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cobaya-install cosmo -m /home/rance/research/cobaya
Has anyone had a similar issue?
Short error message:
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2020-05-11 02:01:38,684 [camb] Importing *local* CAMB from /home/rance/research/CAMB
2020-05-11 02:01:38,749 [exception handler] ---------------------------------------
Traceback (most recent call last):
File "/home/rance/.local/bin/cobaya-run", line 11, in <module>
sys.exit(run_script())
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/run.py", line 154, in run_script
run(info)
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/run.py", line 79, in run
timing=updated_info.get(_timing), allow_renames=False) as model:
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/model.py", line 92, in __init__
self._updated_info.get(_theory), modules=modules, timing=timing)
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/likelihood.py", line 307, in __init__
self[like].initialize()
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/likelihoods/_base_classes/_planck_clik_prototype.py", line 84, in initialize
self.lensing = clik.try_lensing(self.clik_file)
AttributeError: module 'clik' has no attribute 'try_lensing'
-------------------------------------------------------------
2020-05-11 02:01:38,749 [exception handler] Some unexpected ERROR occurred. You can see the exception information above.
We recommend trying to reproduce this error with 'debug:True' in the input.
If you cannot solve it yourself and need to report it, include the debug output,
which you can send it to a file setting 'debug_file:[some_file_name]'.
Code: Select all
rance@sue:~/research/cobaya$ cobaya-run --debug -f dry_run.yaml
2020-05-11 02:01:38,370 [output] Output to be read-from/written-into folder '.', with prefix 'dry_run'
2020-05-11 02:01:38,371 [output] Found existing products with the requested ouput prefix: 'dry_run'
2020-05-11 02:01:38,371 [output] Deleting previous chain ('force' was requested).
2020-05-11 02:01:38,528 [input] Parameter 'A_planck' multiply defined.
2020-05-11 02:01:38,528 [input] Parameter 'A_planck' multiply defined.
2020-05-11 02:01:38,528 [input] Parameter 'A_planck' multiply defined.
2020-05-11 02:01:38,561 [run] Input info updated with defaults (dumped to YAML):
theory:
camb:
extra_args:
halofit_version: mead
bbn_predictor: PArthENoPE_880.2_standard.dat
lens_potential_accuracy: 1
num_massive_neutrinos: 1
nnu: 3.046
theta_H0_range:
- 20
- 100
path: /home/rance/research/CAMB
renames:
omegabh2: ombh2
omegach2: omch2
omegal: omega_de
omegak: omk
yhe: YHe
yheused: YHe
YpBBN: Y_p
zrei: zre
speed: 0.3
stop_at_error: false
use_planck_names: false
likelihood:
planck_2018_lowl.TT:
clik_file: baseline/plc_3.0/low_l/commander/commander_dx12_v3_2_29.clik
params:
- A_planck
path: null
product_id: '151902'
renames:
- lowl
speed: 3000
stop_at_error: false
planck_2018_lowl.EE:
clik_file: baseline/plc_3.0/low_l/simall/simall_100x143_offlike5_EE_Aplanck_B.clik
