Use the Latest Version of lblrtm/lnfl/aer_line_file#

IGRINS RV Step 1 use telfit package to model atmosphere absolution lines (telluric lines), and telfit use the LBLTRM model to generate telluric spectrum. Currently, telfit is using lblrtm v12.2.1, lnfl v2.6, and aer_line_file v3.2 on this zenodo. However, on May 20, 2022, the latest version are lblrtm v12.11, lnfl v3.2, and aer_line_file v3.8.1 on Atmospheric and Environmental Research R&C (AER-RC)’s Github repository.

Using the latest version of lblrtm/lnfl/aer IS NOT REQUIRED to run IGRINS RV, however, the updated lblrtm/lnfl/aer can help fix several reported issue while running telfit.

Benefits of using the latest version of lblrtm/lnfl/aer_line_file#

  1. Fixes occasional error while running Step 1 (calling telfit under the hood) using ifort compiler with lblrtm v12.2.1, lnfl v2.6, and aer_line_file v3.2.

  2. Running telfit with ifort fixes the End of File Runtime Error (see issue #9). The End of File Runtime Error seems to occur when using gfortran compiler.

Make sure the default installation of telfit is working#

Before you try to update lblrtm/lnfl/aer files, please first make sure you followed Packages installation (part 2) - Telfit and that `telfit is working.

Update telfit to use latest lblrtm/lnfl/aer_line_file#

The lblrtm/lnfl/aer files telfit used are saved under a hidden folder .Telfit at the home dir. Do

~$ cd ~/.Telfit

to enter the folder. Under ./Telfit, the folder structure is like:

~/.Telfit
├── aer_v_3.2.tar.gz
├── aerlbl_v12.2.1.tar.gz
├── aerlnfl_v2.6.tar.gz
├── lnfl
│   ├── build
│   ├── docs
│   └── ...
├── lblrtm
│   ├── build
│   ├── src
│   └── ...
├── aer_v_3.2
│   ├── line_files_By_Molecule
│   ├── line_file
│   └── ...
└── rundir#
└── ...

1. Getting the latest version of lblrtm/lnfl/aer_line_file#

All files can be found on Atmospheric and Environmental Research R&C (AER-RC).
More specifically, follow the clone/tarball_download instruction on each of the github README pages below

to get folders: LNFL(-3.2), LBLRTM(-12.11), and AER_Line_File (take lblrtm v12.11, lnfl v3.2, and aer_line_file v3.8.1 for example).

It is important to follow all instructions on their github README pages. Stuff related to submodule is critical to whether the update of lblrtm & lnfl is successful or not! Also, for LBLRTM, when doing git checkout tags/v12.11, make sure to switch to v12.11, instead of v12.13. There might be error popping up when building lblrtm if with v12.13 (lasted update Oct. 9, 2022).

2. Replacement with new version#

For lblrtm and lnfl, simply delete all stuff under ~/.Telfit/lblrtm/* and ~/.Telfit/lnfl/* then copy everything in the LBLRTM(-12.11)/* to ~/.Telfit/lblrtm/* and everything in the LNFL(-3.2)/* to ~/.Telfit/lnfl/*.

As for AER_Line_File, remember to follow the Dependencies and Downloading and Staging the Line File steps on aer_line_file to download the line files. If you follow the instruction, under AER_Line_File you will have:

./AER_Line_File/
├── LICENSE
├── get_line_file.py
├── aer_v_3.8.tar.gz
├── AER_Line_File
│   ├── RELEASE_NOTES_aer_linefile
│   ├── line_file
│   ├── spd_dep
│   ├── extra_brd_params
│   ├── line_files_By_Molecule
│   └── spectral_lines_for_MonoRTM
└── ...

Rename ./AER_Line_File/AER_Line_File to ./AER_Line_File/aer_v_3.8, then move the aer_v_3.8 folder under ~/.Telfit/..

So, now, under your ~/.Telfit you have:

~/.Telfit
├── aer_v_3.2.tar.gz
├── aerlbl_v12.2.1.tar.gz
├── aerlnfl_v2.6.tar.gz
├── lnfl
├── lblrtm
├── aer_v_3.2
├── aer_v_3.8
└── rundir#
└── ...

3. Update the setup.py#

–

  1. Change the order of compilers in /Telluric-Fitter(-master)/setup.py line 117 to 122 from

    compilers = ["gfortran",
                 "ifort",
                 "g95"]
    comp_strs = ["GNU",
                 "INTEL",
                 "G95"]

to

    compilers = ["ifort",
                 "gfortran",
                 "g95"]
    comp_strs = ["INTEL",
                 "GNU",
                 "G95"]

–

  1. In /Telluric-Fitter(-master)/setup.py line 193, change

linfile = u"{0:s}/aer_v_3.2/line_file/aer_v_3.2".format(TELLURICMODELING)

to

linfile = u"{0:s}/aer_v_3.8/line_file/aer_v_3.8".format(TELLURICMODELING)

–

  1. Then comment (#) out line 230 to line 237:

    #Get/Unpack the tar files
    # for fname in ['aer_v_3.2.tar.gz', 'aerlnfl_v2.6.tar.gz', 'aerlbl_v12.2.1.tar.gz']:
    #     if fname not in os.listdir(TELLURICMODELING):
    #         url = '{}{}'.format(DATA_URL, fname)
    #         print('Downloading data from {} and putting it in directory {}'.format(url, TELLURICMODELING))
    #         download_file(url, '{}{}'.format(TELLURICMODELING, fname))
    #     print("Un-packing {}".format(fname))
    #     subprocess.check_call(["tar", "-xzf", '{}{}'.format(TELLURICMODELING, fname), '-C', TELLURICMODELING])

so that the next time we run (igrins_rv) ~$ python setup.py build the ./lnlf and ./lblrtm won’t be overwritten by the old version!

4. Re-run setup.py#

Enter the igrins_rv environment (within which Telfit must be installed) and cd into Telluric-Fitter(-master), then run

(igrins_rv) ~$ python setup.py build
(igrins_rv) ~$ pip install .

If you see:

Finished processing dependencies for TelFit==1.4.0

then, congratulation, you successfully updated your lblrtm/lnfl/aer_line_file versions!