search

jacopo-chevallard / BEAGLE-general

Basic information to get started with the galaxy spectral modelling tool Beagle
https://www.iap.fr/beagle/
9 stars 0 forks source link

Error running BEAGLE 0.3.5 with fit_photometry_example.param - invalid memory reference at load_fits_catalogue #19

Closed marinatrevisan closed 8 years ago

marinatrevisan commented 8 years ago

I get the following error when using fit_photometry_example.param with Docker Toolbox (version 1.6.2), Beagle 0.3.5 on a machine with Ubuntu 14.04. 

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7F225BB02777
#1  0x7F225BB02D7E
#2  0x7F225B23ED3F
#3  0x7F225BBD8C23
#4  0x485ABC in load_fits_catalogue at photometry.f90:225
#5  0x48A7D4 in __photometry_MOD_load_photometric_catalogue at photometry.f90:193
#6  0x4B032E in __beagle_initialization_MOD_initialize_sed_fitting at BEAGLE_initialization.f90:227 (discriminator 2)
#7  0x4136A2 in beagle at BEAGLE.f90:159

P.S: I am not using nebular emission (i.e., the keywords TEMPLATES NEBULAR, EMISSION LINES CONFIGURATION, and the parameters nebular_logU, nebular_xi, and nebular_Z are not used), and I am using the SSP models available at http://www.bruzual.org/bc03/Updated_version_2016/BC03_miles_kroupa.tgz.

jacopo-chevallard commented 8 years ago

It looks like it has a problem in loading the input FITS catalogue

#4  0x485ABC in load_fits_catalogue at photometry.f90:225

Unfortunately for me it's difficult to test these errors, as I don't have access myself to an Ubuntu machine with Docker... But @eclake and I will try to sort this out asap.

jacopo-chevallard commented 8 years ago

@adelave1 (continues from #20) can you try to run the example for the spectroscopic fitting, i.e. replacing

/opt/BEAGLE/params/fit_photometry_example.param

with 

/opt/BEAGLE/params/fit_spectrum_example.param
alex-delavega commented 8 years ago

Below is the output when running fit_spectrum_example.param:

docker run --rm -it -v ~/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle 1 /opt/BEAGLE/params/fit_spectrum_example.param
  [ WARNING: messages are not correctly printed to stderr (they stay in the buffer)        unless you set (in gfortran) "setenv GFORTRAN_UNBUFFERED_PRECONNECTED Y" ] 
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fixed                         current_sfr_timescale                      0
 ---> fitted                        nebular_logU                               0
 ---> fixed                         nebular_xi                                 0
 ---> fitted                        nebular_Z                                  0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 ---> fitted                        specific_sfr                               1
 ---> fitted                        formation_redshift                         1
 n_fitted:            8
 fileName: example_spec_1.fits                                                                                                                                                                                                                                             
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  [ ERROR: Trying to open file example_spec_1.fits, but the file does not exist ] 
  [      IN : "open_fits_file" ] 
  [ MODULE  : "fits_io" ] 
  [ BACKTRACE:   
#0  0x7FCB46494777
#1  0x511642 in print_backtrace at lib_messages.f90:183
#2  0x4A22A0 in __fits_io_MOD_open_fits_file at fits_io.f90:124 (discriminator 2)
#3  0x440425 in read_fits_table_spectrum at io_spectra.f90:664
#4  0x414C5B in beagle at BEAGLE.f90:250 (discriminator 1)
  ] 
  [ EXITING FUNCTION / SUBROUTINE ] 
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 Do you want to conitnue with the execution of the program? [y/n]
n

But example_spec_1.fits exists:

ls ~/Desktop/BEAGLE/BEAGLE-general-master/data/spectra/
example_spec_0.fits example_spec_1.fits example_spec_2.fits spectra.list
jacopo-chevallard commented 8 years ago

It does, but Beagle needs the full path to the file. Can you try to modify the data/spectra/spectra.list file by adding before each line BEAGLE_virtual_workdir/data/spectra?

Also, did you modify on purpose this command

docker run --rm -it -v ~/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE

which originally was 

docker run --rm -it -v /Path/to/your/BEAGLE_workdir:/BEAGLE_virtual_workdir

where /Path/to/your/BEAGLE_workdir will be replaces by the full path to the repository on your local machine (with no tilde)

alex-delavega commented 8 years ago

When executing docker run --rm etc., I would write out the full path to the repository without a tilde; I added the tilde when commenting on issues, but I've no need to continue doing so.