params:
- A_planck
path: null
product_id: '151902'
renames:
- lowE
speed: 4000
stop_at_error: false
planck_2018_highl_plik.TTTEEE:
clik_file: baseline/plc_3.0/hi_l/plik/plik_rd12_HM_v22b_TTTEEE.clik
params:
- A_planck
- calib_100T
- calib_217T
- A_pol
- calib_100P
- calib_143P
- calib_217P
- cib_index
- A_cib_217
- xi_sz_cib
- A_sz
- ksz_norm
- gal545_A_100
- gal545_A_143
- gal545_A_143_217
- gal545_A_217
- A_sbpx_100_100_TT
- A_sbpx_143_143_TT
- A_sbpx_143_217_TT
- A_sbpx_217_217_TT
- ps_A_100_100
- ps_A_143_143
- ps_A_143_217
- ps_A_217_217
- galf_TE_index
- galf_TE_A_100
- galf_TE_A_100_143
- galf_TE_A_100_217
- galf_TE_A_143
- galf_TE_A_143_217
- galf_TE_A_217
- galf_EE_index
- galf_EE_A_100
- galf_EE_A_100_143
- galf_EE_A_100_217
- galf_EE_A_143
- galf_EE_A_143_217
- galf_EE_A_217
- A_cnoise_e2e_100_100_EE
- A_cnoise_e2e_143_143_EE
- A_cnoise_e2e_217_217_EE
- A_sbpx_100_100_EE
- A_sbpx_100_143_EE
- A_sbpx_100_217_EE
- A_sbpx_143_143_EE
- A_sbpx_143_217_EE
- A_sbpx_217_217_EE
path: null
product_id: '151902'
renames:
- plikHM_TTTEEE
speed: 7
stop_at_error: false
planck_2018_lensing.clik:
clik_file: baseline/plc_3.0/lensing/smicadx12_Dec5_ftl_mv2_ndclpp_p_teb_consext8.clik_lensing
params:
- A_planck
path: null
product_id: '151902'
renames:
- lensing
speed: 600
stop_at_error: false
sampler:
mcmc:
Rminus1_cl_level: 0.95
Rminus1_cl_stop: 0.2
Rminus1_last: .inf
Rminus1_single_split: 4
Rminus1_stop: 0.01
blocking: null
blocks: null
burn_in: 20d
callback_every: null
callback_function: null
check_every: 40d
converged: null
covmat: auto
covmat_params: null
drag: true
drag_limits:
- 1
- 10
i_last_slow_block: null
learn_proposal: true
learn_proposal_Rminus1_max: 2.0
learn_proposal_Rminus1_max_early: 30.0
learn_proposal_Rminus1_min: 0.0
max_samples: .inf
max_tries: 40d
mpi_size: null
output_every: 20
oversample: false
oversampling_factors: null
proposal_scale: 1.9
seed: null
prior:
SZ: 'lambda ksz_norm, A_sz: stats.norm.logpdf(ksz_norm+1.6*A_sz, loc=9.5, scale=3.0)'
params:
logA:
prior:
min: 1.61
max: 3.91
ref:
dist: norm
loc: 3.05
scale: 0.001
proposal: 0.001
latex: \log(10^{10} A_\mathrm{s})
drop: true
As:
value: 'lambda logA: 1e-10*np.exp(logA)'
latex: A_\mathrm{s}
derived: true
ns:
prior:
min: 0.8
max: 1.2
ref:
dist: norm
loc: 0.965
scale: 0.004
proposal: 0.002
latex: n_\mathrm{s}
theta_MC_100:
prior:
min: 0.5
max: 10
ref:
dist: norm
loc: 1.04109
scale: 0.0004
proposal: 0.0002
latex: 100\theta_\mathrm{MC}
drop: true
renames: theta
cosmomc_theta:
value: 'lambda theta_MC_100: 1.e-2*theta_MC_100'
derived: false
H0:
latex: H_0
min: 20
max: 100
derived: true
ombh2:
prior:
min: 0.005
max: 0.1
ref:
dist: norm
loc: 0.0224
scale: 0.0001
proposal: 0.0001
latex: \Omega_\mathrm{b} h^2
renames:
- omegabh2
omch2:
prior:
min: 0.001
max: 0.99
ref:
dist: norm
loc: 0.12
scale: 0.001
proposal: 0.0005
latex: \Omega_\mathrm{c} h^2
renames:
- omegach2
omegam:
latex: \Omega_\mathrm{m}
derived: true
omegamh2:
derived: 'lambda omegam, H0: omegam*(H0/100)**2'
latex: \Omega_\mathrm{m} h^2
mnu:
value: 0.06
omega_de:
latex: \Omega_\Lambda
derived: true
renames:
- omegal
YHe:
latex: Y_\mathrm{P}
derived: true
renames:
- yhe
- yheused
Y_p:
latex: Y_P^\mathrm{BBN}
derived: true
renames:
- YpBBN
DHBBN:
derived: 'lambda DH: 10**5*DH'
latex: 10^5 \mathrm{D}/\mathrm{H}
tau:
prior:
min: 0.01
max: 0.8
ref:
dist: norm
loc: 0.055
scale: 0.006
proposal: 0.003
latex: \tau_\mathrm{reio}
zre:
latex: z_\mathrm{re}
derived: true
renames:
- zrei
sigma8:
latex: \sigma_8
derived: true
s8h5:
derived: 'lambda sigma8, H0: sigma8*(H0*1e-2)**(-0.5)'
latex: \sigma_8/h^{0.5}
s8omegamp5:
derived: 'lambda sigma8, omegam: sigma8*omegam**0.5'
latex: \sigma_8 \Omega_\mathrm{m}^{0.5}
s8omegamp25:
derived: 'lambda sigma8, omegam: sigma8*omegam**0.25'
latex: \sigma_8 \Omega_\mathrm{m}^{0.25}
A:
derived: 'lambda As: 1e9*As'
latex: 10^9 A_\mathrm{s}
clamp:
derived: 'lambda As, tau: 1e9*As*np.exp(-2*tau)'
latex: 10^9 A_\mathrm{s} e^{-2\tau}
age:
latex: '{\rm{Age}}/\mathrm{Gyr}'
derived: true
rdrag:
latex: r_\mathrm{drag}
derived: true
chi2__CMB:
derived: 'lambda chi2__planck_2018_lowl_TT, chi2__planck_2018_lowl_EE, chi2__planck_2018_highl_plik_TTTEEE,
chi2__planck_2018_lensing_clik: sum([chi2__planck_2018_lowl_TT, chi2__planck_2018_lowl_EE,
chi2__planck_2018_highl_plik_TTTEEE, chi2__planck_2018_lensing_clik])'
latex: \chi^2_\mathrm{CMB}
A_planck:
prior:
dist: norm
loc: 1
scale: 0.0025
ref:
dist: norm
loc: 1
scale: 0.002
proposal: 0.0005
latex: y_\mathrm{cal}
renames: calPlanck
calib_100T:
prior:
dist: norm
loc: 1.0002
scale: 0.0007
ref:
dist: norm
loc: 1.0002
scale: 0.001
proposal: 0.0005
latex: c_{100}
renames: cal0
calib_217T:
prior:
dist: norm
loc: 0.99805
scale: 0.00065
ref:
dist: norm
loc: 0.99805
scale: 0.001
proposal: 0.0005
latex: c_{217}
renames: cal2
A_pol:
value: 1
calib_100P:
value: 1.021
calib_143P:
value: 0.966
calib_217P:
value: 1.04
cib_index:
value: -1.3
A_cib_217:
prior:
dist: uniform
min: 0
max: 200
ref:
dist: norm
loc: 67
scale: 10
proposal: 1.2
latex: A^\mathrm{CIB}_{217}
renames: acib217
xi_sz_cib:
prior:
dist: uniform
min: 0
max: 1
ref:
dist: halfnorm
loc: 0
scale: 0.1
proposal: 0.1
latex: \xi^{\mathrm{tSZ}\times\mathrm{CIB}}
renames: xi
A_sz:
prior:
dist: uniform
min: 0
max: 10
ref:
dist: norm
loc: 7
scale: 2
proposal: 0.6
latex: A^\mathrm{tSZ}_{143}
renames: asz143
ksz_norm:
prior:
dist: uniform
min: 0
max: 10
ref:
dist: halfnorm
loc: 0
scale: 3
proposal: 1
latex: A^\mathrm{kSZ}
renames: aksz
gal545_A_100:
prior:
dist: norm
loc: 8.6
scale: 2
ref:
dist: norm
loc: 7
scale: 2
proposal: 1
latex: A^\mathrm{dustTT}_{100}
renames: kgal100
gal545_A_143:
prior:
dist: norm
loc: 10.6
scale: 2
ref:
dist: norm
loc: 9
scale: 2
proposal: 1
latex: A^\mathrm{dustTT}_{143}
renames: kgal143
gal545_A_143_217:
prior:
dist: norm
loc: 23.5
scale: 8.5
ref:
dist: norm
loc: 21
scale: 4
proposal: 1.5
latex: A^\mathrm{dustTT}_{\mathrm{143}\times\mathrm{217}}
renames: kgal143217
gal545_A_217:
prior:
dist: norm
loc: 91.9
scale: 20
ref:
dist: norm
loc: 80
scale: 15
proposal: 2
latex: A^\mathrm{dustTT}_{217}
