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CosmoMC can't obtain root.converge_stat
 
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: August 29 2017  Reply with quote

I run CosmoMC on a cluster.
Everything seems to work well except the converge file. I can't get the root.converge_stat when the others are fine such as *.txt, *data, *.log, *.inputparams, etc.
At the meanwhile, there is no feedback about the R−1 showed below, in which there are only such things.
Code:
 Chain:1 drag accpt:  0.4855783     fast/slow   72.54875     slow:       33186
 Chain:13 drag accpt:  0.4834013     fast/slow   72.26221     slow:       33343
 Chain:6 drag accpt:  0.4857524     fast/slow   72.30187     slow:       33418
 Chain:11 drag accpt:  0.4792885     fast/slow   72.25761     slow:       33771
 Chain:9 drag accpt:  0.4833719     fast/slow   72.40794     slow:       33378
 Chain:10 drag accpt:  0.4827319     fast/slow   72.31480     slow:       33427
 Chain:8 drag accpt:  0.4820674     fast/slow   72.17249     slow:       33452
 Chain:3 drag accpt:  0.4805302     fast/slow   72.22508     slow:       33454
 Chain:15 drag accpt:  0.4796885     fast/slow   72.20305     slow:       33578
 Chain:0 drag accpt:  0.4796197     fast/slow   72.22173     slow:       33311
 Chain:12 drag accpt:  0.4818384     fast/slow   72.20877     slow:       33577
 Chain:4 drag accpt:  0.4814351     fast/slow   72.46579     slow:       33350

So I do not know when the program will shutdown, and how much my convergence is. I run CosmoMC for a long time but it never stops.
Anyone has the same problem? How can I fix this? Thanks a lot.
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Ira *Wolfson



Joined: 24 Jan 2013
Posts: 62
Affiliation: BGU

PostPosted: August 29 2017  Reply with quote

Please post the .ini fie you are using.

It is possible you are simulating over a degree of freedom the data do not constrain.

In such a case it will take an inordinate amount of time for the burn in to finish and CosmoMC to produce the .converge_stat file.

It might also be the case if that is indeed what you are doing that convergence will never be achieved....

As a rule for posting, I recommend specifying your machine specs, the compiler you used and the .ini file you use.


– Ira
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: August 30 2017  Reply with quote

Ira *Wolfson wrote:
Please post the .ini fie you are using.

It is possible you are simulating over a degree of freedom the data do not constrain.

In such a case it will take an inordinate amount of time for the burn in to finish and CosmoMC to produce the .converge_stat file.

It might also be the case if that is indeed what you are doing that convergence will never be achieved....

As a rule for posting, I recommend specifying your machine specs, the compiler you used and the .ini file you use.


– Ira

Thank you for reply. I post the ini file below,
Code:
#general settings
#Bicep-Keck-Planck, varying cosmological parameters
DEFAULT(batch2/BKPlanck.ini)

#Planck 2015, default just include native likelihoods (others require clik)
DEFAULT(batch2/plik_dx11dr2_DS_v18_TT.ini)
#DEFAULT(batch2/lowTEB.ini)
DEFAULT(batch2/lowl.ini)
#DEFAULT(batch2/lensing.ini)

#Other Likelihoods
#DEFAULT(batch2/BAO.ini)
#DEFAULT(batch2/WiggleZ_MPK.ini)
#DEFAULT(batch2/MPK.ini)
#DEFAULT(batch2/WL.ini)

#general settings
DEFAULT(batch2/common.ini)

#e.g. to vary r in addition to standard 6:
#(for r>0 also need compute_tensors=T)
#compute_tensors = T
#param[r] = 0.03 0 2 0.04 0.04

