I’m trying to run the basic example in the CmdStan.jl documentation.
However, I’m getting path related errors.
When I try to specify the project folder in the call to stan:
using CmdStan
set_cmdstan_home!(“/Users/yanivabir/cmdstan”)bernoullistanmodel = "
data {
int<lower=0> N;
int<lower=0,upper=1> y[N];
}
parameters {
real<lower=0,upper=1> theta;
}
model {
theta ~ beta(1,1);
y ~ bernoulli(theta);
}
"stanmodel = Stanmodel(name=“bernoulli”, model=bernoullistanmodel);
bernoullidata = Dict(“N” => 10, “y” => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
rc, chns, cnames = stan(stanmodel, bernoullidata, “/Path/to/folder”)
I get the following error:
An error occurred while compiling the Stan program.
Please check your Stan program in variable ‘bernoulli’ and the contents of /Path/to/folder/tmp/bernoulli_build.log.
Note that Stan does not handle blanks in path names.
A tmp folder is made in my project folder, with the files bernoulli.stan, bernoulli_build.log and bernoulli_make.log in it.
When I don’t try to specify the project directory, the stan program compiles, samples are drawn and saved to csv (inside a tmp folder in my cmdstan folder), but then CmdStan.jl gives an error:
I run:
using CmdStan
set_cmdstan_home!(“/Users/yanivabir/cmdstan”)bernoullistanmodel = "
data {
int<lower=0> N;
int<lower=0,upper=1> y[N];
}
parameters {
real<lower=0,upper=1> theta;
}
model {
theta ~ beta(1,1);
y ~ bernoulli(theta);
}
"stanmodel = Stanmodel(name=“bernoulli”, model=bernoullistanmodel);
bernoullidata = Dict(“N” => 10, “y” => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
rc, chns, cnames = stan(stanmodel, bernoullidata)
and get:
Base.IOError(“could not spawn
/Users/yanivabir/cmdstan/bin/stansummary --csv_file=bernoulli_summary.csv bernoulli_samples_1.csv bernoulli_samples_2.csv bernoulli_samples_3.csv bernoulli_samples_4.csv: no such file or directory (ENOENT)”, -2)
Stan.jl caught above exception in Stan’s ‘stansummary’ program.
This is a usually caused by the setting:
Sample(save_warmup=true, thin=n)
in the call to stanmodel() with n > 1.
Looking at the folder, the four sample csv files are there, but there is not summary.csv file.
It then prints chns as if everything is ok.
Any help much appreciated!