ERROR: matrix is not positive definite

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Nafsika Antoniadou

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Apr 30, 2025, 8:55:58 AMApr 30

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Hello,

I am running the following code:

form13 = y ~ -1 + intercept +
f(idx, model="dmatern", locations = loc,
hyper = list(range = list(prior = "pc.range", param = c(30, 0.5)),
theta1 = list(prior="pc.prec", param=c(0.4, 0.05))))

fit_gpd_pred = inla(form13,
data = data_df_gpd_pred,
control.predictor = list(compute=TRUE, link=1),
family = "gp",
control.family = list(list(control.link = list(quantile = q_gpd))),
control.compute = list(dic = TRUE, waic = TRUE, cpo = TRUE, config = TRUE),
control.inla=list(strategy="laplace",int.strategy="ccd"),
verbose=T,debug=T,

num.threads = 2
)

and I get [1] "head(scale)"

NULL
[1] "head(weights)"
NULL
[1] "head(Ntrials)"
NULL
[1] "head(offset)"
NULL
[1] "head(E)"
NULL
[1] "head(strata)"
NULL
[1] "head(lp.scale)"
NULL
[1] "head(link.covariates)"
NULL
[1] "MPredictor 0"
[1] "NPredictor 39957"
[1] "NData 39957"
[1] "y...fake has length 39957"
n.family 1
[1] "Entries with same length:" "station" "CGDmean"
[4] "MAP" "intercept" "Northing"
[7] "Easting" "Ykm" "Xkm"
[10] "idx1" "idx" "y...fake"
[1] "prepare problem section"
Prepare inla file.....inla.create.data.file: n.data = 39957
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274647d1e50"
[1] 0 78696 39348 2 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file22741f9f4895"
[1] 0 1 1 1 0 1 0 1
[1] "prepare data section"
[1] "prepare predictor section"
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366"
[1] 0 79914 39957 2 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43"
[1] 0 79914 39957 2 0 1 0 1
write label[ intercept ]
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25"
[1] 0 79914 39957 2 0 1 0 1
file fixed C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25
1 dmatern
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227412fc5493"
[1] 0 840 840 1 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file22745eaf6625"
[1] 0 79914 39957 2 0 0 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444"
[1] 0 79914 39957 2 0 0 0 1
[1] "n 840"
[1] "nrep 1"
...done
Run inla...[1] "all.args: -s -v -t2:1 -P compact"
Read ntt 2 1 with max.threads 8
Found num.threads = 2:1 max_threads = 2

