Hi all,
When trying to run the sundials-compiled PyStan (following @ahartikainen’s help on the Stan Discourse) I’ve had some trouble compiling my pystan model.
functions {
real[] SIR(real t, real[] y, real[] theta,
real[] x_r, int[] x_i) {
real S = y[1];
real I = y[2];
real R = y[3];
real beta = theta[1];
real gamma = theta[2];
real dS_dt = -beta * I * S;
real dI_dt = beta * I * S - gamma * I;
real dR_dt = gamma * I;
return {dS_dt, dI_dt, dR_dt};
}
}
data {
int<lower = 1> n_obs; // number of days observed
int<lower = 1> n_pop; // population size
int y[n_obs]; // data, total number of infected individuals
real t0; // initial time point
real ts[n_obs]; // time points observed
int<lower=0> n_pred; // number of cases to predict forward
real ts_pred[n_pred]; // future time points
}
transformed data {
real x_r[0];
int x_i[0];
int n_states = 3;
}
parameters {
real<lower = 0> theta[2]; // theta[1]: beta, theta[2]: gamma
real<lower = 1e-6, upper = 1> S0; // initial fraction of susceptible individuals
}
transformed parameters{
real<lower = -1e-6, upper = 1> y_hat[n_obs, n_states]; // ODE solutions
real<lower = 0, upper = 1> y_init[n_states]; // initial SIR fractions
real<lower = 0> lambda[n_obs];
y_init[1] = S0 - 1e-6;
y_init[2] = 1 - S0 + 1e-6;
y_init[3] = 0;
//y_hat = integrate_ode_rk45(SIR, y_init, t0, ts, theta, x_r, x_i);
y_hat = integrate_ode_bdf(SIR, y_init, t0, ts, theta, x_r, x_i);
for (i in 1:n_obs) {
lambda[i] = ((1-2e-6)*y_hat[i, 2] + 1e-6)* n_pop;
}
}
model {
theta ~ lognormal(0, 1);
S0 ~ beta(1, 1);
y ~ poisson(lambda);
}
generated quantities {
real R_0 = theta[1] / theta[2]; // Basic reproduction number
vector[n_pred] y_pred;
vector[n_pred] lambda_pred;
real y_init_pred[3] = y_hat[n_obs, ]; // New initial conditions
real t0_pred = ts[n_obs]; // New time zero is the last observed time
real y_hat_pred[n_pred, 3];
y_hat_pred = integrate_ode_rk45(SIR, y_init_pred, t0_pred, ts_pred, theta, x_r, x_i);
for (i in 1:n_pred) {
lambda_pred[i] = ((1-2e-6)*y_hat_pred[i, 2] + 1e-6) * n_pop;
y_pred[i] = poisson_rng(lambda_pred[i]);
}
}
When I try compiling my model:
stan_sm = pystan.StanModel(
model_name='sir_model',
model_code=sir_model,
verbose=True
)
I get the following error:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-7-e12ef6b38546> in <module>
2 model_name='sir_model',
3 model_code=sir_model,
----> 4 verbose=True
5 )
~/anaconda3/envs/pystan_stiff/lib/python3.6/site-packages/pystan/model.py in __init__(self, file, charset, model_name, model_code, stanc_ret, include_paths, boost_lib, eigen_lib, verbose, obfuscate_model_name, extra_compile_args, allow_undefined, include_dirs, includes)
524 os.dup2(orig_stderr, sys.stderr.fileno())
525
--> 526 self.module = load_module(self.module_name, lib_dir)
527 self.module_filename = os.path.basename(self.module.__file__)
528 # once the module is in memory, we no longer need the file on disk
~/anaconda3/envs/pystan_stiff/lib/python3.6/site-packages/pystan/model.py in load_module(module_name, module_path)
109 pyximport.install()
110 sys.path.append(module_path)
--> 111 return __import__(module_name)
112 else:
113 import imp
ImportError: dlopen(/var/folders/cz/pj6fdbtj3fn_fylbgqhx86hjlyt4ss/T/pystan__7lohdvk/stanfit4sir_model_22bf53890dbdc229524a10734025e572_3085698279385622801.cpython-36m-darwin.so, 2): Symbol not found: _fkbjac_
Referenced from: /var/folders/cz/pj6fdbtj3fn_fylbgqhx86hjlyt4ss/T/pystan__7lohdvk/stanfit4sir_model_22bf53890dbdc229524a10734025e572_3085698279385622801.cpython-36m-darwin.so
Expected in: flat namespace
in /var/folders/cz/pj6fdbtj3fn_fylbgqhx86hjlyt4ss/T/pystan__7lohdvk/stanfit4sir_model_22bf53890dbdc229524a10734025e572_3085698279385622801.cpython-36m-darwin.so
On my terminal, additionally, I see:
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
Additionally, output for the CC version of clang is as below:
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /anaconda3/envs/pystan_stiff/bin
Output of gcc --version:
gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
- Operating System=Mac OS X
- Python Version=3.6
- PyStan Version=2.19.1.1