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mitim-fusion's Issues

Branch access rights

Running my own local branch on a PPPL cluster but I don't have access rights to push this branch (not to main, but to my own branch). Is this something you would be willing to allow?

.json decode error

Format of config_user.json file has issues on PPPL's spark cluster. Using the suggested template (just for .json format testing) @(https://mitim-fusion.readthedocs.io/en/latest/installation.html#instructions)

"preferences": {
   "tglf":             "engaging",
   "verbose_level":    "5",
   "dpi_notebook":     "80"
},
"engaging": {
   "machine":          "eofe7.mit.edu",
   "username":         "pablorf",
   "partition":        "sched_mit_psfc",
   "identity":         "~/.ssh/id_rsa",
   "scratch":          "/nobackup1/pablorf/scratch/"
   }

and running

python3 $MITIM_PATH/tests/TGLF_workflow.py

gives error

(mitim-env) [jparisi@spark-login2 MITIM-fusion-spark]$ python3 $MITIM_PATH/tests/TGLF_workflow.py
Traceback (most recent call last):
  File "/p/gyro/jparisi/MITIM-fusion-spark/tests/TGLF_workflow.py", line 2, in <module>
    from mitim_tools.misc_tools import IOtools
  File "/p/gyro/jparisi/MITIM-fusion-spark/src/mitim_tools/misc_tools/IOtools.py", line 19, in <module>
    verbose_level = read_verbose_level()
  File "/p/gyro/jparisi/MITIM-fusion-spark/src/mitim_tools/misc_tools/CONFIGread.py", line 21, in read_verbose_level
    s = load_settings()
  File "/p/gyro/jparisi/MITIM-fusion-spark/src/mitim_tools/misc_tools/CONFIGread.py", line 15, in load_settings
    settings = json.load(f)
  File "/usr/lib64/python3.9/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/usr/lib64/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/lib64/python3.9/json/decoder.py", line 340, in decode
    raise JSONDecodeError("Extra data", s, end)
json.decoder.JSONDecodeError: Extra data: line 1 column 14 (char 13)

Slurm submission script requires memory specification

On PPPL's spark cluster, specifying memory in the bash.src script is required, otherwise job fails. I recommend we add something like

    # ******* memory setup
    if memory_req is not None:
        commandSBATCH.append(f"#SBATCH --mem {memory_req}GB")

to FARMINGtools.py.

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