39a87469400fa169507c508366eca6ae7588cfdf - Wed Jun 19 21:58:47 2024 +0900
Report bugs to <he...@r-inla.org>
Set reordering to id=[0] and name=[default]
Process file[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22744fb53505/Model.ini] threads[2] max.threads[8] blas_threads[1] nested[2:1]
inla_build...
number of sections=[10]
parse section=[0] name=[INLA.libR] type=[LIBR]
inla_parse_libR...
section[INLA.libR]
R_HOME=[C:/PROGRA~1/R/R-44~1.1]
parse section=[7] name=[INLA.Expert] type=[EXPERT]
inla_parse_expert...
section[INLA.Expert]
disable.gaussian.check=[0]
Measure dot.product.gain=[No]
cpo.manual=[0]
jp.file=[(null)]
jp.model=[(null)]
parse section=[1] name=[INLA.Model] type=[PROBLEM]
inla_parse_problem...
name=[INLA.Model]
R-INLA version = [24.06.19]
R-INLA build date = [19893]
Build tag = [devel]
System memory = [15.7Gb]
Cores = (Physical= 8, Logical= 8)
'char' is signed
BUFSIZ is 512
openmp.strategy=[default]
pardiso-library installed and working? = [no]
smtp = [taucs]
strategy = [default]
store results in directory=[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22744fb53505/results.files]
output:
gcpo=[0]
num.level.sets=[-1]
size.max=[32]
strategy=[Posterior]
correct.hyperpar=[1]
epsilon=[0.005]
prior.diagonal=[0.0001]
keep=[]
remove.fixed=[1]
remove=[]
cpo=[1]
po=[1]
dic=[1]
kld=[1]
mlik=[1]
q=[0]
graph=[0]
hyperparameters=[1]
config=[1]
config.lite=[0]
likelihood.info=[0]
internal.opt=[1]
save.memory=[0]
summary=[1]
return.marginals=[1]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[3] name=[Predictor] type=[PREDICTOR]
inla_parse_predictor ...
section=[Predictor]
dir=[predictor]
PRIOR->name=[loggamma]
hyperid=[53001|Predictor]
PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR->PARAMETERS=[1, 1e-05]
initialise log_precision[13.8155]
fixed=[1]
user.scale=[1]
n=[39957]
m=[0]
ndata=[39957]
compute=[1]
read offsets from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227462613366] 9/39957 (idx,y) = (9, 0)
read link.fitted.values from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274fc84c43] 9/39957 (idx,y) = (9, 0)
A=[(null)]
Aext=[(null)]
AextPrecision=[1e+08]
output:
summary=[1]
return.marginals=[1]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[2] name=[INLA.Data1] type=[DATA]
inla_parse_data [section 1]...
tag=[INLA.Data1]
family=[GP]
likelihood=[GP]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274647d1e50]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227424d4f3d]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file22741f9f4895]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274484e1daa]
read n=[78696] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274647d1e50]
0/39348 (idx,y,d) = (0, 0.364, 1)
1/39348 (idx,y,d) = (1, 21.064, 1)
2/39348 (idx,y,d) = (2, 6.264, 1)
3/39348 (idx,y,d) = (3, 20.864, 1)
4/39348 (idx,y,d) = (4, 3.464, 1)
5/39348 (idx,y,d) = (5, 1.964, 1)
6/39348 (idx,y,d) = (6, 7.564, 1)
7/39348 (idx,y,d) = (7, 10.464, 1)
8/39348 (idx,y,d) = (8, 22.664, 1)
9/39348 (idx,y,d) = (9, 10.864, 1)
likelihood.variant=[0]
likelihood.quantile=[0.5]
initialise internal_tail[-4]
fixed=[0]
PRIOR->name=[pcgevtail]
hyperid=[101201|INLA.Data1]
PRIOR->from_theta=[function (x, interval = c(low=0, high=0.5)) <<NEWLINE>>interval[1] + (interval[2] - interval[1]) * exp(x)/(1 + exp(x))]
PRIOR->to_theta = [function (x, interval = c(low=0, high=0.5)) <<NEWLINE>>log(-(interval[1] - x)/(interval[2] - x))]
PRIOR->PARAMETERS[0]=[7]
PRIOR->PARAMETERS[1]=[0]
PRIOR->PARAMETERS[2]=[0.5]
gp.tail.interval [0 0.5]
Link model [QUANTILE]
Link order [-1]
Link variant [-1]
Link a [1]
Link ntheta [0]
mix.use[0]
parse section=[5] name=[idx] type=[FFIELD]
inla_parse_ffield...
section=[idx]
dir=[random.effect00000001]
model=[dmatern]
PRIOR0->name=[pcprec]
hyperid=[35101|idx]
PRIOR0->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR0->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR0->PARAMETERS0=[0.4 0.05]
PRIOR1->name=[pcrange]
hyperid=[35102|idx]
PRIOR1->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR1->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR1->PARAMETERS1[0]=[30]
PRIOR1->PARAMETERS1[1]=[0.5]
PRIOR2->name=[loggamma]
hyperid=[35103|idx]
PRIOR2->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR2->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR2->PARAMETERS2=[0.5, 1]
vb.correct n[1] -1
correct=[-1]
constr=[0]
diagonal=[0]
id.names=<not present>
compute=[1]
nrep=[1]
ngroup=[1]
Alocal=[no]
read covariates from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227467144444] 9/39957 (idx,y) = (9, 0)
file for locations=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file227412fc5493]
nlocations=[840]
locations[0]=[1]
locations[1]=[2]
locations[2]=[3]
locations[3]=[4]
locations[4]=[5]
locations[5]=[6]
locations[6]=[7]
locations[7]=[8]
locations[8]=[9]
locations[9]=[10]
cyclic=[0]
initialise log_precision[3]
fixed=[0]
initialise range_intern[0]
fixed=[0]
initialise nu_intern[-0.693147]
fixed=[1]
computed/guessed rank-deficiency = [0]
output:
summary=[1]
return.marginals=[1]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
section=[4] name=[intercept] type=[LINEAR]
inla_parse_linear...
section[intercept]
dir=[fixed.effect00000001]
file for covariates=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 0/39957 (idx,y) = (0, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 1/39957 (idx,y) = (1, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 2/39957 (idx,y) = (2, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 3/39957 (idx,y) = (3, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 4/39957 (idx,y) = (4, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 5/39957 (idx,y) = (5, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 6/39957 (idx,y) = (6, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 7/39957 (idx,y) = (7, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 8/39957 (idx,y) = (8, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files/file2274221c3e25] 9/39957 (idx,y) = (9, 1)
prior mean=[0]
prior precision=[0.001]
compute=[1]
output:
summary=[1]
return.marginals=[1]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[9] name=[INLA.pardiso] type=[PARDISO]
inla_parse_pardiso...
section[INLA.pardiso]
verbose[0]
debug[0]
parallel.reordering[1]
nrhs[-1]
parse section=[8] name=[INLA.lp.scale] type=[LP.SCALE]
inla_parse_lp_scale...
section[INLA.lp.scale]

