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JuliaPy / PyPlot.jl

Plotting for Julia based on matplotlib.pyplot
https://github.com/JuliaPy/PyPlot.jl
MIT License
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signal (11): segmentation fault: 11 #299

Closed ptoche closed 7 years ago

ptoche commented 7 years ago

I'm getting this segmentation fault:11 crash.

If I start a new Julia session and run

using PyPlot

all is well and I can make basic plots without apparent difficulty.

But if I first load my module and execute a function from it, and then afterwards load PyPlot as above, I get a crash. What should I be looking for? Any ideas?

My module executes in about 20 seconds, but mostly it's overhead, so I don't think it would be a memory issue (but then again I know nothing). 

    Process:               julia [586]
    Path:                  /Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia
    Identifier:            julia
    Version:               ???
    Code Type:             X86-64 (Native)
    Parent Process:        Atom Helper [327]
    Responsible:           Atom [269]
    User ID:               502

    Date/Time:             2017-06-10 01:17:36.658 +0800
    OS Version:            Mac OS X 10.10.5 (14F2411)
    Report Version:        11
    Anonymous UUID:        492C9CB7-BC26-304E-C519-9DAE1A82CD90

    Time Awake Since Boot: 460 seconds

    Crashed Thread:        0  Dispatch queue: com.apple.main-thread

    Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
    Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000008

    VM Regions Near 0x8:
    --> 
        __TEXT                 000000010e17f000-000000010e181000 [    8K] r-x/rwx SM=COW  /Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia

    Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
    0   libjulia.0.5.2.dylib            0x000000010e1e2c7e julia_type_to_llvm + 46
    1   libjulia.0.5.2.dylib            0x000000010e2019d4 emit_expr(_jl_value_t*, jl_codectx_t*) + 4788
    2   libjulia.0.5.2.dylib            0x000000010e1e7d2e emit_function(_jl_lambda_info_t*, _jl_llvm_functions_t*) + 17774
    3   libjulia.0.5.2.dylib            0x000000010e1e34c2 jl_compile_linfo + 914
    4   libjulia.0.5.2.dylib            0x000000010e202234 emit_expr(_jl_value_t*, jl_codectx_t*) + 6932
    5   libjulia.0.5.2.dylib            0x000000010e20287e emit_expr(_jl_value_t*, jl_codectx_t*) + 8542
    6   libjulia.0.5.2.dylib            0x000000010e2050f1 emit_stmtpos(_jl_value_t*, jl_codectx_t*) + 161
    7   libjulia.0.5.2.dylib            0x000000010e1e871f emit_function(_jl_lambda_info_t*, _jl_llvm_functions_t*) + 20319
    8   libjulia.0.5.2.dylib            0x000000010e1e34c2 jl_compile_linfo + 914
    9   libjulia.0.5.2.dylib            0x000000010e202234 emit_expr(_jl_value_t*, jl_codectx_t*) + 6932
    10  libjulia.0.5.2.dylib            0x000000010e20287e emit_expr(_jl_value_t*, jl_codectx_t*) + 8542
    11  libjulia.0.5.2.dylib            0x000000010e2050f1 emit_stmtpos(_jl_value_t*, jl_codectx_t*) + 161
    12  libjulia.0.5.2.dylib            0x000000010e1e871f emit_function(_jl_lambda_info_t*, _jl_llvm_functions_t*) + 20319
    13  libjulia.0.5.2.dylib            0x000000010e1e34c2 jl_compile_linfo + 914
    14  libjulia.0.5.2.dylib            0x000000010e202234 emit_expr(_jl_value_t*, jl_codectx_t*) + 6932
    15  libjulia.0.5.2.dylib            0x000000010e206312 emit_call(jl_expr_t*, jl_codectx_t*) + 786
    16  libjulia.0.5.2.dylib            0x000000010e201fb8 emit_expr(_jl_value_t*, jl_codectx_t*) + 6296
    17  libjulia.0.5.2.dylib            0x000000010e2050f1 emit_stmtpos(_jl_value_t*, jl_codectx_t*) + 161
    18  libjulia.0.5.2.dylib            0x000000010e1e871f emit_function(_jl_lambda_info_t*, _jl_llvm_functions_t*) + 20319
    19  libjulia.0.5.2.dylib            0x000000010e1e34c2 jl_compile_linfo + 914
    20  libjulia.0.5.2.dylib            0x000000010e19c4a6 jl_compile_for_dispatch + 918
    21  libjulia.0.5.2.dylib            0x000000010e19b672 jl_apply_generic + 1106
    22  libjulia.0.5.2.dylib            0x000000010e1c6b9a jl_module_run_initializer + 282
    23  libjulia.0.5.2.dylib            0x000000010e1c30e8 _jl_restore_incremental + 2184
    24  libjulia.0.5.2.dylib            0x000000010e1c316c jl_restore_incremental + 76
    25  sys.dylib                       0x000000010fcbdd12 julia__include_from_serialized_22632 + 242 (.loading.jl:150)
    26  sys.dylib                       0x000000010fcbe1ec julia__require_from_serialized_22598 + 908 (.loading.jl:187)
    27  sys.dylib                       0x000000010fe0e011 julia__require_search_from_serialized_32311 + 705 (.loading.jl:217)
    28  sys.dylib                       0x000000010fe0e341 jlcall__require_search_from_serialized_32311 + 33
    29  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    30  sys.dylib                       0x000000010fcbf402 julia_require_22458 + 1282 (.loading.jl:371)
    31  sys.dylib                       0x000000010fcc01dc jlcall_require_22458 + 12
    32  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    33  libjulia.0.5.2.dylib            0x000000010e1c5958 read_verify_mod_list + 520
    34  libjulia.0.5.2.dylib            0x000000010e1c29e7 _jl_restore_incremental + 391
    35  libjulia.0.5.2.dylib            0x000000010e1c316c jl_restore_incremental + 76
    36  sys.dylib                       0x000000010fcbdd12 julia__include_from_serialized_22632 + 242 (.loading.jl:150)
    37  sys.dylib                       0x000000010fcbe1ec julia__require_from_serialized_22598 + 908 (.loading.jl:187)
    38  sys.dylib                       0x000000010fe0e011 julia__require_search_from_serialized_32311 + 705 (.loading.jl:217)
    39  sys.dylib                       0x000000010fe0e341 jlcall__require_search_from_serialized_32311 + 33
    40  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    41  sys.dylib                       0x000000010fcbf402 julia_require_22458 + 1282 (.loading.jl:371)
    42  sys.dylib                       0x000000010fcc01dc jlcall_require_22458 + 12
    43  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    44  libjulia.0.5.2.dylib            0x000000010e1c8c95 eval_import_path_ + 565
    45  libjulia.0.5.2.dylib            0x000000010e1c780d jl_toplevel_eval_flex + 797
    46  libjulia.0.5.2.dylib            0x000000010e1a54fe jl_parse_eval_all + 1214
    47  sys.dylib                       0x000000010fe44d1e julia_include_string_33641 + 270 (.loading.jl:441)
    48  sys.dylib                       0x000000010fe44e80 jlcall_include_string_33641 + 16
    49  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    50  libjulia.0.5.2.dylib            0x000000010e1b13b8 do_call + 200
    51  libjulia.0.5.2.dylib            0x000000010e1af73c eval + 860
    52  libjulia.0.5.2.dylib            0x000000010e1b0d5e eval_body + 462
    53  libjulia.0.5.2.dylib            0x000000010e1b12a2 jl_interpret_call + 498
    54  libjulia.0.5.2.dylib            0x000000010e1c7a3d jl_toplevel_eval_flex + 1357
    55  libjulia.0.5.2.dylib            0x000000010e1a9333 jl_toplevel_eval_in_warn + 899
    56  sys.dylib                       0x000000010fc6c64a julia_eval_19854 + 10 (.boot.jl:234)
    57  sys.dylib                       0x000000010fc6c660 jlcall_eval_19854 + 16
    58  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    59  ???                             0x000000031de62922 0 + 13386524962
    60  ???                             0x000000031de62266 0 + 13386523238
    61  ???                             0x000000031de623f3 0 + 13386523635
    62  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    63  ???                             0x000000031de6202a 0 + 13386522666
    64  ???                             0x000000031de62073 0 + 13386522739
    65  ???                             0x000000031de5fe43 0 + 13386513987
    66  libjulia.0.5.2.dylib            0x000000010e19b608 jl_apply_generic + 1000
    67  libjulia.0.5.2.dylib            0x000000010e1b9a54 start_task + 356