I modified data/spectra/spectra.list by adding BEAGLE_virtual_workdir/data/spectra before each line, and I receive the following error when executing with fit_spectrum_example.param: 

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle 1 /opt/BEAGLE/params/fit_spectrum_example.param
  [ WARNING: messages are not correctly printed to stderr (they stay in the buffer)        unless you set (in gfortran) "setenv GFORTRAN_UNBUFFERED_PRECONNECTED Y" ] 
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fixed                         current_sfr_timescale                      0
 ---> fitted                        nebular_logU                               0
 ---> fixed                         nebular_xi                                 0
 ---> fitted                        nebular_Z                                  0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 ---> fitted                        specific_sfr                               1
 ---> fitted                        formation_redshift                         1
 n_fitted:            8
 fileName: /opt/BEAGLE/data/spectra/example_spec_2.fits                                                                                                                                                                                                                    
 *****************************************************
 MultiNest v3.9
 Copyright Farhan Feroz & Mike Hobson
 Release Oct 2014

 no. of live points =  120
 dimensionality =    8
 *****************************************************
 Starting MultiNest
 generating live points

 Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES
 271 filters defined, out of 300                                maximum     ...done
 live points generated, starting sampling
Acceptance Rate:                        0.918919
Replacements:                                170
Total Samples:                               185
Nested Sampling ln(Z):            **************
Acceptance Rate:                        0.817844
Replacements:                                220
Total Samples:                               269
Nested Sampling ln(Z):              10410.995918
Acceptance Rate:                        0.655340
Replacements:                                270
Total Samples:                               412
Nested Sampling ln(Z):              10805.516678

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7FF94316D777
#1  0x7FF94316DD7E
#2  0x7FF9428A9D3F
#3  0x7FF943FA5322
#4  0x7FF943FA58E8
#5  0x7FF943E58C8C
#6  0x7FF9442F8616
#7  0x7FF944319C81
#8  0x7FF94431DEC2
#9  0x7FF944320E04
#10  0x7FF94434E9D8
#11  0x57598C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)
#12  0x576B11 in __utils1_MOD_calcellprop at utils1.f90:359
#13  0x5805C7 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988
#14  0x55212D in __nested_MOD_clusterednest at nested.F90:1451
#15  0x562E84 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)
#16  0x563CDC in __nested_MOD_nestrun at nested.F90:239
#17  0x533FAD in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:133
#18  0x528FAA in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)
#19  0x41414F in beagle at BEAGLE.f90:402 (discriminator 2)
jacopo-chevallard commented 8 years ago

This is a different type of error, but Beagle runs on the example spectroscopic data. @eclake any hint of what could be the problem?

eclake commented 8 years ago

Will try to reproduce the problem now!

eclake commented 8 years ago

OK, my version is happily running on example_spectrum_2.fits after fixing the spectra.list file in the following commit 9eb73a312e5ed54a4edcb3da31b764c30aa80a40 (fixing the problem highlighted in your previous comments in this issue!)

The error might be gdb related rather than BEAGLE related... I'm really not sure but it's worth checking if a reset of docker etc. would produce the same error.

@adelave1 - please could you try fitting again after shutting down docker and restarting it (including restarting the docker machine if you are running from docker-toolbox on a mac)

docker-machine restart default

assuming you haven't manually changed the name of your docker machine it should be called default.

Before re-running BEAGLE make sure to empty the following directory $BEAGLE_RESULTS/fit_spectra_example/

Then let us know if you still get the same error or if it runs through happily (can take a while to fit spectra).

eclake commented 8 years ago

Another thing that is important and that I should fix right away is also, @adelave1, please can you change the command you are using very slightly:

from:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle 1 /opt/BEAGLE/params/fit_spectrum_example.param

to:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle:0.3.5 1 /opt/BEAGLE/params/fit_spectrum_example.param