renames: kgal217
A_sbpx_100_100_TT:
value: 1
A_sbpx_143_143_TT:
value: 1
A_sbpx_143_217_TT:
value: 1
A_sbpx_217_217_TT:
value: 1
ps_A_100_100:
prior:
dist: uniform
min: 0
max: 400
ref:
dist: norm
loc: 257
scale: 24
proposal: 17
latex: A^\mathrm{PS}_{100}
renames: aps100
ps_A_143_143:
prior:
dist: uniform
min: 0
max: 400
ref:
dist: norm
loc: 47
scale: 10
proposal: 3
latex: A^\mathrm{PS}_{143}
renames: aps143
ps_A_143_217:
prior:
dist: uniform
min: 0
max: 400
ref:
dist: norm
loc: 40
scale: 12
proposal: 2
latex: A^\mathrm{PS}_{\mathrm{143}\times\mathrm{217}}
renames: aps143217
ps_A_217_217:
prior:
dist: uniform
min: 0
max: 400
ref:
dist: norm
loc: 104
scale: 13
proposal: 2.5
latex: A^\mathrm{PS}_{217}
renames: aps217
galf_TE_index:
value: -2.4
galf_TE_A_100:
prior:
dist: norm
loc: 0.13
scale: 0.042
ref:
dist: norm
loc: 0.13
scale: 0.1
proposal: 0.1
latex: A^\mathrm{dustTE}_{100}
renames: galfTE100
galf_TE_A_100_143:
prior:
dist: norm
loc: 0.13
scale: 0.036
ref:
dist: norm
loc: 0.13
scale: 0.1
proposal: 0.1
latex: A^\mathrm{dustTE}_{\mathrm{100}\times\mathrm{143}}
renames: galfTE100143
galf_TE_A_100_217:
prior:
dist: norm
loc: 0.46
scale: 0.09
ref:
dist: norm
loc: 0.46
scale: 0.1
proposal: 0.1
latex: A^\mathrm{dustTE}_{\mathrm{100}\times\mathrm{217}}
renames: galfTE100217
galf_TE_A_143:
prior:
dist: norm
loc: 0.207
scale: 0.072
ref:
dist: norm
loc: 0.207
scale: 0.1
proposal: 0.1
latex: A^\mathrm{dustTE}_{143}
renames: galfTE143
galf_TE_A_143_217:
prior:
dist: norm
loc: 0.69
scale: 0.09
ref:
dist: norm
loc: 0.69
scale: 0.1
proposal: 0.1
latex: A^\mathrm{dustTE}_{\mathrm{143}\times\mathrm{217}}
renames: galfTE143217
galf_TE_A_217:
prior:
dist: norm
loc: 1.938
scale: 0.54
ref:
dist: norm
loc: 1.938
scale: 0.2
proposal: 0.2
latex: A^\mathrm{dustTE}_{217}
renames: galfTE217
galf_EE_index:
value: -2.4
galf_EE_A_100:
value: 0.055
latex: A^\mathrm{dustEE}_{100}
renames: galfEE100
galf_EE_A_100_143:
value: 0.04
latex: A^\mathrm{dustEE}_{\mathrm{100}\times\mathrm{143}}
renames: galfEE100143
galf_EE_A_100_217:
value: 0.094
latex: A^\mathrm{dustEE}_{\mathrm{100}\times\mathrm{217}}
renames: galfEE100217
galf_EE_A_143:
value: 0.086
latex: A^\mathrm{dustEE}_{143}
renames: galfEE143
galf_EE_A_143_217:
value: 0.21
latex: A^\mathrm{dustEE}_{\mathrm{143}\times\mathrm{217}}
renames: galfEE143217
galf_EE_A_217:
value: 0.7
latex: A^\mathrm{dustEE}_{217}
renames: galfEE217
A_cnoise_e2e_100_100_EE:
value: 1
A_cnoise_e2e_143_143_EE:
value: 1
A_cnoise_e2e_217_217_EE:
value: 1
A_sbpx_100_100_EE:
value: 1
A_sbpx_100_143_EE:
value: 1
A_sbpx_100_217_EE:
value: 1
A_sbpx_143_143_EE:
value: 1
A_sbpx_143_217_EE:
value: 1
A_sbpx_217_217_EE:
value: 1
modules: /home/rance/research/cobaya/
output: dry_run
debug: true
resume: false
force: true
2020-05-11 02:01:38,682 [prior] Loading external prior 'SZ' from: 'lambda ksz_norm, A_sz: stats.norm.logpdf(ksz_norm+1.6*A_sz, loc=9.5, scale=3.0)'
2020-05-11 02:01:38,682 [prior] *WARNING* External prior 'SZ' loaded. Mind that it might not be normalized!
