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Test failure: devel/sage/sage/modular/modsym/space.py #3

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cschwan opened this issue May 2, 2010 · 15 comments
Closed

Test failure: devel/sage/sage/modular/modsym/space.py #3

cschwan opened this issue May 2, 2010 · 15 comments

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@cschwan
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cschwan commented May 2, 2010

sage -t -force_lib "devel/sage/sage/modular/modsym/space.py"

File "/opt/sage/devel/sage/sage/modular/modsym/space.py", line 1573:
sage: af.intersection_number(ell)
Exception raised:
Traceback (most recent call last):
File "/opt/sage/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/opt/sage/local/bin/sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
File "/opt/sage/local/bin/ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest main.example_45[8]>", line 1, in
af.intersection_number(ell)###line 1573:
sage: af.intersection_number(ell)
File "/usr/lib/python2.6/site-packages/sage/modular/modsym/space.py", line 1581, in intersection_number
B = M.integral_structure()
File "/usr/lib/python2.6/site-packages/sage/modular/modsym/space.py", line 1549, in integral_structure
J = self.free_module().intersection(I)
File "/usr/lib/python2.6/site-packages/sage/modules/free_module.py", line 3003, in intersection
W = B.kernel()
File "matrix2.pyx", line 2288, in sage.matrix.matrix2.Matrix.kernel (sage/matrix/matrix2.c:12765)
File "matrix2.pyx", line 2586, in sage.matrix.matrix2.Matrix.left_kernel (sage/matrix/matrix2.c:14020)
File "matrix_rational_dense.pyx", line 1255, in sage.matrix.matrix_rational_dense.Matrix_rational_dense.right_kernel (sage/matrix/matrix_rational_dense.c:12828)
RuntimeError
@kiwifb
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kiwifb commented May 2, 2010

I don't get that one on my usual x86 set-up.

@cschwan
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cschwan commented May 2, 2010 

sage -t -force_lib -gdb "devel/sage/sage/modular/modsym/space.py"
********************************************************************************
Type r at the (gdb) prompt to run the doctests.
Type bt if there is a crash to see a traceback.
********************************************************************************
GNU gdb (Gentoo 7.1 p1) 7.1
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
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 "i686-pc-linux-gnu".
For bug reporting instructions, please see:
...
Reading symbols from /usr/bin/python...(no debugging symbols found)...done.
(gdb) r
Starting program: /usr/bin/python /home/gnuke/.sage//tmp/.doctest_space.py
process 11287 is executing new program: /usr/bin/python2.6
[Thread debugging using libthread_db enabled]