Index table: number of entries[3], total length[40798]
tag start-index length
Predictor 0 39957
idx 39957 840
intercept 40797 1
List of hyperparameters:
theta[0] = [Intern tail parameter for the gp observations]
theta[1] = [Log precision for idx]
theta[2] = [log range for idx]

parse section=[6] name=[INLA.Parameters] type=[INLA]
inla_parse_INLA...
section[INLA.Parameters]
lincomb.derived.correlation.matrix = [No]
global_node.factor = 2.000
global_node.degree = 2147483647
reordering = -1
constr.marginal.diagonal = 1.49e-08
Contents of ai_param 0000019073d961b0
Optimiser: DEFAULT METHOD
Option for GSL-BFGS2: tol = 0.1
Option for GSL-BFGS2: step_size = 1
Option for GSL-BFGS2: epsx = 0.001
Option for GSL-BFGS2: epsf = 0.002
Option for GSL-BFGS2: epsg = 0.005
Restart: 0
Optimise: try to be smart: Yes
Optimise: use directions: Yes
Mode restart: Yes
Mode fixed: No
Mode use_mode: No
parallel linesearch [0]
Gaussian approximation:
tolerance_func = 0.002
tolerance_step = 5e-06
optpar_fp = 0
optpar_nr_step_factor = -0.1
Gaussian data: No
Strategy: Fit a spline-corrected Gaussian
Fast mode: On
Use linear approximation to log(|Q +c|)? Yes
Method: Compute the derivative exact
Parameters for improved approximations
Number of points evaluate: 9
Step length to compute derivatives numerically: 0.0001
Stencil to compute derivatives numerically: 5
Cutoff value to construct local neigborhood: 0.0001
Log calculations: On
Log calculated marginal for the hyperparameters: On
Integration strategy: Use points from Central Composite Design (CCD)
f0 (CCD only): 1.100
dz (GRID only): 0.750
Adjust weights (GRID only): On
Difference in log-density limit (GRID only): 6.000
Skip configurations with (presumed) small density (GRID only): On
Gradient is computed using Central difference with step-length 0.005000
Hessian is computed using Central difference with step-length 0.070711
Hessian matrix is forced to be a diagonal matrix? [No]
Compute effective number of parameters? [Yes]
Perform a Monte Carlo error-test? [No]
Interpolator [Auto]
CPO required diff in log-density [3]
Stupid search mode:
Status [On]
Max iter [1000]
Factor [1.05]
Numerical integration of hyperparameters:
Maximum number of function evaluations [100000]
Relative error ....................... [1e-05]
Absolute error ....................... [1e-06]
To stabilise the numerical optimisation:
Minimum value of the -Hessian [-inf]
Strategy for the linear term [Keep]
CPO manual calculation[No]
VB correction is [Enabled]
strategy = [mean]
verbose = [Yes]
f_enable_limit_mean = [30]
f_enable_limit_var = [25]
f_enable_limit_mean_max = [1024]
f_enable_limit_variance_max = [768]
iter_max = [25]
emergency = [25.00]
hessian_update = [2]
hessian_strategy = [full]
Misc options:
Hessian correct skewness only [1]
inla_build: check for unused entries in[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22744fb53505/Model.ini]
inla_INLA_preopt_experimental...
Strategy = [DEFAULT]
Mode....................... [Compact]
Setup...................... [2.12s]
Sparse-matrix library...... [taucs]
sort L..................... [no]
OpenMP strategy............ [large]
num.threads................ [2:1]
blas.num.threads........... [1]
Density-strategy........... [Low]
Size of graph.............. [841]
Number of constraints...... [0]
Optimizing sort2_id........ [252]
Optimizing sort2_dd........ [367]
Optimizing Qx-strategy..... serial[0.506] parallel [0.494] choose[serial]
Optimizing pred-strategy... plain [0.935] data-rich[0.065] choose[data-rich]
Optimizing dot-products.... serial[0.551] group[0.449]
==> optimal.mix.strategy[0.010]
serial[89.4] group[10.6]
Found optimal reordering=[metis] nnz(L)=[353221] and use_global_nodes(user)=[no]

