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"SignalError: Illegal instruction" on calling .right_kernel() [closed]

asked 2021-08-31 21:41:52 +0200

Max Alekseyev gravatar image

updated 2023-01-09 23:59:55 +0200

tmonteil gravatar image

UPDATE. I see the same problem in both Sage 9.3 and Sage 9.4 (but not in Sage 9.2), the screenlog below is for Sage 9.4.

I have a particular matrix on which computing .right_kernel() by Sage 9.4 results in SignalError: Illegal instruction. How to deal with such an error?

sage: load("bug_illegal_kernel.sage")                                                                                                                                                                                                                                                                                        
SignalError                               Traceback (most recent call last)
<ipython-input-1-5e05d00e2706> in <module>
----> 1 load("bug_illegal_kernel.sage")

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/misc/persist.pyx in sage.misc.persist.load (build/cythonized/sage/misc/persist.c:2563)()
    172     if sage.repl.load.is_loadable_filename(filename):
--> 173         sage.repl.load.load(filename, globals())
    174         return

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/repl/ in load(filename, globals, attach)
    270                 add_attached_file(fpath)
    271             with open(fpath) as f:
--> 272                 exec(preparse_file( + "\n", globals)
    273     elif ext == '.spyx' or ext == '.pyx':
    274         if attach:

<string> in <module>

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx in sage.matrix.matrix2.Matrix.right_kernel (build/cythonized/sage/matrix/matrix2.c:31019)()
   4716         # Go get the kernel matrix, this is where it all happens
-> 4717         M = self.right_kernel_matrix(*args, **kwds)
   4719         ambient = R**self.ncols()

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx in sage.matrix.matrix2.Matrix.right_kernel_matrix (build/cythonized/sage/matrix/matrix2.c:29656)()
   4316         if M is None:
   4317             try:
-> 4318                 format, M = self._right_kernel_matrix(algorithm=algorithm, proof=proof)
   4319             except AttributeError:
   4320                 pass

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.pyx in sage.matrix.matrix_integer_dense.Matrix_integer_dense._right_kernel_matrix (build/cythonized/sage/matrix/matrix_integer_dense.cpp:22522)()
   2694             proof = kwds.pop('proof', None)
   2695             proof = get_proof_flag(proof, "linear_algebra")
-> 2696             K = self._rational_kernel_iml().transpose().saturation(proof=proof)
   2697             format = 'computed-iml-int'
   2698         else:

/usr/local/SageMath.94/local/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.pyx in sage.matrix.matrix_integer_dense.Matrix_integer_dense._rational_kernel_iml (build/cythonized/sage/matrix/matrix_integer_dense.cpp:32421)()
   3882         time = verbose('computing null space of %s x %s matrix using IML'%(self._nrows, self._ncols))
   3883         cdef mpz_t * m = fmpz_mat_to_mpz_array(self._matrix)
-> 3884         sig_on()
   3885         dim = nullspaceMP(self._nrows, self._ncols, m, &mp_N)
   3886         sig_off()

SignalError: Illegal instruction

lscpu output:

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   46 bits physical, 48 bits virtual
CPU(s):                          40
On-line CPU(s) list:             0-39
Thread(s) per core:              2
Core(s) per socket:              10
Socket(s):                       2
NUMA node(s):                    2
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           62
Model name:                      Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz
Stepping:                        4
CPU MHz:                         2892.940
CPU max MHz:                     3300.0000
CPU min MHz:                     1200.0000
BogoMIPS:                        4987.83
Virtualization:                  VT-x
L1d cache:                       640 KiB
L1i cache:                       640 KiB
L2 cache:                        5 MiB
L3 cache:                        50 MiB
NUMA node0 CPU(s):               0-9,20-29
NUMA node1 CPU(s):               10-19,30-39
Vulnerability Itlb multihit:     KVM: Mitigation: Split huge pages
Vulnerability L1tf:              Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown:          Mitigation; PTI
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Full generic retpoline, IBPB conditional, IBRS_FW, STIBP conditional, RSB filling
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Not affected
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts md_clear flush_l1d
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Closed for the following reason the question is answered, right answer was accepted by Max Alekseyev
close date 2021-09-02 19:19:09.179040


Could you please provide the code that leads to the error, e.g. the content of bug_illegal_kernel.sage ?

tmonteil gravatar imagetmonteil ( 2021-08-31 22:12:30 +0200 )edit

bug_illegal_kernel.sage is available at

Max Alekseyev gravatar imageMax Alekseyev ( 2021-08-31 23:58:06 +0200 )edit

I can't reproduce this: it returns an answer for me. What OS are you using, how did you install Sage, etc.?

John Palmieri gravatar imageJohn Palmieri ( 2021-09-01 00:33:28 +0200 )edit

No error on sagecell either:

tmonteil gravatar imagetmonteil ( 2021-09-01 01:32:06 +0200 )edit

It's Ubuntu 20.04.3 LTS with Sage 9.3 installed from sage-9.3-Ubuntu_20.04-x86_64.tar.bz2, as well as with Sage 9.4 installed from sage-9.4-Ubuntu_20.04-x86_64.tar.bz2

Max Alekseyev gravatar imageMax Alekseyev ( 2021-09-01 02:27:00 +0200 )edit

1 Answer

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answered 2021-09-02 18:08:09 +0200

Max Alekseyev gravatar image

updated 2021-09-02 18:08:24 +0200

I've reported this bug in ticket #32447 which seems to be an instance of a larger problem (seen by others) with OpenBLAS compiling as reported in ticket #32424.

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Asked: 2021-08-31 21:41:52 +0200

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Last updated: Sep 02 '21