Compile error for Lagrangian particle tracking on the hub

[NoraLoose]

Discussed in #137

^{Originally posted by NoraLoose March 28, 2024}
I am trying to do Lagrangian particle tracking with the python package parcels on the LEAP pangeo hub, but upon

pset.execute(
    kernel,  # the kernel (which defines how particles move)
    runtime=timedelta(days=359),  # the total length of the run
    dt=timedelta(days=1),  # the timestep of the kernel
    output_file=output_file,
)

I get

RuntimeError: Error during compilation:
Compilation command: ['/srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc', '-Wall', '-fPIC', '-std=gnu11', '-I/srv/conda/envs/notebook/lib/python3.11/site-packages/parcels/include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', '/tmp/parcels-1000/lib5e10b83c66a2e94be7fac34be5fdd62e_0.so', '/tmp/parcels-1000/5e10b83c66a2e94be7fac34be5fdd62e_0.c', '-shared', '-lm', '-m64']
Source/Destination file: /tmp/parcels-1000/5e10b83c66a2e94be7fac34be5fdd62e_0.c
Log file: /tmp/parcels-1000/5e10b83c66a2e94be7fac34be5fdd62e_0.log
Log output: /srv/conda/envs/notebook/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lgcc: No such file or directory
/srv/conda/envs/notebook/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lgcc: No such file or directory
collect2: error: ld returned 1 exit status


If you are on macOS, it might help to type 'export CC=gcc'

I would have to put a little bit of effort into providing a minimal (reproducible) example. Before doing so, I wanted to hear if anyone has an immediate idea what is going wrong?

[jbusecke]

My bet is that we are missing the gcc compiler in the environment here.

[jbusecke]

How did you install parcels?

[NoraLoose]

Thanks for the quick reply @jbusecke! I actually used the pre-installed Python 3 (ipykernel), which has parcels installed at the location /srv/conda/envs/notebook/lib/python3.11/site-packages.

Also, I have gotten it to work on a different machine/platform. So there is no urgency in digging into this deeper at this point unless another user is having the same issue.

[jbusecke]

I would be generally curious to enable this on the hub. If you want to spend a few cycles on this at some point please ping me.