List of hyperparameters:
theta[0] = [Intern tail parameter for the gp observations]
theta[1] = [Log precision for idx]
theta[2] = [log range for idx]

Compute initial values...
Iter[0] RMS(err) = 1.000, update with step-size = 0.570
Iter[1] RMS(err) = 0.676, update with step-size = 0.822
Iter[2] RMS(err) = 0.948, update with step-size = 0.578
Iter[3] RMS(err) = 0.995, update with step-size = 0.892
Initial values computed in 0.2642 seconds
x[0] = 0.2136
x[1] = 0.2037
x[2] = 0.2146
x[3] = 0.2070
x[4] = 0.2157
x[836] = -0.0812
x[837] = -0.0812
x[838] = -0.0812
x[839] = -0.0812
x[840] = 0.1023

Optimise using DEFAULT METHOD
Smart optimise part I: estimate gradient using forward differences
maxld= -103170.0330 fn= 1 theta= -3.9950 3.0000 0.0000 [1.97, 4.896]
maxld= -103169.7343 fn= 3 theta= -4.0000 3.0000 0.0050 [1.97, 4.114]
maxld= -100375.0668 fn= 5 theta= -4.0009 2.0001 0.0141 [2.20, 3.598]
maxld= -100374.9601 fn= 8 theta= -4.0009 2.0001 0.0191 [2.20, 3.358]
maxld= -98367.4970 fn= 10 theta= -4.0091 -6.9990 0.1415 [2.32, 5.433]
maxld= -98367.4685 fn= 11 theta= -4.0041 -6.9990 0.1415 [2.34, 5.291]
maxld= -98367.3447 fn= 13 theta= -4.0091 -6.9990 0.1465 [2.34, 5.104]
maxld= 163659942357279725940390899638283010048.0000 fn= 15 theta= -4.0831 -87.9909 1.2875 [2.26, 4.827]

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

gsl: cholesky.c:645: ERROR: matrix is not positive definite
Default GSL error handler invoked.
..done

*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
[1] "MPredictor 0"
[1] "NPredictor 39957"
[1] "NData 39957"
[1] "y...fake has length 39957"
n.family 1
[1] "Entries with same length:" "station" "CGDmean"
[4] "MAP" "intercept" "Northing"
[7] "Easting" "Ykm" "Xkm"
[10] "idx1" "idx" "y...fake"
[1] "prepare problem section"
Prepare inla file.....inla.create.data.file: n.data = 39957
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22743b586335"
[1] 0 78696 39348 2 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747b441a2b"
[1] 0 1 1 1 0 1 0 1
[1] "prepare data section"
[1] "prepare predictor section"
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73"
[1] 0 79914 39957 2 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0"
[1] 0 79914 39957 2 0 1 0 1
write label[ intercept ]
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e"
[1] 0 79914 39957 2 0 1 0 1
file fixed C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e
1 dmatern
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227434a7735f"
[1] 0 840 840 1 0 1 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22744e5b2c6f"
[1] 0 79914 39957 2 0 0 0 1
[1] "\nOpen file to write C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea"
[1] 0 79914 39957 2 0 0 0 1
[1] "n 840"
[1] "nrep 1"
...done
Run inla...[1] "all.args: -s -v -t2:1 -P compact"
Read ntt 2 1 with max.threads 8
Found num.threads = 2:1 max_threads = 2