I'll look at fixing the docker version now so that it always runs the latest version as default. It's possible you might have to pull this specific version as well if you previously used

docker pull eclake/beagle

rather than

docker pull eclake/beagle:0.3.5

The need for this is related to issue #22

eclake commented 8 years ago

Interestingly this is the same error that was reported in #7

alex-delavega commented 8 years ago

@eclake, terribly sorry for the delay! I restarted my docker machine, I pulled BEAGLE again (after the latest tag had been applied to 0.3.5), emptied $BEAGLE_RESULTS/fit_spectra_example/ retried with fit_spectrum_example.param, and still received an error:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle 1 /opt/BEAGLE/params/fit_spectrum_example.param
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fixed                         current_sfr_timescale                      0
 ---> fitted                        nebular_logU                               0
 ---> fixed                         nebular_xi                                 0
 ---> fitted                        nebular_Z                                  0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 ---> fitted                        specific_sfr                               1
 ---> fitted                        formation_redshift                         1
 n_fitted:            8
 fileName: /opt/BEAGLE/data/spectra/example_spec_0.fits                                                                                                                                                                                                                    
 *****************************************************
 MultiNest v3.9
 Copyright Farhan Feroz & Mike Hobson
 Release Oct 2014

 no. of live points =  120
 dimensionality =    8
 *****************************************************
 Starting MultiNest
 generating live points

 Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES
 271 filters defined, out of 300                                maximum     ...done
 live points generated, starting sampling
Acceptance Rate:                        0.934066
Replacements:                                170
Total Samples:                               182
Nested Sampling ln(Z):            **************
Acceptance Rate:                        0.808824
Replacements:                                220
Total Samples:                               272
Nested Sampling ln(Z):            **************
Acceptance Rate:                        0.669975
Replacements:                                270
Total Samples:                               403
Nested Sampling ln(Z):            **************

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7F72F34DA777
#1  0x7F72F34DAD7E
#2  0x7F72F2C16CAF
#3  0x7F72F40DF322
#4  0x7F72F40DF8E8
#5  0x7F72F3F92C8C
#6  0x7F72F4432616
#7  0x7F72F4453C81
#8  0x7F72F4457EC2
#9  0x7F72F445AE04
#10  0x7F72F44889D8
#11  0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)
#12  0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359
#13  0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988
#14  0x5934DD in __nested_MOD_clusterednest at nested.F90:1451
#15  0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)
#16  0x5A508C in __nested_MOD_nestrun at nested.F90:239
#17  0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134
#18  0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)
#19  0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)

I emptied $BEAGLE_RESULTS/fit_spectra_example/ and retried with BEAGLE 0.3.5 anyway and still encountered an error:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle:0.3.5 1 /opt/BEAGLE/params/fit_spectrum_example.param
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fixed                         current_sfr_timescale                      0
 ---> fitted                        nebular_logU                               0
 ---> fixed                         nebular_xi                                 0
 ---> fitted                        nebular_Z                                  0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 ---> fitted                        specific_sfr                               1
 ---> fitted                        formation_redshift                         1
 n_fitted:            8
 fileName: /opt/BEAGLE/data/spectra/example_spec_0.fits                                                                                                                                                                                                                    
 *****************************************************
 MultiNest v3.9
 Copyright Farhan Feroz & Mike Hobson
 Release Oct 2014

 no. of live points =  120
 dimensionality =    8
 *****************************************************
 Starting MultiNest
 generating live points

 Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES
 271 filters defined, out of 300                                maximum     ...done
 live points generated, starting sampling
Acceptance Rate:                        0.934066
Replacements:                                170
Total Samples:                               182
Nested Sampling ln(Z):            **************
Acceptance Rate:                        0.808824
Replacements:                                220
Total Samples:                               272
Nested Sampling ln(Z):            **************
Acceptance Rate:                        0.669975
Replacements:                                270
Total Samples:                               403
Nested Sampling ln(Z):            **************

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7FF1E5FDE777
#1  0x7FF1E5FDED7E
#2  0x7FF1E571AD3F
#3  0x7FF1E6BE3322
#4  0x7FF1E6BE38E8
#5  0x7FF1E6A96C8C
#6  0x7FF1E6F36616
#7  0x7FF1E6F57C81
#8  0x7FF1E6F5BEC2
#9  0x7FF1E6F5EE04
#10  0x7FF1E6F8C9D8
#11  0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)
#12  0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359
#13  0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988
#14  0x5934DD in __nested_MOD_clusterednest at nested.F90:1451
#15  0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)
#16  0x5A508C in __nested_MOD_nestrun at nested.F90:239
#17  0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134
#18  0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)
#19  0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)
eclake commented 8 years ago

Thank you @adelave1, that's really helpful! It shows that this happens regardless of the spectrum it's running on and with the latest version.

