Installation

[mulaura]

I installed now TelFit. However when I try to run it I always get this Warning / Error:

>>>>import os
>>>>os.environ["PYSYN_CDBS"] = "/home/path/PySynphot"
>>>>from telfit import TelluricFitter, DataStructures
>>>>fitter = TelluricFitter()

WARNING:root:Un-locked directory not found! Waiting 10 seconds...

The error repeats every 10s and when I stop the program I get:

----> 1 fitter = TelluricFitter()

/usr/local/lib/python3.10/dist-packages/TelluricFitter.py in init(self, debug, debug_level, print_lblrtm_output) 107 self.debug = debug 108 self.debug_level = debug_level #Number from 1-5, with 5 being the most verbose --> 109 self.Modeler = MakeModel.Modeler(debug=self.debug, print_lblrtm_output=print_lblrtm_output) 110 self.parvals = [[] for i in range(len(self.parnames))] 111 self.chisq_vals = []

/usr/local/lib/python3.10/dist-packages/MakeModel.py in init(self, debug, TelluricModelingDirRoot, nmolecules, print_lblrtm_output) 133 134 #Determine working directories --> 135 self.FindWorkingDirectory() 136 TelluricModelingDir = self.TelluricModelingDir 137 ModelDir = self.ModelDir

/usr/local/lib/python3.10/dist-packages/MakeModel.py in FindWorkingDirectory(self) 319 if not found: 320 logging.warn("Un-locked directory not found! Waiting 10 seconds...") --> 321 time.sleep(10) 322 logging.debug('Telluric Modeling Directory = {}'.format(TelluricModelingDir)) 323 logging.debug('Mode Directory = {}'.format(ModelDir))

Kind regards, Laura

[kgullikson88]

Sorry for the slow reply! TelFit uses 4 "modeling directories" to run LBLRTM in. While running, it marks the directory as running, so that another process doesn't come in and overwrite the various LBLRTM input files. If something breaks while running LBLRTM or reading the output file, that lockfile will remain. So, long story short you should be able to get past this by manually removing the *.lock files within ~/.telfit

[mulaura]

Sorry for the slow reply! TelFit uses 4 "modeling directories" to run LBLRTM in. While running, it marks the directory as running, so that another process doesn't come in and overwrite the various LBLRTM input files. If something breaks while running LBLRTM or reading the output file, that lockfile will remain. So, long story short you should be able to get past this by manually removing the *.lock files within ~/.telfit

Hey Thanks for the Help! I know can start the program, if implement os.system('rm $HOME/.TelFit/*.lock') into my code.

However, if I try to fit, I get the following error (also in the exmaples from GitHub):

Parameter      	Value		Fitting?	Bounds
-------------	-----		-----		-----
h2o            	3.10000E+01	True		1 - 99
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
/usr/local/lib/python3.8/dist-packages/MakeModel.py in MakeModel(self, pressure, temperature, lowfreq, highfreq, angle, humidity, co2, o3, n2o, co, ch4, o2, no, so2, no2, nh3, hno3, lat, alt, wavegrid, resolution, save, libfile, vac2air)
    469             if self.print_lblrtm_output:
--> 470                 command = subprocess.check_call(cmd, shell=True)
    471             if not self.print_lblrtm_output:

/usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs)
    363             cmd = popenargs[0]
--> 364         raise CalledProcessError(retcode, cmd)
    365     return 0

CalledProcessError: Command 'cd /home/mulaura/.TelFit/rundir1/;sh runlblrtm_v3.sh' returned non-zero exit status 127.

During handling of the above exception, another exception occurred:

TypeError                                 Traceback (most recent call last)
<ipython-input-6-8f4bcd98a807> in <module>
    132 
    133         # Perform the fit
--> 134         primary, model, R = fitter.Fit(data=order.copy(),
    135                                        #Can give data here as well as separately like in the simpler fit example
    136                                        resolution_fit_mode="gauss",

/usr/local/lib/python3.8/dist-packages/TelluricFitter.py in Fit(self, data, resolution_fit_mode, fit_primary, return_resolution, adjust_wave, continuum_fit_order, wavelength_fit_order, air_wave, fit_source, source_fcn, source_args, source_kwargs)
    522         bfgs_optdict = {'disp': 2, 'pgtol': 1e-8, 'epsilon': 1, 'approx_grad': True}
    523         slsqp_optdict = {'disp': 2, 'eps': 1e-1}
--> 524         output = leastsq(self.FitErrorFunction, fitpars, full_output=True, epsfcn=1e-1)
    525 
    526         fitpars = output[0]

~/.local/lib/python3.8/site-packages/scipy/optimize/_minpack_py.py in leastsq(func, x0, args, Dfun, full_output, col_deriv, ftol, xtol, gtol, maxfev, epsfcn, factor, diag)
    408     if not isinstance(args, tuple):
    409         args = (args,)
--> 410     shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
    411     m = shape[0]
    412 

~/.local/lib/python3.8/site-packages/scipy/optimize/_minpack_py.py in _check_func(checker, argname, thefunc, x0, args, numinputs, output_shape)
     22 def _check_func(checker, argname, thefunc, x0, args, numinputs,
     23                 output_shape=None):
---> 24     res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
     25     if (output_shape is not None) and (shape(res) != output_shape):
     26         if (output_shape[0] != 1):

/usr/local/lib/python3.8/dist-packages/TelluricFitter.py in FitErrorFunction(self, fitpars)
    569         """
    570         if self.return_resolution:
--> 571             model, resolution = self.GenerateModel(fitpars, return_resolution=True)
    572         else:
    573             model = self.GenerateModel(fitpars)

/usr/local/lib/python3.8/dist-packages/TelluricFitter.py in GenerateModel(self, pars, nofit, separate_source, return_resolution, broaden, model, air_wave)
    674         #Generate the model:
    675         if model is None:
--> 676             model = self.Modeler.MakeModel(pressure, temperature, wavenum_start, wavenum_end, angle, h2o, co2, o3, n2o, co,
    677                                            ch4, o2, no, so2, no2, nh3, hno3, lat=lat, alt=alt, wavegrid=None,
    678                                            resolution=None, vac2air=air_wave_overwrite)

/usr/local/lib/python3.8/dist-packages/MakeModel.py in MakeModel(self, pressure, temperature, lowfreq, highfreq, angle, humidity, co2, o3, n2o, co, ch4, o2, no, so2, no2, nh3, hno3, lat, alt, wavegrid, resolution, save, libfile, vac2air)
    473 
    474         except subprocess.CalledProcessError:
--> 475             raise subprocess.CalledProcessError("Error: Command '{}' failed in directory {}".format(cmd, TelluricModelingDir))
    476 
    477         #Read in TAPE12, which is the output of LBLRTM

TypeError: __init__() missing 1 required positional argument: 'cmd'

Do you know a solution for that?

Kind regards, Laura

[kgullikson88]

That looks like LBLRTM itself failed. Those are always super obscure since LBLRTM doesn't have great error message and is hard to debug. You can try running cd /home/mulaura/.TelFit/rundir1/;sh runlblrtm_v3.sh directly to see if you can get the error that LBLRTM is indicating.

It has been a long time, but I think I remember things like that usually come down to trying to create a model with some crazy parameter (temperature = 10,000 or something). So you could also try to debug and see what the inputs to MakeModel or LBLRTM are.