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anandijain opened this issue Feb 28, 2021 · 1 comment
Closed

using SbmlInterface functions with SciMLBase.tmap #10

anandijain opened this issue Feb 28, 2021 · 1 comment

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@anandijain
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I was getting limited by speed testing on the sbml test suite so I wanted to multithread.

SciMLBase has a threaded map here. MWE here.

This is the nefarious line.

SciMLBase.tmap(getmodel, all_files)

This could be a PyCall, a SciMLBase, or an SbmlInterface issue. I'm opening it here for @paulflang to weigh in.
We can move it later, just want ur eyes since you know PyCall better than me.

trace

signal (11): Segmentation fault
in expression starting at REPL[14]:1

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)

signal (11): Segmentation fault

signal (sion starting at REPL[14]:1

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)
unknown function (ip: 0x7fae857ec717)

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)

signal (11): Segmentation fault
in expression starting at REPL[14]:1
unknown function (ip: 0x7fae85834a10)
unknown function (ip: 0x7fae857ec717)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_GetSwigThis at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
_wrap_SBMLDocument_getNumErrors at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
_wrap_SBMLDocument_getNumErrors at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7fae85850356)
_PyEval_EvalFrameDefault at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_PyEval_EvalCodeWithName at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_PyFunction_Vectorcall at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
unknown function (ip: 0x7fae858509e6)
PyVectorcall_Call at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
macro expansion at /home/sippycups/.julia/packages/PyCall/tqyST/src/exception.jl:95 [inlined]
nknown function (ip: 0x7fae85850356)
#109 at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:43 [inlined]
disable_sigint at ./c.jl:458 [inlined]
__pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:42 [inlined]
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:29
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:11 [inlined]
#_#116 at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:86 [inlined]
PyObject at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:86
unknown function (ip: 0x7faf02cd1f26)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
getmodel at /home/sippycups/.julia/dev/SbmlInterface/src/sbml2modelingtoolkit.jl:116
macro expansion at /home/sippycups/.julia/packages/SciMLBase/eghDQ/src/ensemble/basic_ensemble_solve.jl:221 [inlined]
#446#threadsfor_fun at ./threadingconstructs.jl:81
#446#threadsfor_fun at ./threadingconstructs.jl:48
unknown function (ip: 0x7faf02cd01ac)
_PyEval_EvalFrameDefault at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
_PyEval_EvalCodeWithName at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_PyFunction_Vectorcall at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
unknown function (ip: 0x7fae858509e6)
PyVectorcall_Call at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
macro expansion at /home/sippycups/.julia/packages/PyCall/tqyST/src/exception.jl:95 [inlined]
#109 at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:43 [inlined]
disable_sigint at ./c.jl:458 [inlined]
__pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:42 [inlined]
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:29
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:11 [inlined]
#_#116 at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:86 [inlined]
PyObject at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:86
unknown function (ip: 0x7faf02cd1f26)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
getmodel at /home/sippycups/.julia/dev/SbmlInterface/src/sbml2modelingtoolkit.jl:116
macro expansion at /home/sippycups/.julia/packages/SciMLBase/eghDQ/src/ensemble/basic_ensemble_solve.jl:221 [inlined]
#446#threadsfor_fun at ./threadingconstructs.jl:81
#446#threadsfor_fun at ./threadingconstructs.jl:48
unknown function (ip: 0x7faf02cd01ac)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
_wrap_SBMLDocument_getErrorLog at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7fae85850356)
_PyEval_EvalFrameDefault at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_PyEval_EvalCodeWithName at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
_PyFunction_Vectorcall at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
unknown function (ip: 0x7fae85850aea)
PyVectorcall_Call at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
macro expansion at /home/sippycups/.julia/packages/PyCall/tqyST/src/exception.jl:95 [inlined]
#109 at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:43 [inlined]
disable_sigint at ./c.jl:458 [inlined]
__pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:42 [inlined]
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:29
_pycall! at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:11 [inlined]
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at l/tqyST/src/pyfncall.jl:86 [inlined]
SWIG_Python_ConvertPtrAndOwn.constprop.3403 at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
PyObject at /home/sippycups/.julia/packages/PyCall/tqyST/src/pyfncall.jl:86
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
getmodel at /home/sippycups/.julia/dev/SbmlInterface/src/sbml2modelingtoolkit.jl:122
macro expansion at /home/sippycups/.julia/packages/SciMLBase/eghDQ/src/ensemble/basic_ensemble_solve.jl:221 [inlined]
#446#threadsfor_fun at ./threadingconstructs.jl:81
#446#threadsfor_fun at ./threadingconstructs.jl:48
unknown function (ip: 0x7faf02cd01ac)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2238 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2420
_wrap_SBMLDocument_getNumErrors at /usr/local/lib/python3.8/dist-packages/libsbml/_libsbml.cpython-38-x86_64-linux-gnu.so (unknown line)
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
start_task at /buildworker/worker/package_linux64/build/src/task.c:839
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
start_task at /buildworker/worker/package_linux64/build/src/task.c:839
unknown function (ip: 0x7fae85850356)
_PyEval_EvalFrameDefault at /usr/lib/x86_64-linux-gnu/libpython3.8.so.1.0 (unknown line)
unknown function (ip: (nil))
Allocations: 19003754 (Pool: 18999326; Big: 4428); GC: 19
fish: '/home/sippycups/julia-1.6.0-rc1…' terminated by signal SIGSEGV (Address boundary error)
@anandijain
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opened in pycall JuliaPy/PyCall.jl#885. for sure not an sbml issue

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