[BART-devel] shared memory issue

[aj-foster]

The following is an archived message from the BART-devel mailing list, which has now closed.

From: ja***@ph*** (Jasmina Blecic)
Date: Mon, 20 Jul 2015 19:14:48 -0400
Subject: [BART-devel] shared memory issue

Hi AJ and Pato,

last week (Thursday 16th) I had several runs where BART breaks and reports:
Memory exhausted.

Those runs were done with opacity files and tli files that were
previously running fine.

Pato suggested that I check my files, because he had similar experinece
if the tli file is not compatible with current BART.

I cloned BART two days ago, and I rerun pylineread and transit with new
tli file.

1. Pylineread runs fine.
2. Transit runs with no problems producing the opacity file and final
   outputs.
3. BART breaks and reports: memory exhausted

Since I have never seen this before, I run the same BART.cfg on the
BART cloned on 8 July.
The only change I made is that func calls old BARTfunc:

func = hack BARTfunc /home/jasmina/ast/esp01/BART/BART-8Jul2015/code

And it does not break.

I am guessing just one thing, something may be wrong with shared
memory, because BARTfunc was changed only on 10 July.

AJ, do you mind taking a lo***@th***?

Attached is the BART.cfg that breaks witj new cloned BART:

Thanks
Jasmina

=================================
Here is the error message after BART is run:

Transit copies the existing opacity file from:
'/home/jasmina-exo/ast/esp01/BART/BART-17Jul2015/opacity-
files/opacity_file_7mol_061-55_300_3000K_1e100.dat'.

Start MCMC:
There are 100 layers and 13 species.
/usr/bin/python: Memory exhausted

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[MCMC]

===== LOCATE SOURCE AND WORKING DIRECTORIES =====

Location of the output directory:

loc_dir = ./7mol_7specs/

Tepfile name:

tep_name = /home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/tep/WASP-43b.tep

Stellar Kurucz file:

kurucz = /home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/kurucz/WASP43b-fp00ak2odfnew.pck

Atmospheric pressure layers: :::::::::::::::::::::::::::::::::::::::

Pressure filename (.pres extenesion):

press_file = WASP-43b.pres

Number of layers:

n_layers = 100

Pr***@th***op of the atmosphere (in bars):

p_top = 1e-5

Pr***@th***ottom of the atmosphere (in bars):

p_bottom = 100.0

Use log (True) or linear (False) pressure scale:

log = True

Elemental-abundances file ::::::::::::::::::::::::::::::::::::::::::

Basic elemental abundances file:

abun_basic = /home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/abundances_Asplund2009.txt

Multiplication factor for heavy-element abundances:

solar_times = 1

Swap C/O abundance ratio (True) or not (False):

COswap = False

Elemental abundances file name (.abn extension):

abun_file = solar1x.abn

Temperature profile ::::::::::::::::::::::::::::::::::::::::::::::::

Set the type of model ('line' or 'madhu'):

PTtype = line

Set the parameters for the initial profile:

Line Etal 2013: [log10(kappa) log10(gamma1) log10(gamma2) alpha beta]

Madhu Etal 2009 non-inverted: [a1 a2 p1 p3 T3]

Madhu Etal 2009 inverted: [a1 a2 p1 p2 p3 T3]

ideal profile for WASP-43b solar from Kevin's paper

PTinit = -0.6 -0.4 0.0 0.0 1.09
#PTinit = 0.993 0.20 0.05 3.0 1700 ; for madhu

Atmospheric Elemental Abundances (pre-atmospheric) File ::::::::::::

Pre atmospheric filename (.atm extenstion):

preatm_file = WASP43b_preatm.atm

Elemental species:

in_elem = H He C N O

Output species:

- MUST use names produced by JANAF.py

- see TEA/conversion-record-sort.txt for the correct names

- MUST include all elemental species

out_spec = H_g He_ref C_g N_g O_g H2_ref CO_g CO2_g CH4_g H2O_g NH3_g HCN_g C2H2_g

If not None, set uniform mole mixing ratios for each out_spec, e.g.:

uniform = 1e-9 0.15 1e-9 1e-9 1e-9 0.85 1e-4 1e-4 1e-4 1e-4 1e-9 1e-9 1e-9

uniform = None

Atmospheric File (P, T, species-abundances) ::::::::::::::::::::::::

TEA output file (the 'atmospheric file') name:

atmfile = /home/jasmina/ast/esp01/BART/BART-20Jul2015/run/7mol_7specs/WASP43b_7mol_myPT.tea

:::::::::: MCMC arguments ::::::::::::::::::::::::::::::::::::::::::

