Hey,
Rstan is again not working on the Linux server I am using :(
Here the output, any suggestions? Thanks!
> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
> # options(mc.cores = parallel::detectCores())
> # rstan_options(auto_write = TRUE)
>
> utils::sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /software/R/lib64/R/lib/libRblas.so
LAPACK: /software/R/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.21.2 ggplot2_3.3.2 StanHeaders_2.21.0-7
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.7 compiler_4.0.3 prettyunits_1.1.1
[5] tools_4.0.3 pkgbuild_1.1.0 jsonlite_1.7.1 lifecycle_0.2.0
[9] tibble_3.0.4 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.9
[13] cli_2.2.0 parallel_4.0.3 curl_4.3 loo_2.3.1
[17] gridExtra_2.3 withr_2.3.0 dplyr_1.0.2 generics_0.1.0
[21] vctrs_0.3.5 stats4_4.0.3 grid_4.0.3 tidyselect_1.1.0
[25] glue_1.4.2 inline_0.3.16 R6_2.5.0 processx_3.4.4
[29] fansi_0.4.1 callr_3.5.1 purrr_0.3.4 magrittr_2.0.1
[33] codetools_0.2-16 scales_1.1.1 ps_1.4.0 ellipsis_0.3.1
[37] matrixStats_0.57.0 assertthat_0.2.1 colorspace_2.0-0 V8_3.4.0
[41] RcppParallel_5.0.2 munsell_0.5.0 crayon_1.3.4
>
> system("g++ --version")
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> Sys.which("g++")
g++
"/bin/g++"
>
> readLines(file.path(getwd(), ".R", "Makevars"))
[1] "# created by rstan"
[2] "CXX14FLAGS=-O3 -march=native -mtune=native -fPIC"
[3] "CXX14=/opt/rh/devtoolset-8/root/usr/bin/g++"
[4] ""
>
> modelscript <- "
+ // saved as schools.stan
+ data {
+ int<lower=0> J; // number of schools
+ real y[J]; // estimated treatment effects
+ real<lower=0> sigma[J]; // standard error of effect estimates
+ }
+ parameters {
+ real mu; // population treatment effect
+ real<lower=0> tau; // standard deviation in treatment effects
+ vector[J] eta; // unscaled deviation from mu by school
+ }
+ transformed parameters {
+ vector[J] theta = mu + tau * eta; // school treatment effects
+ }
+ model {
+ target += normal_lpdf(eta | 0, 1); // prior log-density
+ target += normal_lpdf(y | theta, sigma); // log-likelihood
+ }
+
+ "
>
> schools_dat <- list(J = 8,
+ y = c(28, 8, -3, 7, -1, 1, 18, 12),
+ sigma = c(15, 10, 16, 11, 9, 11, 10, 18))
>
> fit <- stan(model_code = modelscript, data = schools_dat)
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: dyn.load(libLFile)
2: cxxfunction(sig = sig, body = body, plugin = plugin, includes = includes, settings = settings, ..., verbose = verbose)
3: pkgbuild::with_build_tools(cxxfunction(sig = sig, body = body, plugin = plugin, includes = includes, settings = settings, ..., verbose = verbose), required = rstan_options("required") && !identical(Sys.getenv("WINDOWS"), "TRUE") && !identical(Sys.getenv("R_PACKAGE_SOURCE"), ""))
4: cxxfunctionplus(signature(), body = paste(" return Rcpp::wrap(\"", model_name, "\");", sep = ""), includes = inc, plugin = "rstan", save_dso = save_dso | auto_write, module_name = paste("stan_fit4", model_cppname, "_mod", sep = ""), verbose = verbose)
5: stan_model(file, model_name = model_name, model_code = model_code, stanc_ret = NULL, boost_lib = boost_lib, eigen_lib = eigen_lib, save_dso = save_dso, verbose = verbose)
6: stan(model_code = modelscript, data = schools_dat)
An irrecoverable exception occurred. R is aborting now ...