (sage/libs/gap/util.c:3489)() RuntimeError: libGAP initialization failed You are running a GAP kernel which does not fit with the library. Probably you forgot to apply the kernel part or the library part of a bugfix? If you are using Windows, make sure you installed the file wbin4r5n7.zoo (or .zip), Macintosh users make sure the file bin4r5n7-PPC.sit (or -68k.sit) is installed, Unix users please recompile. Error before error-handling is initialized: Update to correct kernel version!
comment:160 in reply to: ↑ 159 Changed 8 years ago by
Replying to mmarco:
Indeed, the actual version of libgap is incompatible with the gap-4.5.7 spkg:
SPKG.txt contains brief instructions about upgrading. You'll need to increase the version and rerun autotools to produce new spkg. I never tried this myself though.
comment:161 follow-up: ↓ 162 Changed 8 years ago by
I'm working on it.
comment:162 in reply to: ↑ 161 ; follow-up: ↓ 163 Changed 8 years ago by
Replying to vbraun:
I'm working on it.
I've built the new package from your bitbucket repo, and it at least installs OK.
comment:163 in reply to: ↑ 162 Changed 8 years ago by
Replying to dimpase:
Replying to vbraun:
I'm working on it.
I've built the new package from your bitbucket repo, and it at least installs OK.
http://boxen.math.washington.edu/home/dima/packages/libgap-4.5.7.p1.spkg
It also passes the tests in sage/libs/gap
To create the package on MacOSX, I had to install GNU findtools
, for the native find
has different options.
comment:164 Changed 8 years ago by
- Milestone changed from sage-5.7 to sage-duplicate/invalid/wontfix
comment:165 Changed 8 years ago by
So the patches to the sage library and the root repository should be moved to #13588, right?
I am techically unable to review the code, all i can do is test it and report.
comment:166 Changed 8 years ago by
Yes, I've moved the patches from here to #13588 to make Jeroen's life easier.
comment:167 Changed 8 years ago by
- Resolution set to duplicate
- Status changed from positive_review to closed
comment:168 Changed 8 years ago by
- Reviewers changed from Dima Pasechnik, Ivan Andrus, Volker Braun, William Stein to Dmitrii Pasechnik, Ivan Andrus, Volker Braun, William Stein
To try out the first demo libgap.a use of GAP as a library:
Then