test case error - a spherical cloud

[Taysun Kimm]

Hi,

I've just started playing with Sunrise, and installed it and others (i.e. boost, blitz..)
with intel-compilers (11.1) following the instruction on this website.
As a next step, I am trying to run a test simulation ( ir_thick_test) ,
but I've got some error which I can't understand very well.
Does anyone come across this before?
Basically, Blitz was installed nicely, so I'm wondering what I've done wrong.
Any input will be appreciated.

Best,
Taysun

[kimm@service1:~/soft/sunrise/test]$ ./ir_thick_test --output-file res.out --grain_data_dir=/home/kimm/soft/sunrise/crosssections
Optically thick cloud with central point source test problem. Parameters:
output-file = res.out
n_rays = 1000000
n_rays_temp = 1000000
n_rays_ir = 1000000
integrate_ir = 1
rays_per_cell = 2
save_temps = 0
n_threads = 12
maxlevel = 6
i_max = 10
i_min = 0.01
do_ir = 1
ir_tol = 0.1
ir_lumfrac = 0.01
tau_tol = 100
lambda_min = 1e-07
lambda_max = 0.001
n_lambda = 50
seed = 42
wd01_parameter_set = DL07_MW3.1_60
nscat_min = 0
nscat_max = 2147483647
rt_method = standard
n_seeds = 10000
n_metro = 100
n_mut = 1000000
nc_max = 2147483647
ns_max = 2147483647
reflambda = 5.5e-07
source_temp = 5800
source_lum = 1
radius = 5
tau = 100
grain_model = wd01_Brent_PAH

Using dust data from grain model: wd01_Brent_PAH
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/PAH_neutral_DL07.fits
Selecting size range 3.548e-10 - 1e-08
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/PAH_ionized_DL07.fits
Selecting size range 3.548e-10 - 1e-08
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/PAH_neutral_DL07.fits
Selecting size range 3.548e-10 - 1e-08
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/PAH_ionized_DL07.fits
Selecting size range 3.548e-10 - 1e-08
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/graphite.fits
Selecting size range 1.122e-08 - 1e-05
Reading grain cross-sections from file /home/kimm/soft/sunrise/crosssections/suv_silicate.fits
Selecting size range 1e-09 - 1e-05
Using WD01 graphite size distribution DL07_MW3.1_60
Using WD01 silicate size distribution DL07_MW3.1_60
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Downsampling grain opacities onto wavelength grid
Resampling emission quantities
Resampling absorption quantities
Calculating extinction curve
Creating cameras. Translating origin by (0,0,0)
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
thread starting
Final grid contains 22352 cells
Allocating a (22352, 1) memory block for cell densities, 0.000166535 GB.
Allocating a (22352, 50) memory block for cell intensities, 0.00832677 GB.
Total dust mass: 4.49778e-08
shooting
Spawning 12 shooting threads
Shooting complete
CAMERA0-PARAMETERS
CAMERA0-STAR
Normalizing image
Writing image

Reading CAMERA0-STAR
Integrating image
Bolometric luminosity: 4.167e+23
Allocating a (22352, 50) memory block for cell emission, 0.00832677 GB.
Calculating dust equilibrium temperatures

Iteration 1
Calculating grain temperatures and emission SEDs
Don't worry about length unit warning that follows:
Warning: Inconsistent units for length: au and m
Calculating dust emission SED for model 0
Calculating dust emission SED for grain species 0
Calculating grain template emission
Calculating dust emission SED for grain species 1
Calculating grain template emission
Calculating dust emission SED for grain species 2
Setting up temperature interpolation tables
Spawning 12 threads
Threads done.
Calculating dust emission SED for grain species 3
Setting up temperature interpolation tables
Spawning 12 threads
Threads done.
Calculating dust emission SED for grain species 4
Setting up temperature interpolation tables
Spawning 12 threads
Threads done.
Calculating dust emission SED for grain species 5
Setting up temperature interpolation tables
Spawning 12 threads
Threads done.
Updating SED arrays
Calculating emission weights
Grid luminosity in this iteration: 0
Shooting
Not using immediate reemission
Spawning 12 shooting threads
ASSERT_ALL failure at element 44/50
ir_thick_test: ../src/mcrx-debug.h:63: bool xassert_all(const blitz::_bz_ArrayExpr<T> &) [with T = blitz::_bz_ArrayExprBinaryOp<blitz::_bz_ArrayExpr<blitz::FastArrayIterator<double, 1>>, blitz::_bz_ArrayExpr<blitz::_bz_ArrayExprConstant<double>>, blitz::Less<double, double>>]: Assertion `0' failed.
Aborted (core dumped)