39a87469400fa169507c508366eca6ae7588cfdf - Wed Jun 19 21:58:47 2024 +0900
Report bugs to <he...@r-inla.org>
Set reordering to id=[0] and name=[default]
Process file[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22742c8f2f2e/Model.ini] threads[2] max.threads[8] blas_threads[1] nested[2:1]
inla_build...
number of sections=[10]
parse section=[0] name=[INLA.libR] type=[LIBR]
inla_parse_libR...
section[INLA.libR]
R_HOME=[C:/PROGRA~1/R/R-44~1.1]
parse section=[7] name=[INLA.Expert] type=[EXPERT]
inla_parse_expert...
section[INLA.Expert]
disable.gaussian.check=[0]
Measure dot.product.gain=[No]
cpo.manual=[0]
jp.file=[(null)]
jp.model=[(null)]
parse section=[1] name=[INLA.Model] type=[PROBLEM]
inla_parse_problem...
name=[INLA.Model]
R-INLA version = [24.06.19]
R-INLA build date = [19893]
Build tag = [devel]
System memory = [15.7Gb]
Cores = (Physical= 8, Logical= 8)
'char' is signed
BUFSIZ is 512
openmp.strategy=[default]
pardiso-library installed and working? = [no]
smtp = [taucs]
strategy = [default]
store results in directory=[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22742c8f2f2e/results.files]
output:
gcpo=[0]
num.level.sets=[-1]
size.max=[32]
strategy=[Posterior]
correct.hyperpar=[1]
epsilon=[0.005]
prior.diagonal=[0.0001]
keep=[]
remove.fixed=[1]
remove=[]
cpo=[0]
po=[0]
dic=[0]
kld=[1]
mlik=[1]
q=[0]
graph=[0]
hyperparameters=[1]
config=[0]
config.lite=[0]
likelihood.info=[0]
internal.opt=[1]
save.memory=[0]
summary=[1]
return.marginals=[0]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[3] name=[Predictor] type=[PREDICTOR]
inla_parse_predictor ...
section=[Predictor]
dir=[predictor]
PRIOR->name=[loggamma]
hyperid=[53001|Predictor]
PRIOR->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR->PARAMETERS=[1, 1e-05]
initialise log_precision[13.8155]
fixed=[1]
user.scale=[1]
n=[39957]
m=[0]
ndata=[39957]
compute=[1]
read offsets from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467933f73] 9/39957 (idx,y) = (9, 0)
read link.fitted.values from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747c372ab0] 9/39957 (idx,y) = (9, 0)
A=[(null)]
Aext=[(null)]
AextPrecision=[1e+08]
output:
summary=[1]
return.marginals=[0]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[2] name=[INLA.Data1] type=[DATA]
inla_parse_data [section 1]...
tag=[INLA.Data1]
family=[GP]
likelihood=[GP]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22743b586335]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22742d405629]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22747b441a2b]
file->name=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2274228213ab]
read n=[78696] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22743b586335]
0/39348 (idx,y,d) = (0, 0.364, 1)
1/39348 (idx,y,d) = (1, 21.064, 1)
2/39348 (idx,y,d) = (2, 6.264, 1)
3/39348 (idx,y,d) = (3, 20.864, 1)
4/39348 (idx,y,d) = (4, 3.464, 1)
5/39348 (idx,y,d) = (5, 1.964, 1)
6/39348 (idx,y,d) = (6, 7.564, 1)
7/39348 (idx,y,d) = (7, 10.464, 1)
8/39348 (idx,y,d) = (8, 22.664, 1)
9/39348 (idx,y,d) = (9, 10.864, 1)
likelihood.variant=[0]
likelihood.quantile=[0.5]
initialise internal_tail[-4]
fixed=[0]
PRIOR->name=[pcgevtail]
hyperid=[101201|INLA.Data1]
PRIOR->from_theta=[function (x, interval = c(low=0, high=0.5)) <<NEWLINE>>interval[1] + (interval[2] - interval[1]) * exp(x)/(1 + exp(x))]
PRIOR->to_theta = [function (x, interval = c(low=0, high=0.5)) <<NEWLINE>>log(-(interval[1] - x)/(interval[2] - x))]
PRIOR->PARAMETERS[0]=[7]
PRIOR->PARAMETERS[1]=[0]
PRIOR->PARAMETERS[2]=[0.5]
gp.tail.interval [0 0.5]
Link model [QUANTILE]
Link order [-1]
Link variant [-1]
Link a [1]
Link ntheta [0]
mix.use[0]
parse section=[5] name=[idx] type=[FFIELD]
inla_parse_ffield...
section=[idx]
dir=[random.effect00000001]
model=[dmatern]
PRIOR0->name=[pcprec]
hyperid=[35101|idx]
PRIOR0->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR0->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR0->PARAMETERS0=[0.4 0.05]
PRIOR1->name=[pcrange]
hyperid=[35102|idx]
PRIOR1->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR1->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR1->PARAMETERS1[0]=[30]
PRIOR1->PARAMETERS1[1]=[0.5]
PRIOR2->name=[loggamma]
hyperid=[35103|idx]
PRIOR2->from_theta=[function (x) <<NEWLINE>>exp(x)]
PRIOR2->to_theta = [function (x) <<NEWLINE>>log(x)]
PRIOR2->PARAMETERS2=[0.5, 1]
vb.correct n[1] -1
correct=[-1]
constr=[0]
diagonal=[0]
id.names=<not present>
compute=[1]
nrep=[1]
ngroup=[1]
Alocal=[no]
read covariates from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 0/39957 (idx,y) = (0, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 1/39957 (idx,y) = (1, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 2/39957 (idx,y) = (2, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 3/39957 (idx,y) = (3, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 4/39957 (idx,y) = (4, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 5/39957 (idx,y) = (5, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 6/39957 (idx,y) = (6, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 7/39957 (idx,y) = (7, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 8/39957 (idx,y) = (8, 0)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227467c9cea] 9/39957 (idx,y) = (9, 0)
file for locations=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file227434a7735f]
nlocations=[840]
locations[0]=[1]
locations[1]=[2]
locations[2]=[3]
locations[3]=[4]
locations[4]=[5]
locations[5]=[6]
locations[6]=[7]
locations[7]=[8]
locations[8]=[9]
locations[9]=[10]
cyclic=[0]
initialise log_precision[3]
fixed=[0]
initialise range_intern[0]
fixed=[0]
initialise nu_intern[-0.693147]
fixed=[1]
computed/guessed rank-deficiency = [0]
output:
summary=[1]
return.marginals=[0]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
section=[4] name=[intercept] type=[LINEAR]
inla_parse_linear...
section[intercept]
dir=[fixed.effect00000001]
file for covariates=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e]
read n=[79914] entries from file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e]
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 0/39957 (idx,y) = (0, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 1/39957 (idx,y) = (1, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 2/39957 (idx,y) = (2, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 3/39957 (idx,y) = (3, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 4/39957 (idx,y) = (4, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 5/39957 (idx,y) = (5, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 6/39957 (idx,y) = (6, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 7/39957 (idx,y) = (7, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 8/39957 (idx,y) = (8, 1)
file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file22741b27178e] 9/39957 (idx,y) = (9, 1)
prior mean=[0]
prior precision=[0.001]
compute=[1]
output:
summary=[1]
return.marginals=[0]
return.marginals.predictor=[0]
nquantiles=[3] [ 0.025 0.5 0.975 ]
ncdf=[0] [ ]
parse section=[9] name=[INLA.pardiso] type=[PARDISO]
inla_parse_pardiso...
section[INLA.pardiso]
verbose[0]
debug[0]
parallel.reordering[1]
nrhs[-1]
parse section=[8] name=[INLA.lp.scale] type=[LP.SCALE]
inla_parse_lp_scale...
section[INLA.lp.scale]