There's two different issues currently followed here, so I just want to re-organise a bit. This error is the same as #7 so I'm moving all discussion of this error to there, and this issue should be specifically for the 

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7F225BB02777
#1  0x7F225BB02D7E
#2  0x7F225B23ED3F
#3  0x7F225BBD8C23
#4  0x485ABC in load_fits_catalogue at photometry.f90:225
#5  0x48A7D4 in __photometry_MOD_load_photometric_catalogue at photometry.f90:193
#6  0x4B032E in __beagle_initialization_MOD_initialize_sed_fitting at BEAGLE_initialization.f90:227 (discriminator 2)
#7  0x4136A2 in beagle at BEAGLE.f90:159

error

jacopo-chevallard commented 8 years ago

I wouldn't worry too much for the error related to the spectrum, that fact that it originates from a matrix diagonalization (as it appears from the multinest backtrace) suggests that this is an algorithmic error, not a bug. I suspect that this can be related to the units of measure, and to the magnitude of the numbers involved in the likelihood computation.

What is more worrisome is the error related to the loading of the photo metric catalogue, which I'm also unable to reproduce.

Sent from my iPhone

On 12 Aug 2016, at 00:56, adelave1 notifications@github.com wrote:

@eclake, terribly sorry for the delay! I restarted my docker machine, I pulled BEAGLE again (after the latest tag had been applied to 0.3.5), emptied $BEAGLE_RESULTS/fit_spectra_example/ retried with fit_spectrum_example.param, and still received an error:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle 1 /opt/BEAGLE/params/fit_spectrum_example.param ---> fixed sfh_type 0 ---> fitted mass 0 ---> fixed current_sfr_timescale 0 ---> fitted nebular_logU 0 ---> fixed nebular_xi 0 ---> fitted nebular_Z 0 ---> fixed attenuation_type 0 ---> fitted tauV_eff 0 ---> fixed mu 0 ---> fitted tau 1 ---> fitted metallicity 1 ---> fitted specific_sfr 1 ---> fitted formation_redshift 1 n_fitted: 8 fileName: /opt/BEAGLE/data/spectra/example_spec_0.fits

MultiNest v3.9 Copyright Farhan Feroz & Mike Hobson Release Oct 2014

no. of live points = 120 dimensionality = 8

Starting MultiNest generating live points

Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES 271 filters defined, out of 300 maximum ...done live points generated, starting sampling Acceptance Rate: 0.934066 Replacements: 170 Total Samples: 182 Nested Sampling ln(Z): ** Acceptance Rate: 0.808824 Replacements: 220 Total Samples: 272 Nested Sampling ln(Z): ** Acceptance Rate: 0.669975 Replacements: 270 Total Samples: 403 Nested Sampling ln(Z): **

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:

0 0x7F72F34DA777

1 0x7F72F34DAD7E

2 0x7F72F2C16CAF

3 0x7F72F40DF322

4 0x7F72F40DF8E8

5 0x7F72F3F92C8C

6 0x7F72F4432616

7 0x7F72F4453C81

8 0x7F72F4457EC2

9 0x7F72F445AE04

10 0x7F72F44889D8

11 0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)

12 0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359

13 0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988

14 0x5934DD in __nested_MOD_clusterednest at nested.F90:1451

15 0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)

16 0x5A508C in __nested_MOD_nestrun at nested.F90:239

17 0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134

18 0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)

19 0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)

I emptied $BEAGLE_RESULTS/fit_spectra_example/ and retried with BEAGLE 0.3.5 anyway and still encountered an error:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle:0.3.5 1 /opt/BEAGLE/params/fit_spectrum_example.param ---> fixed sfh_type 0 ---> fitted mass 0 ---> fixed current_sfr_timescale 0 ---> fitted nebular_logU 0 ---> fixed nebular_xi 0 ---> fitted nebular_Z 0 ---> fixed attenuation_type 0 ---> fitted tauV_eff 0 ---> fixed mu 0 ---> fitted tau 1 ---> fitted metallicity 1 ---> fitted specific_sfr 1 ---> fitted formation_redshift 1 n_fitted: 8 fileName: /opt/BEAGLE/data/spectra/example_spec_0.fits

