odeint with empty derivative vector causes segmentation fault

[roryyorke]

The crash seems to happen in xerrwv, called from lsoda (see backtrace below).

solve_ivp handles the empty derivative vector case fine (see output below).

I found this while investigating the behaviour of signal.lsim2 for feedthrough (empty ABC matrix) systems; calling lsim2 with such a feedthrough system results in this crash.

Reproducing code example:

import numpy as np
import scipy
from scipy import integrate

print(f'{np.__version__ = }')
print(f'{scipy.__version__ = }')

def fprime(x, t):
    return -x

def fprime2(t, x):
    return fprime(x, t)

t_eval = np.linspace(0,1)

for x0 in [[1,1], [1], []]:
    print(f'{x0 = }')
    sivp = integrate.solve_ivp(fprime, [t_eval[0],t_eval[-1]], x0, t_eval=t_eval)
    print(f'  {sivp.y.shape = }')
    print(f'  {sivp.t.shape = }')
    
    xout = integrate.odeint(fprime, x0, np.linspace(0, 1))
    print(f'  {xout.shape = }')

Error message:

Results of above, including a stack trace:

(scipydev) rory@rory-latitude:~/projects/scipy/odeint-crash$ python -X dev odeint_crash.py
np.__version__ = '1.19.2'
scipy.__version__ = '1.7.0.dev0+ec8912c'
x0 = [1, 1]
  sivp.y.shape = (2, 50)
  sivp.t.shape = (50,)
  xout.shape = (50, 2)
x0 = [1]
  sivp.y.shape = (1, 50)
  sivp.t.shape = (50,)
  xout.shape = (50, 1)
x0 = []
  sivp.y.shape = (0, 50)
  sivp.t.shape = (50,)
Fatal Python error: Segmentation fault

Current thread 0x00007fa1d76fe740 (most recent call first):
  File "/home/rory/src/scipy/scipy/integrate/odepack.py", line 241 in odeint
  File "odeint_crash.py", line 22 in <module>
Segmentation fault (core dumped)
(scipydev) rory@rory-latitude:~/projects/scipy/odeint-crash$ gdb $(which python) core 
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Reading symbols from /home/rory/.miniconda3/envs/scipydev/bin/python...