Index table: number of entries[3], total length[40798]
tag start-index length
Predictor 0 39957
idx 39957 840
intercept 40797 1
List of hyperparameters:
theta[0] = [Intern tail parameter for the gp observations]
theta[1] = [Log precision for idx]
theta[2] = [log range for idx]

parse section=[6] name=[INLA.Parameters] type=[INLA]
inla_parse_INLA...
section[INLA.Parameters]
lincomb.derived.correlation.matrix = [No]
global_node.factor = 2.000
global_node.degree = 2147483647
reordering = -1
constr.marginal.diagonal = 1.49e-08
Contents of ai_param 0000023ab45561b0
Optimiser: DEFAULT METHOD
Option for GSL-BFGS2: tol = 0.1
Option for GSL-BFGS2: step_size = 1
Option for GSL-BFGS2: epsx = 0.002
Option for GSL-BFGS2: epsf = 0.004
Option for GSL-BFGS2: epsg = 0.01
Restart: 0
Optimise: try to be smart: No
Optimise: use directions: Yes
Mode restart: Yes
Mode fixed: No
Mode use_mode: No
parallel linesearch [0]
Gaussian approximation:
tolerance_func = 0.004
tolerance_step = 1e-05
optpar_fp = 0
optpar_nr_step_factor = -0.1
Gaussian data: No
Strategy: Use the Gaussian approximation
Fast mode: On
Use linear approximation to log(|Q +c|)? Yes
Method: Compute the derivative exact
Parameters for improved approximations
Number of points evaluate: 9
Step length to compute derivatives numerically: 0.0001
Stencil to compute derivatives numerically: 5
Cutoff value to construct local neigborhood: 0.0001
Log calculations: On
Log calculated marginal for the hyperparameters: On
Integration strategy: Use only the modal configuration (EMPIRICAL_BAYES)
f0 (CCD only): 1.100
dz (GRID only): 0.750
Adjust weights (GRID only): On
Difference in log-density limit (GRID only): 6.000
Skip configurations with (presumed) small density (GRID only): On
Gradient is computed using Central difference with step-length 0.005000
Hessian is computed using Central difference with step-length 0.070711
Hessian matrix is forced to be a diagonal matrix? [Yes]
Compute effective number of parameters? [Yes]
Perform a Monte Carlo error-test? [No]
Interpolator [Auto]
CPO required diff in log-density [3]
Stupid search mode:
Status [On]
Max iter [1000]
Factor [1.05]
Numerical integration of hyperparameters:
Maximum number of function evaluations [100000]
Relative error ....................... [1e-05]
Absolute error ....................... [1e-06]
To stabilise the numerical optimisation:
Minimum value of the -Hessian [inf]
Strategy for the linear term [Keep]
CPO manual calculation[No]
VB-correction is [Disabled]
Misc options:
Hessian correct skewness only [1]
inla_build: check for unused entries in[C:\Users\nafan\AppData\Local\Temp\Rtmpobswht\file22742c8f2f2e/Model.ini]
inla_INLA_preopt_experimental...
Strategy = [DEFAULT]
Mode....................... [Compact]
Setup...................... [2.21s]
Sparse-matrix library...... [taucs]
sort L..................... [no]
OpenMP strategy............ [large]
num.threads................ [2:1]
blas.num.threads........... [1]
Density-strategy........... [Low]
Size of graph.............. [841]
Number of constraints...... [0]
Optimizing sort2_id........ [261]
Optimizing sort2_dd........ [402]
Optimizing Qx-strategy..... serial[0.468] parallel [0.532] choose[serial]
Optimizing pred-strategy... plain [0.927] data-rich[0.073] choose[data-rich]
Optimizing dot-products.... serial[0.554] group[0.446]
==> optimal.mix.strategy[0.010]
serial[89.7] group[10.3]
Found optimal reordering=[metis] nnz(L)=[353221] and use_global_nodes(user)=[no]