Data (eclipse depths):

order: Blecic-Spizter ch1, ch2; Kevin Spitzer ch1, ch2: Wang H, Ks; Gillon 1.19, 2.09; Chen K, i'; Zhou Ks; Kevin HST

data = 0.00347 0.00382
0.003300 0.003827
0.00103 0.00194
0.00079 0.00156
0.00197 0.00037
0.00181
0.000367 0.000431 0.000414 0.000482 0.000460 0.000473 0.000353
0.000313 0.000320 0.000394 0.000439 0.000458 0.000595 0.000614 0.000732

Data 1-sigma uncertainties:

uncert = 0.00013 0.00015
0.000089 0.000084
0.00017 0.00029
0.00032 0.00014
0.00042 0.00022
0.00027
0.000045 0.000039 0.000038 0.000036 0.000037 0.000033 0.000034
0.000030 0.000036 0.000036 0.000033 0.000035 0.000036 0.000037 0.000042

Waveband filters:

filter = /home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/spitzer_irac1_sa.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/spitzer_irac2_sa.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/spitzer_irac1_sa.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/spitzer_irac2_sa.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/Wang-Hband.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/Wang-Kband.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/VLT_1190.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/VLT_2090.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/GROND_K_JB.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/GROND_i_JB.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/Zhou_Ks.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter0.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter1.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter2.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter3.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter4.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter5.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter6.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter7.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter8.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter9.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter10.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter11.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter12.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter13.dat
/home/jasmina/ast/esp01/BART/WASP43b/BART/inputs/filters/WASP43b_filt/grism141-filter14.dat

Fitting function:

func = hack BARTfunc /home/jasmina/ast/esp01/BART/BART-20Jul2015/code

List of moelcules being fit:

molfit = H2O CO2 CO CH4 NH3 HCN C2H2

MCMC temperature boundaries:

Tmin = 300.0
Tmax = 3000.0

Temperature-profile model:

PTtype = line

The model fitting parameters:

log(kappa) log(g1) log(g2) alpha beta log(M1) log(M2) ...

H2O CO2 CO CH4 NH3 HCN C2H2

params = -0.6 -0.4 0.0 0.0 1.09 0.0 0.0 -1.0 -3.5 -3.0 3.0 -4.5
pmin = -2.0 -0.6 -1.3 0.0 1.02 -1.5 -6.0 -6.0 -6.0 -6.0 -6.0 -6.0
pmax = 6.0 0.0 0.7 1.0 1.14 2.0 5.0 6.0 5.0 5.0 5.0 5.0
stepsize = 0.01 0.01 0.0 0.0 0.01 0.01 0.1 0.1 0.1 0.1 0.1 0.1

DEMC setup:

numit = 1e5
nchains = 10
walk = demc
leastsq = False
chisqiscale = False
grtest = True
burnin = 3000
mpi = True
savemodel = ./band_eclipse.npy
plots = True
logfile = MCMC.log

Verbosity level:

verb = 0

:::::::::: Transit Arguments :::::::::::::::::::::::::::::::::::::::

tconfig = transit.cfg
linedb = /home/jasmina-exo/ast/esp01/BART/BART-17Jul2015/tli-files/7mol_061-55.tli
cia = /home/jasmina/ast/esp01/BART/BART-20Jul2015/modules/transit/inputs/CIA_Borysow_H2H2_0060-7000K_0.61-500um.dat
/home/jasmina-exo/ast/esp01/BART/BART-17Jul2015/modules/transit/inputs/CIA_HITRAN_H2He_0200-3000K_0.5-500um.dat
molfile = /home/jasmina/ast/esp01/BART/BART-20Jul2015/modules/transit/inputs/molecules.dat

Spectrum array:

wllow = 0.61
wlhigh = 5.50
wlfct = 1e-4

wndelt = 1.0
wnosamp = 2160
wnfct = 1.0

Reference pressure and radius level (surface-ish) where p(r0) = p0:

refpress = 0.1

solution = eclipse
raygrid = 0 20 40 60 80
toomuch = 10.0
ethresh = 1e-100

nwidth = 20

Opacity grid:

tlow = 300
thigh = 3000
tempdelt = 100
opacityfile = /home/jasmina-exo/ast/esp01/BART/BART-17Jul2015/opacity-files/opacity_file_7mol_061-55_300_3000K_1e100.dat

Output spectrum file name:

outflux = ./7mol_7specs-flux.dat

Output intensity file name:

outintens = ./7mol_7specs-intens.dat

Output file with the radius where the optical depth reached toomuch:

outtoomuch = ./7mol_7specs5-toom.dat

Output file with the samplings info:

outsample = ./7mol_7specs-samp.dat