double free or corruption (out) #394
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I can't reproduce your corruption locally. You can add |
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Thank you for the help @seisman. Here is the output with V='d': |
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I ran pygmt.test() and got a core dump on open_virtual_file: |
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I searched the Google machine for |
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Something else I am suspecting perhaps is the Linux kernel we are on, or the distribution, or some other library. Any suggestions you have would be greatly appreciated! Thanks. |
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Hard to say why it corrupts for you. pygmt is tested on macOS and Linux nightly, and we don't see any corruptions. The |
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Well, pretty sure this is a segmentation fault in one of the modules. I think the key clue is: Would be great to know if there is a difference between the GMT library I have and the one you have. How can we check this? |
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Those are GMT debug messages. It doesn't mean GMT corrupts. You can check the detailed version information with: |
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Thanks! What is your output from that command? |
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@leouieda, any thoughts on this? It seems clear that psxy is trying to free unallocated memory leading to a double free, and Python does not like that. The python interpreter rarely crashes out like this, but it can do so when a C program does something bad with malloc. I wonder if the version of Python we are on is not as lenient about stuff like this as the one you are using for your tests. I am hoping to determine what versions (i.e. builds) of the GMT library you are using, as well as Python. Can you help with this? Thanks! |
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This is my output: |
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@tjcrone ouch. I love how interfacing with C code keeps coming back to bite us :-) The most frustrating part is that these crashes seems to be somewhat random.
That's probably not it since we test with the latest Python 3.7 from conda-forge. I'm guessing you're running this on a Pangeo JupyterHub, right? Any idea what the underlying system is? |
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Thanks for the followup @leouieda. Currently the underlying system of Pangeo is Ubuntu Bionic. But I don't think it's the kernel or the system. I think I might have narrowed it down to an installation of PyAV, which also uses Cython, and may install incompatible libraries. I'll keep you posted if/when I find a fix. Thanks! |
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In case anyone is wondering, it was actually the pyinterp package that somehow includes something that makes gmt=6.0.0 segmentation fault. I never got to the bottom of the issue, just removed pyinterp from the OOI Pangeo notebook image, and it seems to be working okay. Thanks everyone for the help! |
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Thank you for posting, Tim! That's a strange bug and probably something we
didn't specify well enough in the GMT build.
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Hello. I am getting some sort of segmentation-type error when running the points example:
I'm on a Pangeo system and the output of conda list is:
Any thoughts what might be causing this? Thank you for any help you can provide!
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