    Thread 1:
    0   libsystem_kernel.dylib          0x00007fff91a8d75a __sigwait + 10
    1   libjulia.0.5.2.dylib            0x000000010e1e0ddd signal_listener + 45
    2   libsystem_pthread.dylib         0x00007fff940b905a _pthread_body + 131
    3   libsystem_pthread.dylib         0x00007fff940b8fd7 _pthread_start + 176
    4   libsystem_pthread.dylib         0x00007fff940b63ed thread_start + 13

    Thread 2:
    0   libsystem_kernel.dylib          0x00007fff91a884de mach_msg_trap + 10
    1   libsystem_kernel.dylib          0x00007fff91a8764f mach_msg + 55
    2   libsystem_kernel.dylib          0x00007fff91a87f60 mach_msg_server + 468
    3   libjulia.0.5.2.dylib            0x000000010e1e02fd mach_segv_listener + 29
    4   libsystem_pthread.dylib         0x00007fff940b905a _pthread_body + 131
    5   libsystem_pthread.dylib         0x00007fff940b8fd7 _pthread_start + 176
    6   libsystem_pthread.dylib         0x00007fff940b63ed thread_start + 13

    Thread 3:
    0   libsystem_kernel.dylib          0x00007fff91a8d136 __psynch_cvwait + 10
    1   libopenblas64_.dylib            0x00000003150754db blas_thread_server + 171
    2   libsystem_pthread.dylib         0x00007fff940b905a _pthread_body + 131
    3   libsystem_pthread.dylib         0x00007fff940b8fd7 _pthread_start + 176
    4   libsystem_pthread.dylib         0x00007fff940b63ed thread_start + 13

    Thread 4:: Dispatch queue: com.apple.libdispatch-manager
    0   libsystem_kernel.dylib          0x00007fff91a8e232 kevent64 + 10
    1   libdispatch.dylib               0x00007fff8902526e _dispatch_mgr_thread + 52

    Thread 5:
    0   libsystem_kernel.dylib          0x00007fff91a8d3fa __select + 10
    1   libsystem_pthread.dylib         0x00007fff940b905a _pthread_body + 131
    2   libsystem_pthread.dylib         0x00007fff940b8fd7 _pthread_start + 176
    3   libsystem_pthread.dylib         0x00007fff940b63ed thread_start + 13

    Thread 6:
    0   libsystem_kernel.dylib          0x00007fff91a884de mach_msg_trap + 10
    1   libsystem_kernel.dylib          0x00007fff91a8764f mach_msg + 55
    2   com.apple.CoreFoundation        0x00007fff942bacd4 __CFRunLoopServiceMachPort + 212
    3   com.apple.CoreFoundation        0x00007fff942ba19b __CFRunLoopRun + 1371
    4   com.apple.CoreFoundation        0x00007fff942b99f8 CFRunLoopRunSpecific + 296
    5   com.apple.AppKit                0x00007fff9340756b _NSEventThread + 137
    6   libsystem_pthread.dylib         0x00007fff940b905a _pthread_body + 131
    7   libsystem_pthread.dylib         0x00007fff940b8fd7 _pthread_start + 176
    8   libsystem_pthread.dylib         0x00007fff940b63ed thread_start + 13

    Thread 0 crashed with X86 Thread State (64-bit):
      rax: 0x000000010e418b58  rbx: 0x000000010e418b30  rcx: 0x0000000000000006  rdx: 0x00007fff78015070
      rdi: 0x0000000000000010  rsi: 0x0000000000000000  rbp: 0x00007fff51a76190  rsp: 0x00007fff51a76180
       r8: 0x0000000000000010   r9: 0x0000000113134670  r10: 0x00007fff51a76e00  r11: 0x0000000113134790
      r12: 0x0000000000000010  r13: 0x00007fff51a76898  r14: 0x000000011b4b9990  r15: 0x00007fff51a76898
      rip: 0x000000010e1e2c7e  rfl: 0x0000000000010202  cr2: 0x0000000000000008

