--- Generating Stan code ---
functions {
// https://github.com/stan-dev/stan/issues/452
real to_real(real x) { return x; }
}
data {
int x_stan_0_0;
vector[x_stan_0_0] x_stan_0_1;
int<lower=0,upper=1> x_stan_0_3[x_stan_0_0];
}
parameters {
vector[x_stan_0_0] x_stan_0_2;
}
model {
vector[x_stan_0_0] v_0_1;
matrix[x_stan_0_0,x_stan_0_0] v_0_3;
matrix[x_stan_0_0,x_stan_0_0] v_0_4;
vector[x_stan_0_0] v_0_6;
vector[x_stan_0_0] v_0_7;
for (i_1_1 in 1:x_stan_0_0) {
v_0_1[i_1_1] = 0;
}
for (i_1_1 in 1:x_stan_0_0) for (i_1_2 in 1:x_stan_0_0) {
real v_1_0;
real v_1_1;
real v_1_2;
real v_1_3;
real v_1_4;
int v_1_5;
real v_1_6;
real v_1_7;
v_1_0 = x_stan_0_1[i_1_1] - x_stan_0_1[i_1_2];
v_1_1 = v_1_0 .* v_1_0;
v_1_2 = to_real(v_1_1) ./ to_real(2);
v_1_3 = -(v_1_2);
v_1_4 = exp(v_1_3);
v_1_5 = x_stan_0_1[i_1_1] == x_stan_0_1[i_1_2];
v_1_6 = v_1_5 ? 1.0e-6 : 0;
v_1_7 = v_1_4 + v_1_6;
v_0_3[i_1_1, i_1_2] = v_1_7;
}
v_0_4 = cholesky_decompose(to_matrix(v_0_3));
v_0_6 = to_matrix(v_0_4) * to_vector(x_stan_0_2);
v_0_7 = v_0_1 + v_0_6;
for (i_1_1 in 1:x_stan_0_0) {
x_stan_0_2[i_1_1] ~ normal(0, 1);
}
for (i_1_1 in 1:x_stan_0_0) {
x_stan_0_3[i_1_1] ~ bernoulli_logit(v_0_7[i_1_1]);
}
}
make -C /home/jovyan/stochaskell/cmdstan /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f
make[1]: Entering directory '/home/jovyan/stochaskell/cmdstan'
--- Translating Stan model to C++ code ---
bin/stanc --o=/home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.hpp /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.stan
Model name=model_7569d5f54491ccd122205a025152ebf820b7d76f_model
Input file=/home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.stan
Output file=/home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.hpp
--- Compiling, linking C++ code ---
g++ -std=c++1y -pthread -Wno-sign-compare -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c -x c++ -o /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.o /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.hpp
g++ -std=c++1y -pthread -Wno-sign-compare -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION src/cmdstan/main.o stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_idas.a /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f.o -o /home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f
make[1]: Leaving directory '/home/jovyan/stochaskell/cmdstan'
--- Sampling Stan model ---
/home/jovyan/stochaskell/cache/stan/model_7569d5f54491ccd122205a025152ebf820b7d76f method=sample num_samples=1000 num_warmup=1000 save_warmup=0 thin=1 adapt engaged=1 algorithm=hmc engine=nuts max_depth=10 metric=diag_e stepsize=1.0 stepsize_jitter=0.0 data file=/tmp/stan-3387388d1f5fd324/stan.data init=0 output file=/tmp/stan-3387388d1f5fd324/stan.csv
method = sample (Default)
sample
num_samples = 1000 (Default)
num_warmup = 1000 (Default)
save_warmup = 0 (Default)
thin = 1 (Default)
adapt
engaged = 1 (Default)
gamma = 0.050000000000000003 (Default)
delta = 0.80000000000000004 (Default)
kappa = 0.75 (Default)
t0 = 10 (Default)
init_buffer = 75 (Default)
term_buffer = 50 (Default)
window = 25 (Default)
algorithm = hmc (Default)
hmc
engine = nuts (Default)
nuts
max_depth = 10 (Default)
metric = diag_e (Default)
metric_file = (Default)
stepsize = 1 (Default)
stepsize_jitter = 0 (Default)
id = 0 (Default)
data
file = /tmp/stan-3387388d1f5fd324/stan.data
init = 0
random
seed = -1 (Default)
output
file = /tmp/stan-3387388d1f5fd324/stan.csv
diagnostic_file = (Default)
refresh = 100 (Default)
Gradient evaluation took 0.003398 seconds
1000 transitions using 10 leapfrog steps per transition would take 33.98 seconds.