[Chris Hayward]

Hi Taysun,

That error does not indicate that there is an error in your blitz install but rather that the assertion xassert_all failed. This can be at a number of places:

mcrx-debug.h:#define ASSERT_ALL(expression) if(!all(expression)) assert(xassert_all(expression));

[chayward@rclogin03 src]$ grep ASSERT_ALL *.cc

density_generator.cc:  ASSERT_ALL(rho>=0);

full_sed_grid.cc:    ASSERT_ALL(rho>=0);

grain.cc:  ASSERT_ALL(sigma_>=0);

grain.cc:  ASSERT_ALL(sigma_sca_>=0);

grain.cc:  ASSERT_ALL(g_>=-1);

grain.cc:  ASSERT_ALL(g_<=1);

grain.cc:    ASSERT_ALL(new_esigma>=0);

grain.cc:    ASSERT_ALL(new_sigma_s>=0);

grain.cc:    ASSERT_ALL(new_g>=-1);

grain.cc:    ASSERT_ALL(new_g<=1);

grain.cc:    ASSERT_ALL(sigma_>=0);

imops.cc:    ASSERT_ALL (image < blitz::huge (T_float() ));

imops.cc:    ASSERT_ALL (sed < blitz::huge (T_float ()));

polychromatic_grid.cc:    ASSERT_ALL(rho>=0);

polychromatic_grid.cc:    ASSERT_ALL(intens==intens);

polychromatic_grid.cc:    ASSERT_ALL(intens< 1e300);

polychromatic_grid.cc:  ASSERT_ALL(intensities_==intensities_);

polychromatic_grid.cc:  ASSERT_ALL(intensities_< 1e300);

sfrhist_snapshot.cc:    ASSERT_ALL(current_sed<1e60);

sfrhist_snapshot.cc:    ASSERT_ALL(L_bol_set[s]<1e60);

thermal_equilibrium_grain.cc:    ASSERT_ALL(temps==temps);

vecops.cc:    ASSERT_ALL(x>0);

vecops.cc:    ASSERT_ALL(y>=0);

vecops.cc:    ASSERT_ALL(newx>0);

vecops.cc:  ASSERT_ALL(newy==newy);

I can try to figure out why the assertion failed, but I do not have time to do this immediately. (You could start with a backtrace if you want to investigate this.) If you are just trying to get Sunrise to run, I would suggest using the Sbc example you can download from http://code.google.com/p/sunrise/downloads/detail?name=Sbc-example_v4_00.tar.gz&can=2&q=#makechanges. I know that this runs with v4 (there was a previous thread about this), so this should be a good start.

It is possible that the the ir_thick test has not been updated to work with Sunrise v4, but Patrik would have to comment on this. I'll look at this in detail sometime in the near future.

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[Taysun Kimm]

Hi Chris,

Thanks for your suggestion.

I tried to work on Sbc example you attached, and ran it after commenting out a couple of lines related to ICfiles (which made the program terminated bc they don't exist).

And now I got a little different error message, which seems to be parameter-related (not library-related)?

I'll look into the code to see what's going on, but it would be great if you can comment on this. Thanks!

Best,

Taysun

---------------

Welcome to The Stellar Model program, proudly SI compliant.

Reading parameter file: sfrhist-snapshot_010-25999.config

Reading hydro simulation parameter file: ./simpar        

0 IC snapshots defined.                                  

Loading Gadget snapshot type 1 file: snapshot_010        

GADGET file has TJ format                                

Reading GADGET snapshot file snapshot_010                

Warning: Zero parent ID bug detected. Using own ID.      

Error: Invalid number detected in creation mass!         

       Setting creation mass to current mass!            

Error: Invalid number detected in OrigHsml!              

       Using zero (but it's unused anyway so don't worry).

