Hello, Has this ever been addressed? Five years later this is still happening. Something appears to be fundamentally broken in the way that Sage is using the Singular C library; in particular it seems to have undefined behavior in subsequent calls after it has been interrupted by alarm().
Things I have observed: 1. Memory leaks. (In a long series of calculations, the ones that run too long are interrupted. Even though all variables are redefined, garbage collection appears to miss cleaning up the calculations that are interrupted, because the machine runs out of memory unless the kernel is restarted occasionally.) 2. A string of redefinition messages to standard error such as // ** redefining # (parameter def i_par; parameter list #; ) that occur, not when a calculation is interrupted, but only after a different calculation is subsequently started, when the same messages never appear in the case that all calculations complete before their alarms. 3. Unrelated Python-based Sage code hanging (using the CPU but making zero progress) after Groebner basis calculations have been interrupted by an alarm, different Groebner basis calculations have subsequently been executed during some fraction of a second, then control has been passed back to pure Python code. 4. The exact error reported by Fabian Weise below. It makes me worry that the database of calculation results I have been building, many of them having been performed after a different calculation timed out, may not be reliable. Should a warning be added to the alarm() documentation that it is incompatible with computations involving multivariable polynomials? That would be a pity, because having access to alarm() is the difference between my being able to complete my current research project using Sage or not. The thousands of Groebner basis calculations I want to do can be stated in many different ways, and there appears to be a variation of several orders of magnitude in how long they can take, so that the way to complete them all is to interrupt the slow ones and try them again phrased differently. —Tracy Hall On Thursday, May 15, 2014 at 7:24:13 PM UTC-6, Fabian Weise wrote: > > Hello there, > > as you can see below I am defining a polynomial ring, an ideal and > computing its Groebner Basis in a for loop (iterating threw different .xml > files). > > During the computation I set an alarm for 5s (in the example below still > 60s) and let the program print a message in the error case. But since that > happened the next computation raises an error by the groebner_basis() > function. > > In the output below you can see that the first computation is successful, > the seconds aborts and the third raises an error due to some kind of > "basering" definition. Googling I came up with this ( > http://www.gap-system.org/Manuals/pkg/singular/doc/chap1.html#X82260C8E82090E87, > > cp 1-7-5), because I am using the Singular algorithm to compute the > Groebner Basis. > > But since I do not know how to fix this in Sage, I please for your help. > > Thanks for any answers. > > With best regards > > Fabian > > > 1 Cassou_1.xml > > Multivariate Polynomial Ring in b, c, d, e over Rational Field > > Degree reverse lexicographic term order > > 1 loops, best of 1: 219.62 ms per loop > > > > 1 Cohn_2.xml > > Multivariate Polynomial Ring in t, x, y, z over Rational Field > > Degree reverse lexicographic term order > > abort after 60s > > > 1 Curves.curve10_20.xml > > Multivariate Polynomial Ring in x0, x1, x2, x3, x4, x5, x6, x7, x8, x9, > x10, u, v over Rational Field > > Degree reverse lexicographic term order > > // ** redefining i_par ** > > // ** redefining # ** > > // ** redefining P ** > > Exception RuntimeError: RuntimeError('Error raised calling singular > function',) in 'sage.libs.singular.function.LibraryCallHandler.handle_call' > ignored > > --------------------------------------------------------------------------- > > RuntimeError Traceback (most recent call > last) > > /Applications/sage/local/lib/python2.7/site-packages/sage/all_cmdline.pyc > in <module>() > > ----> 1 load('/Users/kenneth/Desktop/example.sage') > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/structure/sage_object.so > > in sage.structure.sage_object.load (sage/structure/sage_object.c:9540)() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/preparser.pyc > in load(filename, globals, attach) > > * 1771* # Preparse in memory only for speed. > > * 1772* exec_file_is(fpath) > > -> 1773 exec preparse_file(open(fpath).read()) + "\n" in > globals > > * 1774* elif fpath.endswith('.spyx') or fpath.endswith('.pyx'): > > * 1775* exec_file_is(fpath) > > > /Applications/sage/local/lib/python2.7/site-packages/sage/all_cmdline.pyc > in <module>() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/sage_timeit_class.so > > in sage.misc.sage_timeit_class.SageTimeit.__call__ > (sage/misc/sage_timeit_class.c:1177)() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/sage_timeit_class.so > > in sage.misc.sage_timeit_class.SageTimeit.eval > (sage/misc/sage_timeit_class.c:965)() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/sage_timeit.pyc > > in sage_timeit(stmt, globals_dict, preparse, number, repeat, precision, > seconds) > > * 241* break > > * 242* > > --> 243 series = [s/number for s in timer.repeat(repeat, number)] > > * 244* best = min(series) > > * 245* > > > /Applications/sage/local/lib/python/timeit.pyc in repeat(self, repeat, > number) > > * 221* r = [] > > * 222* for i in range(repeat): > > --> 223 t = self.timeit(number) > > * 224* r.append(t) > > * 225* return r > > > /Applications/sage/local/lib/python/timeit.pyc in timeit(self, number) > > * 193* gc.disable() > > * 194* try: > > --> 195 timing = self.inner(it, self.timer) > > * 196* finally: > > * 197* if gcold: > > > /Applications/sage/local/lib/python2.7/site-packages/sage/all_cmdline.pyc > in inner(_it, _timer) > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/cachefunc.so > in sage.misc.cachefunc.CachedMethodCaller.__call__ > (sage/misc/cachefunc.c:9194)() > > > /Applications/sage/local/lib/python2.7/site-packages/sage/misc/cachefunc.so > in sage.misc.cachefunc.CachedMethod._instance_call > (sage/misc/cachefunc.c:11887)() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_ideal.pyc > > in groebner_basis(self, algorithm, deg_bound, mult_bound, prot, *args, > **kwds) > > * 3825* if algorithm is '': > > * 3826* try: > > -> 3827 gb = self._groebner_basis_libsingular("groebner", > deg_bound=deg_bound, mult_bound=mult_bound, *args, **kwds) > > * 3828* except (TypeError,NameError) as msg: # conversion > to Singular not supported > > * 3829* try: > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_ideal.pyc > > in wrapper(*args, **kwds) > > * 503* """ > > * 504* with LibSingularDefaultContext(): > > --> 505 return func(*args, **kwds) > > * 506* return wrapper > > * 507* > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_ideal.pyc > > in _groebner_basis_libsingular(self, algorithm, *args, **kwds) > > * 836* S = slimgb_libsingular(self) > > * 837* elif algorithm == "groebner": > > --> 838 S = groebner(self) > > * 839* else: > > * 840* try: > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/libs/singular/function.so > > in sage.libs.singular.function.SingularFunction.__call__ > (sage/libs/singular/function.cpp:13039)() > > > > /Applications/sage/local/lib/python2.7/site-packages/sage/libs/singular/function.so > > in sage.libs.singular.function.call_function > (sage/libs/singular/function.cpp:14576)() > > > RuntimeError: Error in Singular function call 'groebner': > > `basering` is undefined > > error occurred in or before standard.lib::groebner line 887: ` def > P=basering;` > -- You received this message because you are subscribed to the Google Groups "sage-support" group. 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