Parcel Running in Fedora Asahi Linux

[claudioiturra]

Hello, I just installed Parcels via conda on Fedora, but I encountered the following error when trying to run the example: python example_peninsula.py --fieldset 100 100

`(parcels) cl@cl:~/Downloads/parcels_tutorials (v3.1.0)$ python example_peninsula.py --fieldset 100 100
INFO: Generating FieldSet output with basename: peninsula
Peninsula: Advecting 20 particles for 1 day, 0:00:00
Traceback (most recent call last):
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/compilation/codecompiler.py", line 235, in create_compile_process
subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/subprocess.py", line 419, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gcc', '-Wall', '-fPIC', '-std=gnu11', '-I/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', '/tmp/parcels-1000/lib9a76dfda660e6fdd16844dfe78ca2830_0.so', '/tmp/parcels-1000/9a76dfda660e6fdd16844dfe78ca2830_0.c', '-shared', '-lm', '-m64']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/cl/Downloads/parcels_tutorials (v3.1.0)/example_peninsula.py", line 351, in
main()
~~~~^^
File "/home/cl/Downloads/parcels_tutorials (v3.1.0)/example_peninsula.py", line 338, in main
peninsula_example(
~~~~~~~~~~~~~~~~~^
fieldset,
^^^^^^^^^
...<6 lines>...
method=method[args.method],
^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/cl/Downloads/parcels_tutorials (v3.1.0)/example_peninsula.py", line 171, in peninsula_example
pset.execute(k_adv + k_p, runtime=time, dt=dt, output_file=out)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/particleset.py", line 1051, in execute
self._kernel.compile(
~~~~~~~~~~~~~~~~~~~~^
compiler=GNUCompiler(cppargs=cppargs, incdirs=[os.path.join(get_package_dir(), "include"), "."])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/kernel.py", line 483, in compile
compiler.compile(self.src_file, self.lib_file, self.log_file)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/compilation/codecompiler.py", line 311, in compile
super().compile(src, obj, log)
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/compilation/codecompiler.py", line 275, in compile
self.create_compile_process(cc, src, log)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/compilation/codecompiler.py", line 240, in create_compile_process
raise RuntimeError(
...<7 lines>...
)
RuntimeError: Error during compilation:
Compilation command: ['gcc', '-Wall', '-fPIC', '-std=gnu11', '-I/home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/include', '-I.', '-g', '-O3', '-DDOUBLE_COORD_VARIABLES', '-m64', '-o', '/tmp/parcels-1000/lib9a76dfda660e6fdd16844dfe78ca2830_0.so', '/tmp/parcels-1000/9a76dfda660e6fdd16844dfe78ca2830_0.c', '-shared', '-lm', '-m64']
Source/Destination file: /tmp/parcels-1000/9a76dfda660e6fdd16844dfe78ca2830_0.c
Log file: /tmp/parcels-1000/9a76dfda660e6fdd16844dfe78ca2830_0.log
Log output: gcc: error: unrecognized command-line option '-m64'
gcc: error: unrecognized command-line option '-m64'

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

(parcels) cl@cl:~/Downloads/parcels_tutorials (v3.1.0)$ 'export CC=gcc'
bash: export CC=gcc: command not found...

(parcels) cl@cl:~/Downloads/parcels_tutorials (v3.1.0)$ gcc --versiongcc (conda-forge gcc 13.3.0-1) 13.3.0 Copyright (C) 2023 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

is that a problem with my gcc version?, route?

I will appreciate any help¡, thanks

[erikvansebille]

It seems that your compiler (gcc) doesn't understand/recognise the -m64 flag that is used in the compilation command. Not sure why this is.

It's a bit tacky, but what if you into the file at /home/cl/anaconda3/envs/parcels/lib/python3.13/site-packages/parcels/compilation/codecompiler.py and change line 101 from

arch_flag = ["-m64" if calcsize("P") == 8 else "-m32"]

to

arch_flag = []

Can you check if that fixes your issue, and report back?

[claudioiturra]

Dear @erikvansebille

Changing the line 101 arch_flag = ["-m64" if calcsize("P") == 8 else "-m32"] to arch_flag = [] did the trick! Parcels now works. Thank you so much.

[VeckoTheGecko]

I want to dig a bit more into this. @claudioiturra if you run gcc --version what do you get? All good, just saw the line gcc (conda-forge gcc 13.3.0-1) 13.3.0 from your logs