    Logical CPU:     2
    Error Code:      0x00000004
    Trap Number:     14

    Binary Images:
           0x10e17f000 -        0x10e180fff +julia (???) <14C26D69-968A-330E-A43C-FA7B63AA2B19> /Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia
           0x10e189000 -        0x10e312ff7 +libjulia.0.5.2.dylib (0) <4E8849D2-8A7B-3797-9EAC-8CADD9EE1BEE> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/libjulia.0.5.2.dylib
           0x10e5f9000 -        0x10f602ff7 +libLLVM-3.7.dylib (0) <05AE218C-1CE2-32C4-A7B2-952F60F4619C> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libLLVM-3.7.dylib
           0x10fb3b000 -        0x1118eeff7 +sys.dylib (0) <34ABB9C3-A8C2-3924-96FE-CAA963899C1E> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib
           0x3148cd000 -        0x3148cffff +libdSFMT.dylib (0) <7FFA0121-C161-31AA-B74B-9F0E29CDE7A3> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libdSFMT.dylib
           0x3148d2000 -        0x31490bfe7 +libquadmath.0.dylib (0) <FB40BC93-613B-3268-AC2D-8C25846F7323> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libquadmath.0.dylib
           0x31491a000 -        0x31491bff7 +libsuitesparseconfig.dylib (0) <E4FB5166-CE72-31F4-A508-84D12F766481> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libsuitesparseconfig.dylib
           0x31491e000 -        0x31491eff7 +libsuitesparse_wrapper.dylib (0) <244B1012-7E53-3084-A307-69637724EC56> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libsuitesparse_wrapper.dylib
           0x314ae5000 -        0x314b68ff7 +libpcre2-8.0.dylib (4) <DA720706-FB17-3116-904A-8EA1A46DCAB9> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libpcre2-8.0.dylib
           0x314c6d000 -        0x314cdafdf +libgmp.10.dylib (14) <07013073-3AE8-38B3-8AD4-7FED2F599623> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libgmp.10.dylib
           0x314ce6000 -        0x314d3cfff +libmpfr.4.dylib (6.4) <E4016962-CF02-38AB-99E4-18B01156F36A> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libmpfr.4.dylib
           0x314d59000 -        0x318d641d7 +libopenblas64_.dylib (0) <96A0342D-86C6-3ED5-B31C-81AA729C9591> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libopenblas64_.dylib
           0x3190ae000 -        0x3191ccfff +libgfortran.3.dylib (0) <70C14D65-241B-3FB0-A94D-A2A4CAD4BFFC> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libgfortran.3.dylib
           0x31923a000 -        0x31924ffe7 +libgcc_s.1.dylib (1) <E5DB3B80-B5F1-3244-93F8-E6CB4697936A> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libgcc_s.1.dylib
           0x31d2dd000 -        0x31d387ff7 +libgit2.0.24.5.dylib (0) <4DB118AB-0411-395B-A4E8-858E76663B6A> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libgit2.0.24.5.dylib
           0x31d3a6000 -        0x31d3f5fff +libcurl.dylib (9) <E4E7D550-253F-354C-AF08-5E38CBE51D2A> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libcurl.dylib
           0x31d404000 -        0x31d426ff7 +libssh2.dylib (0) <19B6CEDF-9AD1-3BDC-9224-3CE4E2DF8AE5> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libssh2.dylib
           0x31d42f000 -        0x31d44cff7 +libmbedtls.dylib (0) <5DAEFD43-C6E3-3A9D-8EEA-BC82A9A42301> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libmbedtls.dylib
           0x31d455000 -        0x31d462fff +libmbedx509.dylib (0) <08B42A01-52B9-32BB-A404-877F4A4A2E46> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libmbedx509.dylib
           0x31d468000 -        0x31d4a6fff +libmbedcrypto.dylib (0) <49794EE0-4514-35EE-9867-7C1EFE0A69FF> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libmbedcrypto.dylib