warning: core file may not match specified executable file.
[New LWP 194964]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Core was generated by `python odeint_crash.py'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f79e5262e30 in ?? () from /usr/lib/x86_64-linux-gnu/libgfortran.so.5
(gdb) bt
#0  0x00007f79e5262e30 in ?? () from /usr/lib/x86_64-linux-gnu/libgfortran.so.5
#1  0x00007f79e5273d98 in ?? () from /usr/lib/x86_64-linux-gnu/libgfortran.so.5
#2  0x00007f79e41dcbd0 in xerrwv (msg=..., nmes=<optimized out>, nerr=<optimized out>, level=0, ni=1, i1=0, i2=0, nr=0, r1=0, 
    r2=0) at scipy/integrate/odepack/xerrwv.f:84
#3  0x00007f79e41d1b69 in lsoda (f=<optimized out>, neq=..., y=..., t=<optimized out>, tout=0.020408163265306121, itol=1, 
    rtol=..., atol=..., itask=1, istate=1, iopt=1, rwork=..., lrw=22, iwork=..., liw=20, 
    jac=0x7f79e41cf6b0 <ode_jacobian_function>, jt=2) at scipy/integrate/odepack/lsoda.f:1554
#4  0x00007f79e41d08da in odepack_odeint (dummy=<optimized out>, args=<optimized out>, kwdict=<optimized out>)
    at scipy/integrate/_odepackmodule.c:713
#5  0x000055b0ab622f76 in cfunction_call_varargs (kwargs=<optimized out>, args=<optimized out>, func=0x7f79e43bfd10)
    at /tmp/build/80754af9/python_1599203911753/work/Objects/call.c:742
#6  PyCFunction_Call (func=0x7f79e43bfd10, args=<optimized out>, kwargs=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Objects/call.c:772
#7  0x000055b0ab5e085f in _PyObject_MakeTpCall (callable=0x7f79e43bfd10, args=<optimized out>, nargs=<optimized out>, 
    keywords=<optimized out>) at /tmp/build/80754af9/python_1599203911753/work/Objects/call.c:159
#8  0x000055b0ab667f56 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55b0ad65ab10, 
    callable=0x7f79e43bfd10) at /tmp/build/80754af9/python_1599203911753/work/Include/cpython/abstract.h:125
#9  call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x55b0ace19070)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:4963
#10 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:3469
#11 0x000055b0ab62da92 in _PyEval_EvalCodeWithName (_co=0x7f79e43c3c90, globals=<optimized out>, locals=<optimized out>, 
    args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x7f79f39495d8, kwcount=<optimized out>, kwstep=1, 
    defs=0x7f79e44a57d8, defcount=19, kwdefs=0x0, closure=0x0, name=0x7f79f38429f0, qualname=0x7f79f38429f0)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:4298
#12 0x000055b0ab62e943 in _PyFunction_Vectorcall (func=<optimized out>, stack=0x7f79f39495c0, nargsf=<optimized out>, 
    kwnames=<optimized out>) at /tmp/build/80754af9/python_1599203911753/work/Objects/call.c:435
#13 0x000055b0ab5a377f in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7f79f39495c0, 
    callable=0x7f79e43cd5e0) at /tmp/build/80754af9/python_1599203911753/work/Include/cpython/abstract.h:127
#14 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x55b0ace19070)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:4963
#15 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:3469
#16 0x000055b0ab62da92 in _PyEval_EvalCodeWithName (_co=0x7f79f38cc450, globals=<optimized out>, locals=<optimized out>, 
    args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x0, kwcount=<optimized out>, kwstep=2, defs=0x0, 
    defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:4298
#17 0x000055b0ab62e754 in PyEval_EvalCodeEx (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, 
    args=<optimized out>, argcount=<optimized out>, kws=<optimized out>, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, 
    closure=0x0) at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:4327
#18 0x000055b0ab6bcedc in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Python/ceval.c:718
#19 0x000055b0ab6bcf84 in run_eval_code_obj (co=0x7f79f38cc450, globals=0x7f79f39abdc0, locals=0x7f79f39abdc0)
    at /tmp/build/80754af9/python_1599203911753/work/Python/pythonrun.c:1125
#20 0x000055b0ab6ef1f4 in run_mod (mod=<optimized out>, filename=<optimized out>, globals=0x7f79f39abdc0, 
    locals=0x7f79f39abdc0, flags=<optimized out>, arena=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Python/pythonrun.c:1147
#21 0x000055b0ab5b76e1 in PyRun_FileExFlags (fp=0x55b0ace176d0, filename_str=<optimized out>, start=<optimized out>, 
    globals=0x7f79f39abdc0, locals=0x7f79f39abdc0, closeit=1, flags=0x7ffec460fc88)
    at /tmp/build/80754af9/python_1599203911753/work/Python/pythonrun.c:1063
#22 0x000055b0ab5b7ac6 in PyRun_SimpleFileExFlags (fp=0x55b0ace176d0, filename=<optimized out>, closeit=1, flags=0x7ffec460fc88)
    at /tmp/build/80754af9/python_1599203911753/work/Python/pythonrun.c:428
#23 0x000055b0ab5b898b in pymain_run_file (cf=0x7ffec460fc88, config=0x55b0ace180c0)
    at /tmp/build/80754af9/python_1599203911753/work/Modules/main.c:387
#24 pymain_run_python (exitcode=0x7ffec460fc80) at /tmp/build/80754af9/python_1599203911753/work/Modules/main.c:612
#25 Py_RunMain () at /tmp/build/80754af9/python_1599203911753/work/Modules/main.c:691
#26 0x000055b0ab6f1d19 in Py_BytesMain (argc=<optimized out>, argv=<optimized out>)
    at /tmp/build/80754af9/python_1599203911753/work/Modules/main.c:1137
#27 0x00007f79f413e0b3 in __libc_start_main (main=0x55b0ab5b9460 <main>, argc=2, argv=0x7ffec460fe88, init=<optimized out>, 
    fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7ffec460fe78) at ../csu/libc-start.c:308
#28 0x000055b0ab681e93 in _start () at ../sysdeps/x86_64/elf/start.S:103

Scipy/Numpy/Python version information:

1.7.0.dev0+ec8912c 1.19.2 sys.version_info(major=3, minor=8, micro=5, releaselevel='final', serial=0)

[WarrenWeckesser]

@roryyorke, thanks for reporting the issue. When I give an empty sequence for y0 (on a Mac and on Linux, both with Python 3.7), I get a warning, not a crash, but even a warning is a bug.

I'll have a pull request that fixes this ready soon.

[roryyorke]

I'm testing on Ubuntu 20.04, with the commit noted in the output. Given that the segfault happens in the error-reporting function, I suppose this could be an ABI mismatch? I can run the unit tests successfully, so whatever is causing this problem doesn't obviously affect LAPACK and BLAS calls.

I've tested the 1.6.0rc2 wheel (scipy-1.6.0rc2-cp38-cp38-manylinux1_x86_64.whl), and it produces the warning, as you said, and not a segfault.