Program received signal SIGFPE, Arithmetic exception.
0xb7fff424 in ?? ()
(gdb) bt
\#0  0xb7fff424 in ?? ()
\#1  0x4b5346be in __gmp_invalid_operation () from /usr/lib/libgmp.so.3
\#2  0x4b549aaf in __gmpz_set_d () from /usr/lib/libgmp.so.3
\#3  0xb46a5277 in ChineseRemainder () from /usr/lib/libiml.so.0 
\#4  0xb46a2779 in iml_lift () from /usr/lib/libiml.so.0
\#5  0xb46a0e30 in nonsingSolvLlhsMM () from /usr/lib/libiml.so.0
\#6  0xb46a768c in nullspaceMP () from /usr/lib/libiml.so.0
\#7  0xb4701964 in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix_integer_dense.so
\#8  0x41066408 in PyCFunction_Call () from /usr/lib/libpython2.6.so.1.0
\#9  0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#10 0xb4645e95 in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix_rational_dense.so
\#11 0x410663d9 in PyCFunction_Call () from /usr/lib/libpython2.6.so.1.0
\#12 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#13 0x410bb713 in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.6.so.1.0
\#14 0xb489fe5e in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix2.so
\#15 0xb48a04d5 in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix2.so
\#16 0x410663d9 in PyCFunction_Call () from /usr/lib/libpython2.6.so.1.0
\#17 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#18 0x410bb713 in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.6.so.1.0
\#19 0xb489fe5e in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix2.so
\#20 0xb48a07dc in ?? () from /usr/lib/python2.6/site-packages/sage/matrix/matrix2.so
\#21 0x410663d9 in PyCFunction_Call () from /usr/lib/libpython2.6.so.1.0
\#22 0x410c148e in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#23 0x410c1e47 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#24 0x410c1e47 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#25 0x410c1e47 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#26 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#27 0x410c3305 in PyEval_EvalCode () from /usr/lib/libpython2.6.so.1.0
\#28 0x410c12f9 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#29 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#30 0x41053f04 in ?? () from /usr/lib/libpython2.6.so.1.0
\#31 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#32 0x410398fc in ?? () from /usr/lib/libpython2.6.so.1.0
\#33 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#34 0x410bf2c5 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#35 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#36 0x410c1907 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#37 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#38 0x41053f04 in ?? () from /usr/lib/libpython2.6.so.1.0
\#39 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#40 0x410398fc in ?? () from /usr/lib/libpython2.6.so.1.0
\#41 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#42 0x410bf2c5 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#43 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#44 0x410c1907 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#45 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#46 0x41053fe8 in ?? () from /usr/lib/libpython2.6.so.1.0
\#47 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#48 0x410398fc in ?? () from /usr/lib/libpython2.6.so.1.0
\#49 0x41029c7a in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
\#50 0x410bf2c5 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#51 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
---Type  to continue, or q  to quit---
\#52 0x410c1907 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#53 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#54 0x410c1907 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#55 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#56 0x410c1907 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
\#57 0x410c31b6 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
\#58 0x410c3305 in PyEval_EvalCode () from /usr/lib/libpython2.6.so.1.0
\#59 0x410ddba2 in ?? () from /usr/lib/libpython2.6.so.1.0
\#60 0x410ddc5c in PyRun_FileExFlags () from /usr/lib/libpython2.6.so.1.0
\#61 0x410df2d5 in PyRun_SimpleFileExFlags () from /usr/lib/libpython2.6.so.1.0
\#62 0x410dfa1a in PyRun_AnyFileExFlags () from /usr/lib/libpython2.6.so.1.0
\#63 0x410ec276 in Py_Main () from /usr/lib/libpython2.6.so.1.0
\#64 0x080486b2 in main ()

@kiwifb
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kiwifb commented Aug 1, 2010

The Chineseremainder code is identical between iml-1.0.1 and iml-1.0.3.
sage do not apply any relevant patch. gmp bug?

@kiwifb
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kiwifb commented Sep 10, 2010

It looks like a "phantom" failing test. Entering the test data manually into sage produces the right results. This could be a sign of a problem into the doctest framework. There are other examples of similar problems popping up occasionally on sage-devel.

@kiwifb
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kiwifb commented Oct 9, 2010

So in alpha2 we noticed that the long form of sage/modular/abvar/abvar.py breaks in the same point. My current build of alpha3 has more failures at that point.

At this stage I think it is not a problem with iml or gmp as I thought at first. I now think it is a memory leak from a matrix*.pyx file proper. At the entry point. I spotted some warnings in the build log that are probably relevant:

In file included from sage/matrix/matrix_integer_dense.c:214:
/usr/include/csage/gmp_globals.h:6:1: warning: "EXTERN" redefined
In file included from sage/matrix/matrix_integer_dense.c:205:
/usr/include/csage/ntl_wrap.h:34:1: warning: this is the location of the previous definition
sage/matrix/matrix_integer_dense.c: In function ‘__pyx_pf_4sage_6matrix_20matrix_integer_dense_20Matrix_integer_dense__rational_kernel_iml’:
sage/matrix/matrix_integer_dense.c:25891: warning: passing argument 3 of ‘nullspaceMP’ from incompatible pointer type
/usr/include/iml.h:134: note: expected ‘const struct __mpz_struct (*)[1]’ but argument is of type ‘struct __mpz_struct (*)[1]’
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix2.o -L/usr/lib -L/usr/lib -lcsage -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix2.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_integer_sparse.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_integer_sparse.o
sage/matrix/matrix_integer_sparse.c: In function ‘__pyx_pf_4sage_6matrix_21matrix_integer_sparse_21Matrix_integer_sparse___init__’:
sage/matrix/matrix_integer_sparse.c:7843: warning: assignment from incompatible pointer type
sage/matrix/matrix_integer_sparse.c: In function ‘__pyx_f_4sage_6matrix_21matrix_integer_sparse_21Matrix_integer_sparse__mod_int_c’:
sage/matrix/matrix_integer_sparse.c:9802: warning: assignment from incompatible pointer type
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_integer_sparse.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_integer_sparse.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_mod2_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_mod2_dense.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_mod2_dense.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lm4ri -lgd -lpng14 -lz -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_mod2_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_modn_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_modn_dense.o
sage/matrix/matrix_modn_dense.c: In function ‘__pyx_pf_4sage_6matrix_17matrix_modn_dense_17Matrix_modn_dense___cinit__’:
sage/matrix/matrix_modn_dense.c:3375: warning: left shift count >= width of type
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_modn_dense.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_modn_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_modn_sparse.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_modn_sparse.o
sage/matrix/matrix_modn_sparse.c: In function ‘__pyx_pf_4sage_6matrix_18matrix_modn_sparse_18Matrix_modn_sparse___init__’:
sage/matrix/matrix_modn_sparse.c:8562: warning: assignment from incompatible pointer type
sage/matrix/matrix_modn_sparse.c: In function ‘__pyx_f_4sage_6matrix_18matrix_modn_sparse_18Matrix_modn_sparse__init_linbox’:
sage/matrix/matrix_modn_sparse.c:12791: warning: passing argument 5 of ‘__pyx_v_4sage_6matrix_18matrix_modn_sparse_linbox->__pyx_vtab->set’ from incompatible pointer type
sage/matrix/matrix_modn_sparse.c:12791: note: expected ‘struct __pyx_t_4sage_4libs_6linbox_6linbox_c_vector_modint *’ but argument is of type ‘struct __pyx_t_4sage_6matrix_18matrix_modn_sparse_c_vector_modint *’
sage/matrix/matrix_modn_sparse.c: In function ‘__pyx_pf_4sage_6matrix_18matrix_modn_sparse_18Matrix_modn_sparse__solve_right_nonsingular_square’:
sage/matrix/matrix_modn_sparse.c:14104: warning: passing argument 2 of ‘__pyx_v_4sage_6matrix_18matrix_modn_sparse_linbox->__pyx_vtab->solve’ from incompatible pointer type
sage/matrix/matrix_modn_sparse.c:14104: note: expected ‘struct __pyx_t_4sage_4libs_6linbox_6linbox_c_vector_modint **’ but argument is of type ‘struct __pyx_t_4sage_6matrix_18matrix_modn_sparse_c_vector_modint **’
sage/matrix/matrix_modn_sparse.c:14104: warning: passing argument 3 of ‘__pyx_v_4sage_6matrix_18matrix_modn_sparse_linbox->__pyx_vtab->solve’ from incompatible pointer type
sage/matrix/matrix_modn_sparse.c:14104: note: expected ‘struct __pyx_t_4sage_4libs_6linbox_6linbox_c_vector_modint *’ but argument is of type ‘struct __pyx_t_4sage_6matrix_18matrix_modn_sparse_c_vector_modint *’
sage/matrix/matrix_modn_sparse.c: In function ‘__pyx_pf_4sage_6matrix_18matrix_modn_sparse_18Matrix_modn_sparse_lift’:
sage/matrix/matrix_modn_sparse.c:14319: warning: assignment from incompatible pointer type
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_integer_dense.o -L/usr/lib -L/usr/lib -lcsage -liml -lgmp -lm -lpari24 -lcblas -latlas -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_integer_dense.so
i686-pc-linux-gnu-g++ -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include/singular -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_mpolynomial_dense.cpp -o build/temp.linux-i686-2.6/sage/matrix/matrix_mpolynomial_dense.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_modn_sparse.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_modn_sparse.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_rational_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_rational_dense.o
i686-pc-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_mpolynomial_dense.o -L/usr/lib -L/usr/lib -lcsage -lm -lreadline -lsingular -lgivaro -lgmpxx -lgmp -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_mpolynomial_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_rational_sparse.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_rational_sparse.o
In file included from sage/matrix/matrix_rational_sparse.c:207:
/usr/include/csage/gmp_globals.h:6:1: warning: "EXTERN" redefined
In file included from sage/matrix/matrix_rational_sparse.c:205:
/usr/include/csage/ntl_wrap.h:34:1: warning: this is the location of the previous definition
sage/matrix/matrix_rational_sparse.c: In function ‘__pyx_pf_4sage_6matrix_22matrix_rational_sparse_22Matrix_rational_sparse___init__’:
sage/matrix/matrix_rational_sparse.c:10298: warning: assignment from incompatible pointer type
sage/matrix/matrix_rational_sparse.c: In function ‘__pyx_pf_4sage_6matrix_22matrix_rational_sparse_22Matrix_rational_sparse__clear_denom’:
sage/matrix/matrix_rational_sparse.c:12525: warning: passing argument 1 of ‘__pyx_f_4sage_6matrix_22matrix_rational_sparse_mpz_vector_set_entry’ from incompatible pointer type
sage/matrix/matrix_rational_sparse.c:3970: note: expected ‘struct __pyx_t_4sage_6matrix_22matrix_rational_sparse_mpz_vector *’ but argument is of type ‘struct __pyx_t_4sage_6matrix_21matrix_integer_sparse_mpz_vector *’
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_rational_sparse.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_rational_sparse.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/lib/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_real_double_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_real_double_dense.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_real_double_dense.o -L/usr/lib -L/usr/lib -lcsage -lcblas -latlas -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_real_double_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_sparse.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_sparse.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_rational_dense.o -L/usr/lib -L/usr/lib -lcsage -lgmp -lpari24 -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_rational_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_symbolic_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_symbolic_dense.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_sparse.o -L/usr/lib -L/usr/lib -lcsage -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_sparse.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_window.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_window.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_window.o -L/usr/lib -L/usr/lib -lcsage -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_window.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/matrix_window_modn_dense.c -o build/temp.linux-i686-2.6/sage/matrix/matrix_window_modn_dense.o
i686-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG build/temp.linux-i686-2.6/sage/matrix/matrix_symbolic_dense.o -L/usr/lib -L/usr/lib -lcsage -lstdc++ -lntl -lpari24 -lgmp -lpython2.6 -o build/lib.linux-i686-2.6/sage/matrix/matrix_symbolic_dense.so
i686-pc-linux-gnu-gcc -pthread -O2 -march=native -fomit-frame-pointer -pipe -fno-strict-aliasing -fno-strict-aliasing -DNDEBUG -fPIC -I/usr/include -I/usr/include/csage -Isage/ext -I/usr/include/python2.6 -c sage/matrix/misc.c -o build/temp.linux-i686-2.6/sage/matrix/misc.o
In file included from sage/matrix/misc.c:209:
/usr/include/csage/gmp_globals.h:6:1: warning: "EXTERN" redefined
In file included from sage/matrix/misc.c:207:
/usr/include/csage/ntl_wrap.h:34:1: warning: this is the location of the previous definition
sage/matrix/misc.c: In function ‘__pyx_pf_4sage_6matrix_4misc_matrix_integer_sparse_rational_reconstruction’:
sage/matrix/misc.c:13320: warning: assignment from incompatible pointer type
sage/matrix/misc.c:13329: warning: assignment from incompatible pointer type

