R session aborts when using the 'control' argument

I have been successfully running stan models while specifying control arguments (e.g. adapt_delta, max_treedepth) without issue until yesterday. The only thing I can think of that could have affected it is that I installed the mixOmics package via Bioconductor using the steps outlined here: GitHub - mixOmicsTeam/mixOmics: Development repository for the Bioconductor package 'mixOmics '

After this installation, whenever I run a model where I specify the ‘control’ argument, I get an error via an Rstudio popup:
Screen Shot 2021-07-16 at 12.58.37 PM

If I run chains in parallel using

options(mc.cores = detectCores())

Then the chains start sampling and I see the following output and error:

starting worker pid=25403 on localhost:11771 at 13:08:20.600
starting worker pid=25417 on localhost:11771 at 13:08:20.798

SAMPLING FOR MODEL 'simple-model' NOW (CHAIN 1).
Error in unserialize(socklist[[n]]) : error reading from connection

SAMPLING FOR MODEL 'simple-model' NOW (CHAIN 2).

These both happen with the stan() function and the sampling() function.

I have a 2017 Macbook Pro running Big Sur (11.4). Here is my session info after loading the ‘stan’ and ‘parallel’ libraries:

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rstan_2.21.2         ggplot2_3.3.5        StanHeaders_2.21.0-7

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7         pillar_1.6.1       compiler_4.1.0     prettyunits_1.1.1 
 [5] tools_4.1.0        pkgbuild_1.2.0     jsonlite_1.7.2     lifecycle_1.0.0   
 [9] tibble_3.1.2       gtable_0.3.0       pkgconfig_2.0.3    rlang_0.4.11      
[13] DBI_1.1.1          cli_3.0.0          curl_4.3.2         loo_2.4.1         
[17] gridExtra_2.3      withr_2.4.2        dplyr_1.0.7        generics_0.1.0    
[21] vctrs_0.3.8        stats4_4.1.0       grid_4.1.0         tidyselect_1.1.1  
[25] glue_1.4.2         inline_0.3.19      R6_2.5.0           processx_3.5.2    
[29] fansi_0.5.0        purrr_0.3.4        callr_3.7.0        magrittr_2.0.1    
[33] codetools_0.2-18   matrixStats_0.59.0 scales_1.1.1       ps_1.6.0          
[37] ellipsis_0.3.2     assertthat_0.2.1   colorspace_2.0-2   V8_3.4.2          
[41] utf8_1.2.1         RcppParallel_5.1.4 munsell_0.5.0      crayon_1.4.1   

I uninstalled R and Rstudio and stan and reinstalled them all (making sure to delete all libraries, especially all of the ones that were installed when I installed mixOmics), and shut down and restarted my computer numerous times. The problem persists.

I can fit models perfectly without specifying and control arguments—I can specify ‘chians’, ‘iter’, ‘thin’, etc. and it works, both parallel and serial.

In case it matters, my Makevars file is the following:

CXX14FLAGS += -O3 -mtune=native -arch x86_64 -ftemplate-depth-256

Here is a minimal reproducible example for what’s going on. My stan code is:

data {
  int<lower=0> N;
  vector[N] y;

parameters {
  real mu;
  real<lower=0> sigma;

model {
  y ~ normal(mu, sigma);

My R code is:

library(rstan); library(parallel);

mu <- 1
sigma <- 1
N <- 100
y <- rnorm(N, mu, sigma)
dat_list <- list(N = N, y = y)

# this works!
res <- stan(file = "/Users/austin/Desktop/simple-model.stan",
            data = dat_list)

# this has an error and aborts R
res <- stan(file = "/Users/austin/Desktop/simple-model.stan",
            data = dat_list, 
            control = list(adapt_delta = 0.95))

# for parallel
options(mc.cores = detectCores())

# this works!
res <- stan(file = "/Users/austin/Desktop/simple-model.stan",
            data = dat_list)

# this has an error: "Error in unserialize(socklist[[n]]) : error reading from connection"
res <- stan(file = "/Users/austin/Desktop/simple-model.stan",
            data = dat_list, 
            control = list(adapt_delta = 0.95))

I’m thoroughly baffled by this, especially due to the full reinstallation of R, Rstudio, and Stan. Any ideas and help would be gladly appreciated.

1 Like

I can confirm this on my laptop with OS X. However, I usually don’t run rstan anymore but use cmdstan instead:

m0 <- cmdstan_model("~/Downloads/simple-model.stan")
res <- m0$sample(dat_list, adapt_delta=0.95)

works great.


Does everything run ok if you run R from Terminal? If so, then this is a good reproducible example to use in an issue at the RStudio GitHub repo.

Correction. This is what I get. RStudio does not crash for me.

@torkar Thanks for the help! I successfully ran the model with the adapt_delta argument using cmdstan. I’d never used cmdstan before so I downloaded the cmdstanr R package and installed cmdstan fresh via the install_cmdstan() function. So at least now I can run models using cmdstan. Regular stan still doesn’t work.

@mike-lawrence When I ran stan in the Terminal, it tried to start sampling but then had an error:

SAMPLING FOR MODEL 'simple-model' NOW (CHAIN 1).
Segmentation fault: 11

So I guess it’s not an RStudio issue but instead something else…