Compilation error using brms

Interfaces brms
1

Hi!,
I am fitting a Poisson regression with brms, but I am having problems with the compilation of my model in a cluster. I got the following error message:

Compiling Stan program...
'config' variable 'CPP' is deprecated
icc -E
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from /home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/stan/math/rev/mat/functor/idas_forward_system.hpp(9),
                 from /home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/stan/math/rev/mat/functor/integrate_dae.hpp(5),
                 from /home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/stan/math/rev/mat.hpp(72),
                 from /home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/stan/math.hpp(4),
                 from /home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/src/stan/model/model_header.hpp(4),
                 from file286011e0d7630.cpp(14):
/home/jomartinez/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/stan/math/rev/mat/functor/idas_system.hpp(283): warning #858: type qualifier on return type is meaningless
    const size_t n() { return N_; }
    ^

In file included f
In addition: Warning messages:
1: In system(paste(CPP, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  error in running command
2: In system(cmd, intern = !verbose) :
  running command '/workspace/easybuild/x86_64/software/R/4.0.0-intel-2019b/lib64/R/bin/R CMD SHLIB file286011e0d7630.cpp 2> file286011e0d7630.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

The code that I am running is:

library(brms)
prior1 <- prior(normal(0,10), class = b) +
+   prior(cauchy(0,2), class = sd)
> fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient),
+             data = epilepsy, family = poisson(), prior = prior1)

Some session Info:
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Version of relevant libraries:
[1] brms_2.15.0 Rcpp_1.0.4.6 rstan_2.21.3
[4] ggplot2_3.3.0 StanHeaders_2.21.0-7

Many thanks for your help.
Best,
Joaquín.

2

Hi,
just to be clear - are you able to compile some models in the cluster or are you unable to compile any models?

Will tag @rok_cesnovar as I have little experience with installation issues on Linux

3

Hi!,

Thanks for answering!

I am not able to compile any model… Just took this Poisson regression as an example.

4

Bumping this up, hopefully somebody with more expertise can answer.

5

Sorry we were not able to help you so far. A quick suggestion: you can try if you can get cmdstanr to work (Getting started with CmdStanR • cmdstanr) which is often easier to get going. You can then use options(brms.backend = "cmdstanr") to have brms use cmdstanr instead of rstan

1 Like
6

Sorry for missing this! I’d second @martinmodrak’s suggestion to install cmdstanr and use that as a backend, as it uses a more recent version of Stan which has more features and optimisations.

But let me know if you’d like to troubleshoot the existing rstan installation, and I can help with that as well