List of hyperparameters:
theta[0] = [Intern tail parameter for the gp observations]
theta[1] = [Log precision for idx]
theta[2] = [log range for idx]

Compute initial values...
Iter[0] RMS(err) = 1.000, update with step-size = 0.570
Iter[1] RMS(err) = 0.676, update with step-size = 0.822
Iter[2] RMS(err) = 0.948, update with step-size = 0.578
Iter[3] RMS(err) = 0.995, update with step-size = 0.892
Initial values computed in 0.2480 seconds
x[0] = 0.2136
x[1] = 0.2037
x[2] = 0.2146
x[3] = 0.2070
x[4] = 0.2157
x[836] = -0.0812
x[837] = -0.0812
x[838] = -0.0812
x[839] = -0.0812
x[840] = 0.1023

Optimise using DEFAULT METHOD
maxld= -103170.0330 fn= 1 theta= -3.9950 3.0000 0.0000 [1.97, 5.279]
maxld= -103169.9975 fn= 3 theta= -4.0050 3.0000 -0.0000 [1.97, 5.014]
maxld= -103150.2521 fn= 4 theta= -4.0000 2.9950 -0.0000 [1.98, 4.189]
maxld= -100375.0668 fn= 7 theta= -4.0009 2.0001 0.0141 [2.20, 4.513]
maxld= -100375.0304 fn= 8 theta= -4.0059 2.0001 0.0141 [2.20, 4.460]
maxld= -100366.1070 fn= 9 theta= -4.0009 1.9951 0.0141 [2.20, 4.156]
maxld= -98367.5012 fn= 14 theta= -4.0090 -6.9990 0.1409 [2.32, 5.627]
maxld= -98367.4125 fn= 15 theta= -4.0140 -6.9990 0.1409 [2.34, 5.527]
maxld= -98363.1408 fn= 16 theta= -4.0090 -7.0040 0.1409 [2.34, 5.279]
maxld= 163671538004487110451944551720478048256.0000 fn= 21 theta= -4.0822 -87.9909 1.2825 [2.26, 4.707]
maxld= 163671542960015753825727491154666061824.0000 fn= 24 theta= -4.0872 -87.9909 1.2825 [2.26, 4.273]
maxld= 164491945002793713774845291367088783360.0000 fn= 25 theta= -4.0822 -87.9959 1.2825 [2.26, 4.115]

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 0
Failed to factorize Q. I will try to fix it...

Function: GMRFLib_factorise_sparse_matrix_TAUCS(), Line: 923, Thread: 1
Failed to factorize Q. I will try to fix it...

gsl: cholesky.c:645: ERROR: matrix is not positive definite
Default GSL error handler invoked.
..done
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
If this does not help, please contact the developers at <he...@r-inla.org>.
The inla program failed and the maximum number of tries has been reached.

