[INSTRM-1785] Fix conda gcc linking of external libraries.

Relates — Mon, 14 Nov 2022 23:16:43 +0000

The agcc actor requires building a cython module for the external FLI camera library. That library uses the external libusb-1.0.so to actually connect to the device.

With rubin3-ics, the extension .so is built but does not then load libusb.

Bad:

(conda-ics) pfs-data@AGCC-OptiPlex-755:ics_agccActor-pfsdata$ ldd fli_camera.cpython-38-x86_64-linux-gnu.so
	linux-vdso.so.1 =>  (0x00007ffd177d8000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9688095000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f968845e000)

Good:

(conda-ics) pfs-data@AGCC-OptiPlex-755:ics_agccActor-pfsdata$ ldd fli_camera.cpython-38-x86_64-linux-gnu.so
	linux-vdso.so.1 =>  (0x00007ffcde7f6000)
	libusb-1.0.so.0 => /software/conda/envs/rubin3_ics/lib/libusb-1.0.so.0 (0x00007f2fc1bad000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2fc165d000)
	libudev.so.1 => /software/conda/envs/rubin3_ics/lib/./libudev.so.1 (0x00007f2fc1b60000)
	libatomic.so.1 => /software/conda/envs/rubin3_ics/lib/./libatomic.so.1 (0x00007f2fc1b54000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2fc143f000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f2fc1a26000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f2fc1237000)

rubin3-ics switched from using the system compilers to using the conda compiler packages. These are set up by /software/conda/envs/rubin3_ics/etc/conda/activate.d/activate-gcc_linux-64.sh

One flag which conda adds is Wl,as-needed, and that is what causes the external libraries to be trimmed. I have not figured if that is really correct, nor how to bypass it. You can add -Wl,-no-as-needed to the extra_ld_args Extension arguments, but that is added too late in the gcc call: that argument needs to come before the listings of the object files and libraries. So the distutils quick fix does not work here, and I have not found a better one.

This cannot be right. Surely many Extensions out there require external libraries. So I am missing something.

If this is right, we can simply edit the /software/conda/envs/rubin3_ics/etc/conda/activate.d/activate-gcc_linux-64.sh file. Yuck.

PFS-JIRA

[INSTRM-1785] Fix conda gcc linking of external libraries.