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Bitgroom test now dies with symbol-not-found error on Charlie's MacOS11 #91

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czender opened this issue Dec 3, 2020 · 4 comments
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@czender
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czender commented Dec 3, 2020

Within the last few weeks the BitGroom portion of "make check" began to fail for me. During this time I upgraded to MacOS11, and @edwardhartnett implemented the run_tests.sh mechanism. The BitGroom test now fails on my Macbook (and still works on Linux). Running the contents of run_tests.sh manually on my Macbook reveals a symbol not found error:

zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ export HDF5_PLUGIN_PATH=../src/.libs
zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ ./h5ex_d_bitgroom
BitGroom filter is available for quantization and decoding.
....Create dataset ................
....Writing BitGroom-quantized data ................
dyld: lazy symbol binding failed: Symbol not found: _ccr_bgr
  Referenced from: ../src/.libs/libh5bgr.dylib
  Expected in: flat namespace

dyld: Symbol not found: _ccr_bgr
  Referenced from: ../src/.libs/libh5bgr.dylib
  Expected in: flat namespace

Abort trap: 6
zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ 

This symbol, ccr_bgr, both has a prototype and is defined in the BitGroom filter H5Zbitgroom.c.
@edwardhartnett do you understand what the issue might be?
It is probably an issue with my transition to MacOS11, because everything works fine on Linux.

@czender czender added bug Something isn't working test Testing labels Dec 3, 2020
@czender czender self-assigned this Dec 3, 2020
@edwardhartnett
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Can you do a make distclean and try again with the latest develop branch?

Tests are building and working on GitHub macos-latest...

@czender
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czender commented Dec 4, 2020

Unfortunately the same problem still occurs. Looking a bit deeper, the symbol in question appears to me to be in the library in question:

zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ ls -l ../src/.libs/libh5bgr.dylib
lrwxr-xr-x 1 zender staff 16 Dec  4 09:49 ../src/.libs/libh5bgr.dylib -> libh5bgr.0.dylib*
zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ ls -l ../src/.libs/libh5bgr.0.dylib
-rwxr-xr-x 1 zender staff 51480 Dec  4 09:49 ../src/.libs/libh5bgr.0.dylib*
zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ nm ../src/.libs/libh5bgr.0.dylib | grep ccr_bgr
00000000000036d0 T _ccr_bgr
zender@sastrugi:~/ccr/hdf5_plugins/BITGROOM/example$ 

This is causing me major headaches! I think the upgrade to MacOS11 is interacting in a fatal way with my MacPorts paths so that some tools like ar and ld are using inconsistent versions.

@edwardhartnett
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Is this issue still active?

@edwardhartnett edwardhartnett added this to To do in Version 1.2.0 via automation May 11, 2021
@czender
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czender commented May 11, 2021

So long as you have this working on the MacOS pipeline, I will assume this issue was just restricted to my laptop, which is now MacOS12 not 11 so I am closing this issue.

@czender czender closed this as completed May 11, 2021
Version 1.2.0 automation moved this from To do to Done May 11, 2021
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