[CosmoMC] (custom-run) chain not found

Use of Healpix, camb, CLASS, cosmomc, compilers, etc.
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Mason Ng
Posts: 26
Joined: May 17 2017
Affiliation: The University of Auckland

[CosmoMC] (custom-run) chain not found

Post by Mason Ng » June 19 2017

Sorry for the many questions - I'm just about mostly set-up for CosmoMC.

I have run (as a test) CosmoMC on the cluster and got back some chains. I am now trying to use GetDist on Python to analyze the chains. However, I am getting the error that the chain is not found even though I've basically gone back to an earlier thread (http://cosmocoffee.info/viewtopic.php?t=2836&highlight=) I asked in and followed the instructions:

Below is the Python code used

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g = plots.getSubplotPlotter(chain_dir='/Users/masonng/Documents/University/Honours Project/cosmomc/chains/')
roots = ['base_plikHM_TT_lowl', 'second_planck_best_fit', 'seventh_planck_best_fit']
#TT_lowl uses both the high-l likelihood from plik
#and the low-l likelihood from Commander
params = ['theta', 'omegabh2', 'omegach2', 'logA', 'ns', 'tau']
param_3d = None
g.triangle_plot(roots, params, plot_3d_with_param=param_3d, filled_compare=True, shaded=False)
g.export('/Users/masonng/Documents/University/Honours Project/tests.pdf')

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[local host information]:chains masonng$ cd second
[local host information]:second masonng$ ls
second_planck_best_fit.converge_stat	second_planck_best_fit_2.data		second_planck_best_fit_4.txt		second_planck_best_fit_7.data
second_planck_best_fit.inputparams	second_planck_best_fit_2.log		second_planck_best_fit_5.chk		second_planck_best_fit_7.log
second_planck_best_fit.likelihoods	second_planck_best_fit_2.txt		second_planck_best_fit_5.data		second_planck_best_fit_7.txt
second_planck_best_fit.paramnames	second_planck_best_fit_3.chk		second_planck_best_fit_5.log		second_planck_best_fit_8.chk
second_planck_best_fit.ranges		second_planck_best_fit_3.data		second_planck_best_fit_5.txt		second_planck_best_fit_8.data
second_planck_best_fit_1.chk		second_planck_best_fit_3.log		second_planck_best_fit_6.chk		second_planck_best_fit_8.log
second_planck_best_fit_1.data		second_planck_best_fit_3.txt		second_planck_best_fit_6.data		second_planck_best_fit_8.txt
second_planck_best_fit_1.log		second_planck_best_fit_4.chk		second_planck_best_fit_6.log
second_planck_best_fit_1.txt		second_planck_best_fit_4.data		second_planck_best_fit_6.txt
second_planck_best_fit_2.chk		second_planck_best_fit_4.log		second_planck_best_fit_7.chk
[local host information]:second masonng$ pwd
/Users/masonng/Documents/University/Honours Project/cosmomc/chains/second
One difference is that in params.ini, I've used, for the file root:

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file_root = planck_best_fit
I did manually rename the chains (added prefix second_ for example). Is this the cause of the problem? The end goal is to scp the files from the cluster to my desktop (particularly into the /Users/masonng/Documents/University/Honours Project/cosmomc/chains/ folder) and then use Python to generate the joint posterior distributions and parameter posterior distributions as before.

Antony Lewis
Posts: 1369
Joined: September 23 2004
Affiliation: University of Sussex

Re: [CosmoMC] (custom-run) chain not found

Post by Antony Lewis » June 19 2017

You'll need to set chain_dir to a list of directories to search for the chains.

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