Opened 3 years ago
Closed 3 years ago
#24701 closed defect (duplicate)
Crash in linbox compiled with clang-3.8
Reported by: | rws | Owned by: | |
---|---|---|---|
Priority: | critical | Milestone: | sage-duplicate/invalid/wontfix |
Component: | packages: standard | Keywords: | |
Cc: | Merged in: | ||
Authors: | Reviewers: | ||
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
On OpenSuSE with clang-3.8 and CC=clang CXX=clang++
sage: A = random_matrix(GF(127),200,200,density=0.01,sparse=True) sage: A.rank() --------------------------------------------------------------------------- SignalError Traceback (most recent call last) <ipython-input-12-4b1a2344e717> in <module>() ----> 1 A.rank() /home/ralf/sage/src/sage/matrix/matrix_modn_sparse.pyx in sage.matrix.matrix_modn_sparse.Matrix_modn_sparse.rank (build/cythonized/sage/matrix/matrix_modn_sparse.c:9389)() 788 if is_prime(self.p): 789 if gauss is False: --> 790 return self._rank_linbox(0) 791 elif gauss is True: 792 return self._rank_linbox(1) /home/ralf/sage/local/lib/python2.7/site-packages/sage/misc/decorators.pyc in wrapper(*args, **kwds) 720 kwds[new_name] = kwds[old_name] 721 del kwds[old_name] --> 722 return func(*args, **kwds) 723 724 return wrapper /home/ralf/sage/src/sage/matrix/matrix_modn_sparse.pyx in sage.matrix.matrix_modn_sparse.Matrix_modn_sparse._rank_linbox (build/cythonized/sage/matrix/matrix_modn_sparse.c:9008)() 728 return x 729 self._init_linbox() --> 730 sig_on() 731 # the returend pivots list is currently wrong 732 #r, pivots = linbox.rank(1) SignalError: Segmentation fault #0 0x00007fffe58f1422 in std::ostream::sentry::sentry(std::ostream&) () from /usr/lib64/libstdc++.so.6 #1 0x00007fffe58f1a38 in std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long) () from /usr/lib64/libstdc++.so.6 #2 0x00007ffdbc8d7b06 in std::operator<< <std::char_traits<char> > ( __out=..., __s=<optimized out>) at /usr/bin/../lib64/gcc/x86_64-suse-linux/4.8/../../../../include/c++/4.8/ostream:535 #3 LinBox::GaussDomain<Givaro::Modular<unsigned int, unsigned int> >::InPlaceLinearPivoting<LinBox::SparseMatrix<Givaro::Modular<unsigned int, unsigned int>, LinBox::SparseMatrixFormat::SparseSeq> > (this=<optimized out>, Rank=<optimized out>, determinant=<optimized out>, LigneA=..., Ni=200, Nj=200) at ../../linbox/algorithms/gauss/gauss.inl:505 #4 0x00007ffdbc8d6ab9 in linbox_modn_sparse_matrix_rank ( modulus=<optimized out>, numrows=200, numcols=200, rows=<optimized out>, gauss=0) at linbox-sage.C:119 #5 0x00007ffdbaab26ea in __pyx_f_4sage_4libs_6linbox_6linbox_18Linbox_modn_sparse_rank (__pyx_v_self=<optimized out>, __pyx_v_gauss=46130704) at build/cythonized/sage/libs/linbox/linbox.cpp:2826 #6 0x00007ffdbe89162f in __pyx_pf_4sage_6matrix_18matrix_modn_sparse_18Matrix_modn_sparse_28_rank_linbox (__pyx_v_self=0x7ffd9c6f69e0, __pyx_v_algorithm=) at build/cythonized/sage/matrix/matrix_modn_sparse.c:9018 #7 0x00007ffff7a44d01 in PyObject_Call
Change History (11)
comment:1 Changed 3 years ago by
comment:2 Changed 3 years ago by
I can't even replace that library but using a libc++ if the system has it would be nice.
comment:3 Changed 3 years ago by
- Summary changed from Segfault in linbox when compiled with clang-3.8 to configure should make sure that on Linux libc++ is used with clang
comment:4 Changed 3 years ago by
That's a tall order as a check. Here it is also possible that the problem is the age of the gcc's libstdc++. Although I think it is better to use libc++/libcxx and that may be easier to enforce even it turns to be overbroad.
comment:5 follow-up: ↓ 6 Changed 3 years ago by
Where we are now is that the right flags seem to be
export CC="clang" export CXX="clang++ --stdlib=libc++" export CXXFLAGS="$CXXFLAGS --stdlib=libc++" export LDFLAGS="$LDFLAGS -lc++ --stdlib=libc++"
The stdlib directive is needed on all three variables because 1. without it in CXX several packages ignore CXXFLAGS and so it's not applied with clang++ (the compiler), 2. CXXFLAGS um well it belongs there, and 3. without it in LDFLAGS several packages link with libstdc++ (fpylll, sagelib).
comment:6 in reply to: ↑ 5 Changed 3 years ago by
Replying to rws:
Where we are now is that the right flags seem to be
export CC="clang" export CXX="clang++ --stdlib=libc++" export CXXFLAGS="$CXXFLAGS --stdlib=libc++" export LDFLAGS="$LDFLAGS -lc++ --stdlib=libc++"
Actually I also need to add -I/usr/include/libcxxabi/
for otherwise brial won't find a certain header (on my computer at least).
The stdlib directive is needed on all three variables because 1. without it in CXX several packages ignore CXXFLAGS and so it's not applied with clang++ (the compiler), 2. CXXFLAGS um well it belongs there, and 3. without it in LDFLAGS several packages link with libstdc++ (fpylll, sagelib).
comment:7 follow-up: ↓ 9 Changed 3 years ago by
- Milestone changed from sage-8.2 to sage-duplicate/invalid/wontfix
- Status changed from new to needs_review
So this ticket is wontfix. Use these flags:
export CC="clang" export CXX="clang++" export CLANG_DEFAULT_CXX_STDLIB="libc++"
comment:8 Changed 3 years ago by
- Status changed from needs_review to positive_review
comment:9 in reply to: ↑ 7 Changed 3 years ago by
comment:10 Changed 3 years ago by
- Status changed from positive_review to needs_review
- Summary changed from configure should make sure that on Linux libc++ is used with clang to Crash in linbox compiled with clang-3.8
#24716 looks similar. Duplicate?
comment:11 Changed 3 years ago by
- Resolution set to duplicate
- Status changed from needs_review to closed
Hum, still clang using gcc's libstdc++ from gcc 4.8 in this case. Would sage want to build its own gcc on that box if there is just gcc-4.8?