Please ensure you are following the instructions in Conda on O2 when attempting to install your own Conda packages. Below is a list of known packages and situations the O2 user community has troubleshooted with Research Computing and their solutions resolutions (this list will be updated as new instances are encountered).
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$ cd path/to/env/bin
$ ln -s x86_64-conda-linux-gnu-gcc gcc
$ ln -s x86_64-conda-linux-gnu-g++ g++ |
You should now see the following additional entries in the bin directory:
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lrwxrwxrwx 1 *** *** 26 Jul 12 15:05 g++ -> x86_64-conda-linux-gnu-g++ lrwxrwxrwx 1 *** *** 26 Jul 12 15:04 gcc -> x86_64-conda-linux-gnu-gcc |
In most cases, this should get you far enough. If you encounter build errors that are looking for something like gcc-ar, you will need to set up a similar softlink for that as well. In any case, once you have the above softlinks (at a minimum) created, your conda environment should be able to reliably use your installed gcc installation to build packages instead of inadvertently using the one located at /usr/bin.
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