Adjust your expectations accordingly!
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Elapsed Time: 35.3845 seconds (Warm-up)
22.6767 seconds (Sampling)
58.0612 seconds (Total)
Stan took 58.08748379s
# stan_version_major = 2
# stan_version_minor = 20
# stan_version_patch = 0
# model = model_7569d5f54491ccd122205a025152ebf820b7d76f_model
# method = sample (Default)
# sample
# num_samples = 1000 (Default)
# num_warmup = 1000 (Default)
# save_warmup = 0 (Default)
# thin = 1 (Default)
# adapt
# engaged = 1 (Default)
# gamma = 0.050000000000000003 (Default)
# delta = 0.80000000000000004 (Default)
# kappa = 0.75 (Default)
# t0 = 10 (Default)
# init_buffer = 75 (Default)
# term_buffer = 50 (Default)
# window = 25 (Default)
# algorithm = hmc (Default)
# hmc
# engine = nuts (Default)
# nuts
# max_depth = 10 (Default)
# metric = diag_e (Default)
# metric_file = (Default)
# stepsize = 1 (Default)
# stepsize_jitter = 0 (Default)
# id = 0 (Default)
# data
# file = /tmp/stan-3387388d1f5fd324/stan.data
# init = 0
# random
# seed = -1 (Default)
# output
# file = /tmp/stan-3387388d1f5fd324/stan.csv
# diagnostic_file = (Default)
# refresh = 100 (Default)
# Adaptation terminated
# Step size = 0.307326
# Diagonal elements of inverse mass matrix:
# 0.454784, 0.609914, 0.892531, 0.966999, 0.975292, 0.813568, 0.984162, 1.12342, 0.791994, 0.867618, 1.05041, 0.97575, 0.893809, 0.841702, 1.12326, 0.842975, 0.919122, 0.968328, 0.965005, 0.985369, 1.04096, 1.03149, 1.04123, 0.96826, 0.933623, 0.949133, 1.01007, 0.946262, 0.889816, 1.06354, 0.783898, 1.04882, 1.02299, 0.792839, 0.916242, 0.744308, 1.03046, 0.849252, 0.926423, 0.955199, 0.888793, 0.855933, 1.03896, 1.06476, 0.829021, 0.981326, 1.05203, 0.818894, 0.715086, 0.763326, 0.99942, 1.00893, 0.918666, 0.93359, 1.00808, 1.14396, 0.888619, 1.01575, 0.837915, 0.97647, 0.853298, 0.777611, 0.806646, 0.861312, 0.893244, 1.03236, 0.990303, 1.00321, 0.954213, 0.904326, 0.957451, 1.01408, 0.920718, 0.87331, 0.820142, 0.902128, 1.14986, 0.867055, 1.05263, 0.887892, 0.893434, 1.02279, 0.98857, 1.10319, 1.07899, 1.0448, 1.02726, 1.00964, 1.01895, 1.0081, 1.00302, 0.899133, 1.00881, 1.0358, 1.01014, 0.985071, 0.990859, 0.900477, 1.02481, 0.970945, 0.956314, 1.04053
#
# Elapsed Time: 35.3845 seconds (Warm-up)
# 22.6767 seconds (Sampling)
# 58.0612 seconds (Total)
#
Extracting: v_0_7
--- Removing temporary files ---