#high for new runs
MPI_Max_R_ProposeUpdate = 30

propose_matrix= planck_covmats/base_TT_lowTEB_plik.covmat

#Folder where files (chains, checkpoints, etc.) are stored
root_dir = tTT+lowP/
#Root name for files produced
file_root=Planck TT+lowP
#action= 0 runs chains, 1 importance samples, 2 minimizes
#use action=4 just to quickly test likelihoods
action = 0

#expected result for -(log like)
test_check_compare = 28.337

num_threads = 0

#if you want to get theory cl for test point
#test_output_root = output_cl_root

start_at_bestfit =F
feedback=1
use_fast_slow = T

checkpoint = T

#sampling_method=7 is a new fast-slow scheme good for Planck
sampling_method = 7
dragging_steps  = 3
propose_scale = 2

#Set >0 to make data files for importance sampling
indep_sample=10

#these are just small speedups for testing
get_sigma8=T

#Uncomment this if you don't want one 0.06eV neutrino by default
#num_massive_neutrinos=
#to vary parameters set param[name]= center, min, max, start width, propose width
#param[mnu] = 0 0 0 0 0


#for PICO install from https://pypi.python.org/pypi/pypico and download data file
#cosmology_calculator=PICO
#pico_datafile = pico3_tailmonty_v34.dat
ico_verbose=F

The system is CentOS 6.6 and I compiled via ifort 17.0.3. Any advice? I am not familiar with these.
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Yutong Wang



Joined: 06 May 2014
Posts: 7
Affiliation: university of Chinese Academy of Sciences

PostPosted: August 31 2017  Reply with quote

I met the same problem, when I use the old version of ifort, there is no problems, and when I change the ifort 17.0.3,there are some problems,such as there is no .chk file,and can't obtain root.converge_stat

And by the way, what's your version number of MPI? I suspect the problem may be cause by the lastest MPI
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: August 31 2017  Reply with quote

Yutong Wang wrote:
I met the same problem, when I use the old version of ifort, there is no problems, and when I change the ifort 17.0.3,there are some problems,such as there is no .chk file,and can't obtain root.converge_stat

And by the way, what's your version number of MPI? I suspect the problem may be cause by the lastest MPI

You reminded me that when I used the the old version 16.0.0, there was no problem. However after I ran it on a new cluster with ifort 17.0.3, it happened.
Now I use the Intel MPI version 2017 update 2. Before, I used the Open MPI 1.6.2, and there was no problem. Any idea?
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Ira *Wolfson



Joined: 24 Jan 2013
Posts: 62
Affiliation: BGU

PostPosted: August 31 2017  Reply with quote

I was having the same problems.

I was finally reduced to using the last version (November release),
with ifort compiler 16.3.


I don't know what's the deal with the code and ifort 17.xxx is...


Maybe Antony can clarify this...
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: September 01 2017  Reply with quote

Ira *Wolfson wrote:
I was having the same problems.

I was finally reduced to using the last version (November release),
with ifort compiler 16.3.


I don't know what's the deal with the code and ifort 17.xxx is...


Maybe Antony can clarify this...

So it is the problem between the latest ifort version and CosmoMC. I will try the 16 one. Thank you.
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: September 04 2017  Reply with quote

Ira *Wolfson wrote:
I was having the same problems.

I was finally reduced to using the last version (November release),
with ifort compiler 16.3.


I don't know what's the deal with the code and ifort 17.xxx is...


Maybe Antony can clarify this...

I can get the .chk now with ifort 16.0.4. However there was no .converge_stat still.
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Ira *Wolfson



Joined: 24 Jan 2013
Posts: 62
Affiliation: BGU

PostPosted: September 04 2017  Reply with quote

Have you seen an output saying that "burn-in" is done?
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Tian Qiu



Joined: 01 Jun 2017
Posts: 7
Affiliation: University of Science and Technology of China

PostPosted: September 04 2017  Reply with quote

Ira *Wolfson wrote:
Have you seen an output saying that "burn-in" is done?

Oh, it was obtained after a while. Maybe my machine works slowly. lol
Thank you.
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