           0x31dc59000 -        0x31dd3bfff +libcholmod.dylib (0) <F6D862C5-3835-3B26-B07C-F7922B206FF4> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libcholmod.dylib
           0x31dd43000 -        0x31dd49ff7 +libcolamd.dylib (0) <635F709B-0F08-3964-AA99-D5186E2C43A4> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libcolamd.dylib
           0x31dd4c000 -        0x31dd53ff7 +libamd.dylib (0) <ACBEB50D-317C-3B53-AAD4-B57F95510B55> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libamd.dylib
           0x31dd56000 -        0x31dd5dff7 +libcamd.dylib (0) <ACC69CE0-B0BE-3A40-BA16-D358598D87F0> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libcamd.dylib
           0x31dd60000 -        0x31dd69fff +libccolamd.dylib (0) <C623EF8B-6F83-37F4-A029-C652C8854982> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libccolamd.dylib
           0x31dd6c000 -        0x31de16ff7 +libumfpack.dylib (0) <093546D7-5C61-3DBE-A4B3-E2E8A96BC710> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libumfpack.dylib
           0x31de1e000 -        0x31de43ff7 +libspqr.dylib (0) <D595D476-1720-3C81-AF2E-011FB3388726> /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/libspqr.dylib
           0x31e14d000 -        0x31e154ff7  libCGCMS.A.dylib (790) <64ACC63D-93FC-3D11-AF9C-A2A84A34FE35> /System/Library/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGCMS.A.dylib
           0x31ebb0000 -        0x31ecfefff +libpython2.7.dylib (2.7) <7A3497FC-961C-3662-9881-47819053E095> /Users/USER/*/libpython2.7.dylib
           0x31ee5f000 -        0x31ee60fff +_locale.so (???) <D776362E-167F-3844-809E-DF6F0AEA3AB6> /Users/USER/*/_locale.so
           0x31eee4000 -        0x31eee7fff +strop.so (???) <B7D12DC6-45FF-3DEA-A64A-C996C0BACA1B> /Users/USER/*/strop.so
           0x31eeec000 -        0x31eef2fff +itertools.so (???) <E5FB1D56-DD5B-30A9-A80E-9FCA3366C65E> /Users/USER/*/itertools.so
           0x31eefd000 -        0x31ef01fff +operator.so (???) <F9731FEF-575E-35AF-ACB4-87234CCB22EC> /Users/USER/*/operator.so
           0x31ef08000 -        0x31ef0cfff +_collections.so (???) <EA1F8779-1214-3AD6-AEC9-C8A1860182BC> /Users/USER/*/_collections.so
           0x31ef52000 -        0x31ef53ff7 +_heapq.so (???) <25B0AF76-2251-38D0-B85C-546719C2B274> /Users/USER/*/_heapq.so
           0x31ef57000 -        0x31ef6afff +_ctypes.so (???) <D1C6B5E2-D327-3E4A-84E5-F0B9EC43349C> /Users/USER/*/_ctypes.so
           0x31ef7b000 -        0x31ef7ffff +_struct.so (???) <7DADDDF8-D81D-3A32-86A7-472941CA730B> /Users/USER/*/_struct.so
           0x31ef86000 -        0x31ef93fff +datetime.so (???) <F246EB76-D999-3E68-8138-7DACAEF26816> /Users/USER/*/datetime.so
           0x31f08e000 -        0x31f08fff7 +_functools.so (???) <35B7AB72-1B95-3885-97C4-56E74F2D9A95> /Users/USER/*/_functools.so
           0x31f093000 -        0x31f0a6ff7 +_io.so (???) <19A85DA0-1D09-3977-AFBB-5CAF568B8A0D> /Users/USER/*/_io.so
           0x31f0fe000 -        0x31f128ff7 +pyexpat.so (???) <B4978894-B4E8-322A-AC7F-B6120C4A9BB3> /Users/USER/*/pyexpat.so
           0x31f1be000 -        0x31f1c3fff +math.so (???) <05E1AC30-A55F-3DD9-858A-D7A96A633BAC> /Users/USER/*/math.so
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jgoldfar commented 7 years ago

Trying to debug an installation issue on OSX roughly according to https://github.com/JuliaPy/PyPlot.jl/issues/219#issuecomment-222430718 i.e. running

ENV["PYTHON"]=""; map(Pkg.build, ["PyCall", "PyPlot"]); using PyPlot

after checking out the master version of PyPlot. I'm now running into a segfault with the same signal number on Julia v0.7.0-dev; not sure how to debug, or if Julia-0.7.0 support is not expected quite yet...

stevengj commented 7 years ago

Currently, PyCall is broken on 0.7.