Cobaya : installation issue

Use of Healpix, camb, CLASS, cosmomc, compilers, etc.
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Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Cobaya : installation issue

Post by Rance Solomon » May 11 2020

I am installing Cobaya and CAMB on my personal desktop (Ubuntu 18.04.4 LTS ; 64-bit). Both codes have been installed in development mode. I am now trying to run the 'basic cosmology runs' example ( https://cobaya.readthedocs.io/en/latest/cosmo_basic_runs.html#basic-cosmology-runs ). The full debug readout is below where the you can see the set up of the .yaml file. I am using a local installation of CAMB with its path given in the theory block of the .yaml file. I also used

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cobaya-install cosmo -m /home/rance/research/cobaya
in order to install the cosmological data files so a modules block was also added to the .yaml file. I do not know if this would cause the issue.

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]'.
Full debug output:

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]'.
For completeness, I had replaced Windows on my machine with Ubuntu just before trying to do these installs. I think I got all of the prerequisites for both CAMB and Cobaya. Below should be nearly all of the relevant command line inputs I made in order while doing the install (this attempt is showing the non-dev version of Cobaya but the error is the same for both versions):

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
At this point I run the

Code: Select all

 cobaya-run 
on the .yaml file which gives the above errors.

Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 11 2020

Hi Rance,

It's the first time I see that error. Could you please attach the output of cobaya-install?

Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Re: Cobaya : installation issue

Post by Rance Solomon » May 12 2020

Hi Jesus,

Here is the output of the cobaya-install:

Code: Select all

$ cobaya-install cosmo -m /home/rance/research/cobaya/
[install] Installing cosmological modules (input files will be ignored)
[install] Installing modules at '/home/rance/research/cobaya'

================================================================================
theory:camb
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
theory:classy
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:planck_2018_lowl.TT
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:planck_2018_lensing.native
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:bicep_keck_2015
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:sn.pantheon
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:bao.sdss_dr12_consensus_final
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:des_y1.joint
================================================================================

[install] External module already installed.

[install] Doing nothing.


Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 12 2020

Weird!

Maybe the "pip3 install clik" is the culprit? The "clik" package in PyPI has nothing to do with Planck, and maybe Cobaya is trying to import that one instead of the Planck likelihood. Can you do "pip3 uninstall clik" and try again?

Also, all the installation-related commands (about cfitsio and CAMB) should not be necessary: cobaya-install should be taking care of all that.

Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Re: Cobaya : installation issue

Post by Rance Solomon » May 12 2020

After uninstalling clik the cobaya-install gives

Code: Select all

$ cobaya-install cosmo -m /home/rance/research/cobaya/
[install] Installing cosmological modules (input files will be ignored)
[install] Installing modules at '/home/rance/research/cobaya'

================================================================================
theory:camb
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
theory:classy
================================================================================

[install] External module already installed.

[install] Doing nothing.

================================================================================
likelihood:planck_2018_lowl.TT
================================================================================

Failed to import clik
Failed to import clik
[planck_2018_lowl.TT] Installing the clik code.
[clik] Installing pre-requisites...
Collecting cython
  Using cached https://files.pythonhosted.org/packages/e7/d7/510ddef0248f3e1e91f9cc7e31c0f35f8954d0af92c5c3fd4c853e859ebe/Cython-0.29.17-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: cython
Successfully installed cython-0.29.17
Collecting astropy
  Using cached https://files.pythonhosted.org/packages/da/c2/07b8244febf380f8fe43d87ab906bfff70221ba095df3fe85cf89957c63d/astropy-4.0.1.post1-cp36-cp36m-manylinux1_x86_64.whl
Collecting numpy>=1.16 (from astropy)
  Using cached https://files.pythonhosted.org/packages/03/27/e35e7c6e6a52fab9fcc64fc2b20c6b516eba930bb02b10ace3b38200d3ab/numpy-1.18.4-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: numpy, astropy
Successfully installed astropy-4.0.1.post1 numpy-1.18.4
[clik] Downloading...
[sue:04393] *** Process received signal ***
[sue:04393] Signal: Segmentation fault (11)
[sue:04393] Signal code: Address not mapped (1)
[sue:04393] Failing at address: 0x2f839c
Segmentation fault (core dumped)
This was the original reason I had added the 'pip3 install clik' command. The 'cobaya-run' now gives the error message:

Code: Select all

 2020-05-11 16:12:12,633 [planck_2018_lowl.TT] Importing clik from /home/rance/research/cobaya/code/planck
 2020-05-11 16:12:12,656 [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 77, in initialize
    import clik
ModuleNotFoundError: No module named 'clik'
-------------------------------------------------------------

 2020-05-11 16:12:12,656 [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]'.

Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 12 2020

Hi Rance,

I just checked in my system that "pip3 install clik" produces the error you reported. So that part is solved.

It looks the root of your problem is now `wget`. Can you give me the output of `wget --version` in the shell, please?

Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Re: Cobaya : installation issue

Post by Rance Solomon » May 12 2020

Jesus,

Thank you for the help. 'wget --version' returns

Code: Select all

$ wget --version
GNU Wget 1.19.4 built on linux-gnu.

-cares +digest -gpgme +https +ipv6 +iri +large-file -metalink +nls 
+ntlm +opie +psl +ssl/openssl 

Wgetrc: 
    /etc/wgetrc (system)
Locale: 
    /usr/share/locale 
Compile: 
    gcc -DHAVE_CONFIG_H -DSYSTEM_WGETRC="/etc/wgetrc" 
    -DLOCALEDIR="/usr/share/locale" -I. -I../../src -I../lib 
    -I../../lib -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_LIBSSL -DNDEBUG 
    -g -O2 -fdebug-prefix-map=/build/wget-Xb5Z7Y/wget-1.19.4=. 
    -fstack-protector-strong -Wformat -Werror=format-security 
    -DNO_SSLv2 -D_FILE_OFFSET_BITS=64 -g -Wall 
Link: 
    gcc -DHAVE_LIBSSL -DNDEBUG -g -O2 
    -fdebug-prefix-map=/build/wget-Xb5Z7Y/wget-1.19.4=. 
    -fstack-protector-strong -Wformat -Werror=format-security 
    -DNO_SSLv2 -D_FILE_OFFSET_BITS=64 -g -Wall -Wl,-Bsymbolic-functions 
    -Wl,-z,relro -Wl,-z,now -lpcre -luuid -lidn2 -lssl -lcrypto -lpsl 
    ftp-opie.o openssl.o http-ntlm.o ../lib/libgnu.a 

Copyright (C) 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://www.gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Originally written by Hrvoje Niksic <hniksic@xemacs.org>.
Please send bug reports and questions to <bug-wget@gnu.org>.

Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 12 2020

Seem to be up to date. Honestly, I have no idea about what's going on.

Could you try again at some point tomorrow? (We are releasing a new version)

Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Re: Cobaya : installation issue

Post by Rance Solomon » May 12 2020

Sounds good. I will try again tomorrow afternoon. Thanks.

Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 12 2020

Hi Rance,

In case the new version does not work yet, I have created a branch that uses an alternative download tool: swapping_wget_requests. Would you mind giving it a try?

Cheers!

Rance Solomon
Posts: 8
Joined: April 21 2020
Affiliation: University at Buffalo

Re: Cobaya : installation issue

Post by Rance Solomon » May 12 2020

Jesus,

I am not sure what it was but the update seems to have fixed it for me.

Jesus Torrado
Posts: 17
Joined: April 15 2013
Affiliation: RWTH Aachen
Contact:

Re: Cobaya : installation issue

Post by Jesus Torrado » May 13 2020

Glad to hear that! Have fun with it!

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