MultiNest v3.9 Copyright Farhan Feroz & Mike Hobson Release Oct 2014

no. of live points = 120 dimensionality = 8

Starting MultiNest generating live points

Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES 271 filters defined, out of 300 maximum ...done live points generated, starting sampling Acceptance Rate: 0.934066 Replacements: 170 Total Samples: 182 Nested Sampling ln(Z): ** Acceptance Rate: 0.808824 Replacements: 220 Total Samples: 272 Nested Sampling ln(Z): ** Acceptance Rate: 0.669975 Replacements: 270 Total Samples: 403 Nested Sampling ln(Z): **

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:

0 0x7FF1E5FDE777

1 0x7FF1E5FDED7E

2 0x7FF1E571AD3F

3 0x7FF1E6BE3322

4 0x7FF1E6BE38E8

5 0x7FF1E6A96C8C

6 0x7FF1E6F36616

7 0x7FF1E6F57C81

8 0x7FF1E6F5BEC2

9 0x7FF1E6F5EE04

10 0x7FF1E6F8C9D8

11 0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)

12 0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359

13 0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988

14 0x5934DD in __nested_MOD_clusterednest at nested.F90:1451

15 0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)

16 0x5A508C in __nested_MOD_nestrun at nested.F90:239

17 0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134

18 0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)

19 0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

eclake commented 8 years ago

OK, so it's interesting that the system setup that cannot load the photometric catalogue can read in a fits file to be able to fit to the spectrum.

Same thing applies as for #7 - If I know docker toolbox version and virtualbox version I can try and reproduce the error using the exact setup (cannot reproduce on my current setup).

jacopo-chevallard commented 8 years ago

Any news on this @eclake? are you still unable to reproduce the error? I wonder if the problem cannot be in the FITS catalogue itself...perhaps with trying with a different photometric catalogue and parameter file?

marinatrevisan commented 8 years ago

Sorry for my late reply, I was away in the last few days! Following the suggestions here, I managed to run BEAGLE with both fit_spectrum_example.param and fit_photometry_example.param with apparently no errors. In my case, it seems that the problem is solved by specifying the BEAGLE version when running the code (i.e., using eclake/beagle:0.3.5 instead of eclake/beagle, as suggested by @eclake). I used the commands below:

  docker run --rm -it -v /nethome/trevisan/BEAGLE/BEAGLE-general:/BEAGLE_virtual_workdir --env-file env.list eclake/beagle:0.3.5 1 /BEAGLE_virtual_workdir/params/fit_photometry_example.param

and

  docker run --rm -it -v /nethome/trevisan/BEAGLE/BEAGLE-general:/BEAGLE_virtual_workdir --env-file env.list eclake/beagle:0.3.5 1 /BEAGLE_virtual_workdir/params/fit_spectrum_example.param

The parameter files that I used are these ones:

fit_photometry_example.txt fit_spectrum_example.txt

I am using Docker Toolbox version 1.6.2, machine with Ubuntu 14.04.

I had a quick look at the output files, and they seem ok. But it would be nice to have the output from @jacopo-chevallard or @eclake to check the results I've got. Is it possible? :-)

eclake commented 8 years ago

Good idea @marinatrevisan - I'll put them up in this repo today/tomorrow and let you know!

eclake commented 8 years ago

OK, if adding in the version specifically worked for @marinatrevisan but not @adelave1, perhaps I didn't set the new latest flag properly (once we have the BEAGLE version number in the output files it will be easier to verify).

@adelave1, please could you try one more time with the photometry example explicitly writing eclake/beagle:0.3.5 (rather than eclake/beagle).

If that works then I know I still need to fix the latest flag. - sorry this hasn't been a quick answer.

alex-delavega commented 8 years ago

@eclake, here is my output for the photometry fit from using @marinatrevisan's parameter files (except I used the cb15 templates) and BEAGLE:0.3.5: 

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle:0.3.5 1 /opt/BEAGLE/params/fit_photometry_example.param

  All the templates read.

 Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES
 271 filters defined, out of 300                                maximum     ...done
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fitted                        redshift                                   0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 n_fitted:            5
 *****************************************************
 MultiNest v3.9
 Copyright Farhan Feroz & Mike Hobson
 Release Oct 2014

 no. of live points =  150
 dimensionality =    5
 *****************************************************
 Starting MultiNest
 generating live points
 --- LINEAR:  X0 =  2.293E+02 is outside X range --- 9.000E+02 6.010E+04      1666
 ---   Error reported only once. It may occur more than once. ---
 live points generated, starting sampling
Acceptance Rate:                        0.970874
Replacements:                                200
Total Samples:                               206
Nested Sampling ln(Z):               -209.178171
Acceptance Rate:                        0.871080
Replacements:                                250
Total Samples:                               287
Nested Sampling ln(Z):               -207.268980
Acceptance Rate:                        0.735294
Replacements:                                300
Total Samples:                               408
Nested Sampling ln(Z):               -206.746324