Assigning softening 0.1 to Disk particles                 

Assigning softening 0.1 to Bulge particles                

Assigning softening 0.1 to Stars particles                

Assigning softening 0.4 to Halo particles                 

Multiplying star particle radius by 1                     

Multiplying BH particle radius by 1                       

Error opening merger setup file: /data1/tcoxc01/execute/ICs/Sbc4-c11.dat.parameters

Warning: Initial conditions parameter file not found,                              

  No initial conditions will be saved.                                             

Warning: The number of objects in the initial conditions file is different         

 from the number of objects in the snapshot                                        

Calculating centers of galaxies:

Particles not belonging to a galaxy: (-0.131781,-0.0819457,0.294205)

Calculating particle ages and metallicities

Object 1 gas central metallicity 0.032 gradient -0.0690776

Population disk object 1 mode exponential

Population disk object 1 max age 1.39e+10 tau -1.06e+11

Object 1 disk central metallicity 0.032 gradient -0.0690776

Population bulge object 1 mode instantaneous

Population bulge object 1 age 1.39e+10

Object 1 bulge central metallicity 0.032 gradient -0.0690776

Object 1 nstar central metallicity 0.032 gradient -0.0690776

Reading stellar model file: /home/tkimm/soft/sunrise/Patrik-imfKroupa-Zmulti-ml.fits

SED

Reading MAPPINGS SED from file /home/tkimm/soft/sunrise/Smodel.fits

Warning: MAPPINGS reference mass not found in file, assuming 1e7 Msun

Unversioned MAPPINGS file

  Using MAPPINGS PDR fraction 0.2

  Using MAPPINGS cluster mass 5

Reading MAPPINGS SED with size 540000

axes sizes 6 5 5 2 1800

(6,5,5,1800,2)

  Using wavelength range 757 - 1724

Downsampling SEDs onto wavelength grid

Deleting existing output file

  Building grid from snapshot 'snapshot_010'

   Emission information will not be used

Total number of particles used for refinement: 29861

  Fractional unification tolerance: 1.79769e+308 L_bol, 1e+100 gas, 0.1 metals

  Absolute unification tolerance: 1.79769e+308 W, inf M_Sun gas, 23.076 M_Sun metals

  Resolve metal column density of : 33333.3 M_Sun

  Building grid

Starting with 1 initial grid cells

Creating balanced work chunks

Thread starting

Thread starting

Thread starting

Thread starting

Thread starting

Thread starting

Thread exiting

Now beginning work on 246 balanced cells

thread starting

thread starting

thread starting

thread starting

thread starting

thread starting

sfrhist: sphparticle.cc:126: double mcrx::particle_base::project(const blitz::TinyVector<double, 3> &, const blitz::TinyVector<double, 3> &) const: Assertion `(abs(cellsize [0]/cellsize [2]-1.0)<1e-5) && (abs(cellsize [1]/cellsize [2]-1.0)<1e-5)' failed.

7.57.52.5Aborted (core dumped)

[Gregory F Snyder]

Hi Taysun,

Try replacing the default grid_* keywords with the following:

grid_min -60 -60 -60
grid_max 60 60 60
#grid_n 3 3 1

As I understand, the grid_n keyword is obsolete in Version 4, in which
the adaptive grid always begins with exactly one root cell, defined by
the grid_min and grid_max keywords. The code requires that the grid
creates cubic cells (hence this assertion), so it appears for the new
pure octree scheme the initial root cell needs to be a cube.

Greg

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[Taysun Kimm]

Thanks for the info, Greg. It now works.

Taysun

[Patrik Jonsson]

Greg is correct, the cells must be cubic and grid_n is obsolete. Did
the wiki never get updated with this?

/P.

[Smaran Deshmukh]

Hi,

After (finally) installing Sunrise, I tried to get the Sbc example working. However, I have encountered a problem while running sfrhist. The output file is attached here, as well as the stub and config files.

I am getting a negative pressure error. I think this is because my grid does not seem to contain any mass, even though sfrhist does see the mass in the snapshot file.

I would really appreciate any help.

Thanks

[Chris Hayward]

Hi Smaran,

Sorry you're having trouble. I'll try to reproduce your error. First, can you please tell me which compiler you used?

Thanks,

Chris

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[Smaran Deshmukh]

Hi Chris,

I am using intel compilers. I have also attached the script file which I used to install the software.

(While installing Boost, 4 targets were skipped in atomic and locale. Can that be the cause of the error?

Thanks a lot for your help!
Smaran