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kiwifb commented Oct 9, 2010

In fact the first non NTL warning quoted is probably spot on as it involves a call to nullspaceMP from iml.

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kiwifb commented Oct 11, 2010

Did we ever try to correlate that to the python version used?
That could explain why I didn't see it at first, since I stayed on 2.6.4 for some time.

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cschwan commented Oct 12, 2010

If thats the case its an issue with python 2.6.5 !?

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kiwifb commented Oct 12, 2010

It would be, but I don't think it stand scrutiny. One could try 2.6.4 and see what happens of course. I am exploring 2 other routes: bug in ATLAS or different behavior of gmp-mpir.

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kiwifb commented Oct 13, 2010

And I now point my finger to ATLAS (at least 3.9.23-r4 other version may or may not work).
It need to be checked by people not using ATLAS as their cblas.

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kiwifb commented Oct 23, 2010

Returning in 4.6rc0. compiling against gslcblas doesn't seem to do the trick anymore.
I have a few ideas to test to improve the situation. Note that the gslcblas trick is technically a bug in Gentoo.

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kiwifb commented Oct 24, 2010

Will commit a patch in the next few hours enabling the work around to be effective again.

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cschwan commented Jun 5, 2011

Test failure disappeared with Sage 4.7, reference blas and gsl cblas.

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kiwifb commented Jun 5, 2011

It is a failure specific to the usage of cblas-atlas-3.9.xx, doesn't happen with anything else. atlas-3.9 breaks things.

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cschwan commented Jul 25, 2011

I added a warning not to use ATLAS in commit f1d4995

@cschwan cschwan closed this as completed Jul 25, 2011
@CaptainBloodz CaptainBloodz mentioned this issue Mar 24, 2024
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