2020-05-11 02:01:38,683 [likelihood] Parameters were assigned as follows:
2020-05-11 02:01:38,683 [likelihood] - 'planck_2018_lowl.TT':
2020-05-11 02:01:38,683 [likelihood] Input: ['A_planck']
2020-05-11 02:01:38,683 [likelihood] Output: []
2020-05-11 02:01:38,683 [likelihood] - 'planck_2018_lowl.EE':
2020-05-11 02:01:38,683 [likelihood] Input: ['A_planck']
2020-05-11 02:01:38,683 [likelihood] Output: []
2020-05-11 02:01:38,683 [likelihood] - 'planck_2018_highl_plik.TTTEEE':
2020-05-11 02:01:38,683 [likelihood] Input: ['A_planck', 'calib_100T', 'calib_217T', 'A_pol', 'calib_100P', 'calib_143P', 'calib_217P', 'cib_index', 'A_cib_217', 'xi_sz_cib', 'A_sz', 'ksz_norm', 'gal545_A_100', 'gal545_A_143', 'gal545_A_143_217', 'gal545_A_217', 'A_sbpx_100_100_TT', 'A_sbpx_143_143_TT', 'A_sbpx_143_217_TT', 'A_sbpx_217_217_TT', 'ps_A_100_100', 'ps_A_143_143', 'ps_A_143_217', 'ps_A_217_217', 'galf_TE_index', 'galf_TE_A_100', 'galf_TE_A_100_143', 'galf_TE_A_100_217', 'galf_TE_A_143', 'galf_TE_A_143_217', 'galf_TE_A_217', 'galf_EE_index', 'galf_EE_A_100', 'galf_EE_A_100_143', 'galf_EE_A_100_217', 'galf_EE_A_143', 'galf_EE_A_143_217', 'galf_EE_A_217', 'A_cnoise_e2e_100_100_EE', 'A_cnoise_e2e_143_143_EE', 'A_cnoise_e2e_217_217_EE', 'A_sbpx_100_100_EE', 'A_sbpx_100_143_EE', 'A_sbpx_100_217_EE', 'A_sbpx_143_143_EE', 'A_sbpx_143_217_EE', 'A_sbpx_217_217_EE']
2020-05-11 02:01:38,683 [likelihood] Output: []
2020-05-11 02:01:38,683 [likelihood] - 'planck_2018_lensing.clik':
2020-05-11 02:01:38,684 [likelihood] Input: ['A_planck']
2020-05-11 02:01:38,684 [likelihood] Output: []
2020-05-11 02:01:38,684 [likelihood] - 'theory':
2020-05-11 02:01:38,684 [likelihood] Input: ['As', 'ns', 'cosmomc_theta', 'ombh2', 'omch2', 'mnu', 'tau']
2020-05-11 02:01:38,684 [likelihood] Output: ['H0', 'omegam', 'omega_de', 'YHe', 'Y_p', 'zre', 'sigma8', 'age', 'rdrag', 'DH']
2020-05-11 02:01:38,684 [camb] Importing *local* CAMB from /home/rance/research/CAMB
2020-05-11 02:01:38,749 [exception handler] ---------------------------------------
Traceback (most recent call last):
File "/home/rance/.local/bin/cobaya-run", line 11, in <module>
sys.exit(run_script())
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/run.py", line 154, in run_script
run(info)
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/run.py", line 79, in run
timing=updated_info.get(_timing), allow_renames=False) as model:
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/model.py", line 92, in __init__
self._updated_info.get(_theory), modules=modules, timing=timing)
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/likelihood.py", line 307, in __init__
self[like].initialize()
File "/home/rance/.local/lib/python3.6/site-packages/cobaya/likelihoods/_base_classes/_planck_clik_prototype.py", line 84, in initialize
self.lensing = clik.try_lensing(self.clik_file)
AttributeError: module 'clik' has no attribute 'try_lensing'
-------------------------------------------------------------
2020-05-11 02:01:38,749 [exception handler] Some unexpected ERROR occurred. You can see the exception information above.
We recommend trying to reproduce this error with 'debug:True' in the input.
If you cannot solve it yourself and need to report it, include the debug output,
which you can send it to a file setting 'debug_file:[some_file_name]'.
Code: Select all
$ sudo apt-get install python3-pip
$ sudo apt install gfortran
$ sudo pip3 install cobaya --upgrade
$ cd /usr/local/src
$ sudo mv ~/Downloads/cfitsio-3.48.tar.gz .
$ sudo tar zxvf cfitsio-3.48.tar.gz
$ sudo ./configure --prefix=/usr
$ sudo make shared
$ sudo make install
$ sudo make clean
$ sudo apt-get install git
$ pip3 install clik
$ cobaya-install cosmo -m /home/rance/research/cobaya/
$ pip3 install pyside2
$ git clone --recursive https://[my username]@github.com/[my username]/CAMB.git
$ cd CAMB/
$ python3 setup.py build
Code: Select all
cobaya-run