Can you help me debug it?

Helpdesk (Haavard Rue)

unread,

May 3, 2025, 4:13:32 AMMay 3

to Nafsika Antoniadou, R-inla discussion group

coud you please upgrade to R-4.5 and retry with the most recent testing version
of INLA?

> /file2274fc84c43]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 0/39957 (idx,y) = (0, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 1/39957 (idx,y) = (1, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 2/39957 (idx,y) = (2, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 3/39957 (idx,y) = (3, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 4/39957 (idx,y) = (4, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 5/39957 (idx,y) = (5, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 6/39957 (idx,y) = (6, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 7/39957 (idx,y) = (7, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file2274fc84c43] 8/39957 (idx,y) = (8, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f

> read n=[79914] entries from
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files

> /file227467144444]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 0/39957 (idx,y) = (0, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 1/39957 (idx,y) = (1, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 2/39957 (idx,y) = (2, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 3/39957 (idx,y) = (3, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 4/39957 (idx,y) = (4, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 5/39957 (idx,y) = (5, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 6/39957 (idx,y) = (6, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 7/39957 (idx,y) = (7, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f
> b53505/data.files/file227467144444] 8/39957 (idx,y) = (8, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f

> read n=[79914] entries from
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744fb53505/data.files

> /file2274221c3e25]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22744f

> [1] 0 78696 39348 2 0 1 0 1
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 2747b441a2b"

> [1] 0 1 1 1 0 1 0 1
> [1] "prepare data section"
> [1] "prepare predictor section"
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 27467933f73"

> [1] 0 79914 39957 2 0 1 0 1
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 2747c372ab0"

> [1] 0 79914 39957 2 0 1 0 1
> write label[ intercept ]
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 2741b27178e"

> [1] 0 79914 39957 2 0 1 0 1
> file fixed

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 2741b27178e

> 1 dmatern
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 27434a7735f"

> [1] 0 840 840 1 0 1 0 1
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2
> 2744e5b2c6f"

> [1] 0 79914 39957 2 0 0 0 1
> [1] "\nOpen file to write

> C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files/file2

> read n=[79914] entries from

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file227467933f73]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 0/39957 (idx,y) = (0, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 1/39957 (idx,y) = (1, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 2/39957 (idx,y) = (2, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 3/39957 (idx,y) = (3, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 4/39957 (idx,y) = (4, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 5/39957 (idx,y) = (5, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 6/39957 (idx,y) = (6, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 7/39957 (idx,y) = (7, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 8/39957 (idx,y) = (8, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467933f73] 9/39957 (idx,y) = (9, 0)
> read link.fitted.values from
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file22747c372ab0]

> read n=[79914] entries from

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file22747c372ab0]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 0/39957 (idx,y) = (0, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 1/39957 (idx,y) = (1, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 2/39957 (idx,y) = (2, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 3/39957 (idx,y) = (3, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 4/39957 (idx,y) = (4, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 5/39957 (idx,y) = (5, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 6/39957 (idx,y) = (6, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 7/39957 (idx,y) = (7, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22747c372ab0] 8/39957 (idx,y) = (8, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c

> read n=[78696] entries from

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file22743b586335]

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file227467c9cea]

> read n=[79914] entries from

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file227467c9cea]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 0/39957 (idx,y) = (0, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 1/39957 (idx,y) = (1, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 2/39957 (idx,y) = (2, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 3/39957 (idx,y) = (3, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 4/39957 (idx,y) = (4, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 5/39957 (idx,y) = (5, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 6/39957 (idx,y) = (6, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 7/39957 (idx,y) = (7, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 8/39957 (idx,y) = (8, 0)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file227467c9cea] 9/39957 (idx,y) = (9, 0)
> file for
> locations=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.
> files/file227434a7735f]

> read n=[79914] entries from

> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c8f2f2e/data.files
> /file22741b27178e]
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 0/39957 (idx,y) = (0, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 1/39957 (idx,y) = (1, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 2/39957 (idx,y) = (2, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 3/39957 (idx,y) = (3, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 4/39957 (idx,y) = (4, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 5/39957 (idx,y) = (5, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 6/39957 (idx,y) = (6, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 7/39957 (idx,y) = (7, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c
> 8f2f2e/data.files/file22741b27178e] 8/39957 (idx,y) = (8, 1)
> file=[C:/Users/nafan/AppData/Local/Temp/Rtmpobswht/file22742c

> --
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> To unsubscribe from this group and stop receiving emails from it, send an
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> .

--
Håvard Rue
he...@r-inla.org

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