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3d_scalar seg faults on mac #245

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danlipsa opened this Issue Sep 5, 2017 · 11 comments

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danlipsa commented Sep 5, 2017

The following script seg faults on my mac. It works on linux. Upgrading to opengl2 might fix this. @doutriaux1 @aashish24 Do we test 3D plots?

import vcs
import cdms2
f=cdms2.open("http://test.opendap.org/dap/data/nc/coads_climatology.nc")
x=vcs.init()
s=f["AIRT"]
gm=x.get3d_scalar()
x.plot(s,gm)

@doutriaux1 doutriaux1 added the bug label Sep 5, 2017

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doutriaux1 commented Sep 5, 2017

@danlipsa there are some dv3d test in already.

@danlipsa it might be cdtime related, can you check cdtime versions on both your mac and linux, i think cdtime 2.12 is the issue.

@dnadeau4 her'es the mac traceback

Warning, can't open data file 'None'
Process 86845 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=EXC_I386_GPFLT)
    frame #0: 0x0000000113161bbd cdtime.so`PyCdReltime_Compare + 67
cdtime.so`PyCdReltime_Compare:
->  0x113161bbd <+67>: movq   0x8(%rax), %rdx
    0x113161bc1 <+71>: leaq   0x8e918(%rip), %rax       ; CompTimeType
    0x113161bc8 <+78>: cmpq   %rax, %rdx
    0x113161bcb <+81>: jne    0x113161beb               ; <+113>
(lldb) bt
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=EXC_I386_GPFLT)
  * frame #0: 0x0000000113161bbd cdtime.so`PyCdReltime_Compare + 67
    frame #1: 0x0000000113160aec cdtime.so`reltime_cmp2 + 224
    frame #2: 0x000000011316158d cdtime.so`PyCdReltime_Cmp + 119
    frame #3: 0x0000000100142f73 libpython2.7.dylib`PyEval_EvalFrameEx + 30563
    frame #4: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #5: 0x00000001000c40ac libpython2.7.dylib`function_call + 364
    frame #6: 0x000000010009ddc3 libpython2.7.dylib`PyObject_Call + 99
    frame #7: 0x000000010014381c libpython2.7.dylib`PyEval_EvalFrameEx + 32780
    frame #8: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #9: 0x0000000100147996 libpython2.7.dylib`fast_function + 118
    frame #10: 0x000000010014299a libpython2.7.dylib`PyEval_EvalFrameEx + 29066
    frame #11: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #12: 0x0000000100147996 libpython2.7.dylib`fast_function + 118
    frame #13: 0x000000010014299a libpython2.7.dylib`PyEval_EvalFrameEx + 29066
    frame #14: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #15: 0x00000001000c40ac libpython2.7.dylib`function_call + 364
    frame #16: 0x000000010009ddc3 libpython2.7.dylib`PyObject_Call + 99
    frame #17: 0x000000010014381c libpython2.7.dylib`PyEval_EvalFrameEx + 32780
    frame #18: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #19: 0x00000001000c40ac libpython2.7.dylib`function_call + 364
    frame #20: 0x000000010009ddc3 libpython2.7.dylib`PyObject_Call + 99
    frame #21: 0x000000010014381c libpython2.7.dylib`PyEval_EvalFrameEx + 32780
    frame #22: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #23: 0x00000001000c40ac libpython2.7.dylib`function_call + 364
    frame #24: 0x000000010009ddc3 libpython2.7.dylib`PyObject_Call + 99
    frame #25: 0x000000010014381c libpython2.7.dylib`PyEval_EvalFrameEx + 32780
    frame #26: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #27: 0x00000001000c40ac libpython2.7.dylib`function_call + 364
    frame #28: 0x000000010009ddc3 libpython2.7.dylib`PyObject_Call + 99
    frame #29: 0x000000010014381c libpython2.7.dylib`PyEval_EvalFrameEx + 32780
    frame #30: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #31: 0x0000000100147996 libpython2.7.dylib`fast_function + 118
    frame #32: 0x000000010014299a libpython2.7.dylib`PyEval_EvalFrameEx + 29066
    frame #33: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #34: 0x0000000100147996 libpython2.7.dylib`fast_function + 118
    frame #35: 0x000000010014299a libpython2.7.dylib`PyEval_EvalFrameEx + 29066
    frame #36: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #37: 0x000000010013ad26 libpython2.7.dylib`PyEval_EvalCode + 54
    frame #38: 0x0000000100169c34 libpython2.7.dylib`PyRun_FileExFlags + 164
    frame #39: 0x000000010013729b libpython2.7.dylib`builtin_execfile + 507
    frame #40: 0x0000000100142f73 libpython2.7.dylib`PyEval_EvalFrameEx + 30563
    frame #41: 0x000000010013b3b2 libpython2.7.dylib`PyEval_EvalCodeEx + 1666
    frame #42: 0x000000010013ad26 libpython2.7.dylib`PyEval_EvalCode + 54
    frame #43: 0x00000001001699b6 libpython2.7.dylib`PyRun_InteractiveOneFlags + 406
    frame #44: 0x000000010016946e libpython2.7.dylib`PyRun_InteractiveLoopFlags + 206
    frame #45: 0x000000010016930b libpython2.7.dylib`PyRun_AnyFileExFlags + 139
    frame #46: 0x000000010017f75c libpython2.7.dylib`Py_Main + 3084
    frame #47: 0x00007fffe5702235 libdyld.dylib`start + 1
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danlipsa commented Sep 5, 2017

@doutriaux1 Indeed, on linux I have cdtime 2.10 on mac I have 2.12.

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dnadeau4 commented Sep 5, 2017

I just pushed a change on cdtime to make sure I deference the pointer correctly.
CDAT/cdtime@1111ec4

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doutriaux1 commented Sep 5, 2017

@dnadeau4 that fixes it on the mac! Thanks!

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danlipsa commented Sep 5, 2017

@doutriaux1 Is this on conda nightly?

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doutriaux1 commented Sep 5, 2017

@danlipsa it is a py3 issue, reverted to py2 only (like v2.10) it's on conda-forge queue should be in overnight

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danlipsa commented Sep 5, 2017

Thanks @doutriaux1 @dnadeau4 I did a python setup.py install and that fixed it.

@danlipsa danlipsa closed this Sep 5, 2017

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doutriaux1 commented Sep 5, 2017

@danlipsa linux cdtime is now on conda-forge, expecting mac version around midnight PDT tonight

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doutriaux1 commented Sep 6, 2017

mac still in conda-forge queue... 17hours... unbelievable...

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danlipsa commented Sep 6, 2017

@doutriaux1 No worries ... I already installed the correct version manually.
I wonder if there is any way to trigger a vcs rounds of tests each time we change one of its conda packages. This way, we'll know if one of the packages broke something.

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doutriaux1 commented Sep 6, 2017

@danlipsa in this case that wouldn't help us because the test suite passed against cdtime. I did manually test vcs on both mac and linux when I put the py3 code in, and we did find some breakage already then. One way to achieve this would be to run vcs, cdms, etc.. as part of cdtime test suite, but it would take a long time...

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