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7FCEA2831777
#1  0x7FCEA2831D7E
#2  0x7FCEA1F6DD3F
#3  0x7FCEA3436322
#4  0x7FCEA34368E8
#5  0x7FCEA32E9C8C
#6  0x7FCEA3789616
#7  0x7FCEA37AAC81
#8  0x7FCEA37AEEC2
#9  0x7FCEA37B1E04
#10  0x7FCEA37DF9D8
#11  0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)
#12  0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359
#13  0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988
#14  0x5934DD in __nested_MOD_clusterednest at nested.F90:1451
#15  0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)
#16  0x5A508C in __nested_MOD_nestrun at nested.F90:239
#17  0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134
#18  0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)
#19  0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)

and for the spectrum fit:

docker run --rm -it -v /Users/vega/Desktop/BEAGLE/BEAGLE-general-master:/opt/BEAGLE --env-file env.list eclake/beagle:0.3.5 1 /opt/BEAGLE/params/fit_spectrum_example.param

  All the templates read.
 ---> fixed                         sfh_type                                   0
 ---> fitted                        mass                                       0
 ---> fixed                         current_sfr_timescale                      0
 ---> fixed                         attenuation_type                           0
 ---> fitted                        tauV_eff                                   0
 ---> fixed                         mu                                         0
 ---> fitted                        tau                                        1
 ---> fitted                        metallicity                                1
 ---> fitted                        specific_sfr                               1
 ---> fitted                        formation_redshift                         1
 n_fitted:            6
 fileName: /opt/BEAGLE/data/spectra/example_spec_0.fits                                                                                                                                                                                                                    
 *****************************************************
 MultiNest v3.9
 Copyright Farhan Feroz & Mike Hobson
 Release Oct 2014

 no. of live points =   90
 dimensionality =    6
 *****************************************************
 Starting MultiNest
 generating live points

 Reading Filter File: /opt/BEAGLE/build/FILTERBIN.RES
 271 filters defined, out of 300                                maximum     ...done
 live points generated, starting sampling
Acceptance Rate:                        0.939597
Replacements:                                140
Total Samples:                               149
Nested Sampling ln(Z):            **************

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7F79E7D4C777
#1  0x7F79E7D4CD7E
#2  0x7F79E7488D3F
#3  0x7F79E8951322
#4  0x7F79E89518E8
#5  0x7F79E8804C8C
#6  0x7F79E8CA4616
#7  0x7F79E8CC5C81
#8  0x7F79E8CC9EC2
#9  0x7F79E8CCCE04
#10  0x7F79E8CFA9D8
#11  0x5B6D3C in __utils1_MOD_diagonalize at utils1.f90:58 (discriminator 2)
#12  0x5B7EC1 in __utils1_MOD_calcellprop at utils1.f90:359
#13  0x5C1977 in __xmeans_clstr_MOD_dinosaur at xmeans_clstr.f90:1988
#14  0x5934DD in __nested_MOD_clusterednest at nested.F90:1451
#15  0x5A4234 in __nested_MOD_nestsample at nested.F90:365 (discriminator 1)
#16  0x5A508C in __nested_MOD_nestrun at nested.F90:239
#17  0x57E18D in __nested_sampling_MOD_run_nested_sampling at nested_sampling.f90:134
#18  0x57356A in __prosit_MOD_sample_pdf at PROSIT.f90:235 (discriminator 1)
#19  0x4157A6 in beagle at BEAGLE.f90:464 (discriminator 2)
eclake commented 8 years ago

Thank you so much @adelave1 ! This means 3 things - first that I failed to attach the latest flag to the correct image - therefore reopening #22 - second that the original fits input error was a BEAGLE version specific problem and not an operating-system based file access problem, and thirdly that we have to find out the reason for the SIGILL error and solve #7 - any ideas @jacopo-chevallard ?

I think regarding the invalid_memory_reference issue, this has been solved so please close this issue if you agree @jacopo-chevallard and we can continue the disc. on #7

jacopo-chevallard commented 8 years ago

Agreed, we'll continue on #7 for SIGILL