Hi everyone,
I am trying to run brms (package version 2.13.0) on a SAS Grid computing cluster (x86_64 GNU/Linux). After some initial problems in setting up the C++ toolchain, I successfully tested the RStan C++ toolchain by running
example(stan_model, package = “rstan”, run.dontrun = TRUE)
I also can get the following simple example using the epilepsy data to compile:
data("epilepsy", package = "brms")
fit <- brm(count ~Trt, data = epilepsy, chains = 1, silent = FALSE)
Because I haven’t specified the underlying model, it automatically fits the Gaussian family. However, when I try to choose another family, e.g., Poisson, it seems like it starts and finishes sampling but then hangs up, with no error messages or warnings and without returning the model results after hours:
fit <- brm(count ~Trt, family = poisson(link = "log"), chains = 1, silent = FALSE)
This example runs without problems on my personal computer which makes me think that it might be still a configuration issue. So, possibly it’s an issue with RStan and not brms. I am just not sure what exactly to do now and was wondering if anyone could give me some advice?
Output:
SAMPLING FOR MODEL '0c2f4a4fdf0b3ef31f90532329a52e6b' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 1: Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 1: Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 1: Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 1: Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 1: Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 1: Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 1: Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.1 seconds (Warm-up)
Chain 1: 0.11 seconds (Sampling)
Chain 1: 0.21 seconds (Total)
Chain 1:
Here are some information about the compiler and the session, in case it’s helpful:
gcc (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
**Session info**
setting value
version R version 3.6.0 (2019-04-26)
os Red Hat Enterprise Linux
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2024-12-17
**Packages**
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 3.6.0)
askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 3.6.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0)
bayesplot 1.7.2 2020-05-28 [1] CRAN (R 3.6.0)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 3.6.0)
bridgesampling 1.0-0 2020-02-26 [1] CRAN (R 3.6.0)
brio 1.1.0 2020-08-31 [1] CRAN (R 3.6.0)
brms * 2.13.0 2020-05-27 [1] CRAN (R 3.6.0)
Brobdingnag 1.2-5 2018-03-18 [1] CRAN (R 3.6.0)
callr 3.5.1 2020-10-13 [1] CRAN (R 3.6.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 3.6.0)
cli 3.6.2 2023-12-11 [1] CRAN (R 3.6.0)
coda 0.19-4 2020-09-30 [1] CRAN (R 3.6.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
colourpicker 1.1.0 2020-09-14 [1] CRAN (R 3.6.0)
commonmark 1.9.1 2024-01-30 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 3.6.0)
curl 4.3 2019-12-02 [1] CRAN (R 3.6.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
diffobj 0.3.2 2020-10-05 [1] CRAN (R 3.6.0)
digest 0.6.27 2020-10-24 [1] CRAN (R 3.6.0)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 3.6.0)
DT 0.16 2020-10-13 [1] CRAN (R 3.6.0)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 3.6.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 3.6.0)
evaluate 0.23 2023-11-01 [1] CRAN (R 3.6.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 3.6.0)
future 1.26.1 2022-05-27 [1] CRAN (R 3.6.0)
generics 0.1.0 2020-10-31 [1] CRAN (R 3.6.0)
ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 3.6.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0)
globals 0.15.0 2022-05-09 [1] CRAN (R 3.6.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 3.6.0)
highr 0.8 2019-03-20 [1] CRAN (R 3.6.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 3.6.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 3.6.0)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 3.6.0)
igraph 1.2.6 2020-10-06 [1] CRAN (R 3.6.0)
inline 0.3.16 2020-09-06 [1] CRAN (R 3.6.0)
isoband 0.2.2 2020-06-20 [1] CRAN (R 3.6.0)
jsonlite 1.7.1 2020-09-07 [1] CRAN (R 3.6.0)
knitr 1.46 2024-04-06 [1] CRAN (R 3.6.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 3.6.0)
later 1.1.0.1 2020-06-05 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 3.6.0)
listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0)
loo 2.3.1 2020-07-14 [1] CRAN (R 3.6.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 3.6.0)
markdown 1.12 2023-12-06 [1] CRAN (R 3.6.0)
MASS 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.0)
Matrix 1.6-1.1 2023-09-18 [1] CRAN (R 3.6.0)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 3.6.0)
mgcv 1.8-28 2019-03-21 [1] CRAN (R 3.6.0)
mime 0.9 2020-02-04 [1] CRAN (R 3.6.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 3.6.0)
nleqslv 3.3.2 2018-05-17 [1] CRAN (R 3.6.0)
nlme 3.1-139 2019-04-09 [1] CRAN (R 3.6.0)
openssl 1.4.3 2020-09-18 [1] CRAN (R 3.6.0)
packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.0)
parallelly 1.32.0 2022-06-07 [1] CRAN (R 3.6.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 3.6.0)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 3.6.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 3.6.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.0)
praise 1.0.0 2015-08-11 [1] CRAN (R 3.6.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0)
processx 3.5.3 2022-03-25 [1] CRAN (R 3.6.0)
promises 1.1.1 2020-06-09 [1] CRAN (R 3.6.0)
ps 1.4.0 2020-10-07 [1] CRAN (R 3.6.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 3.6.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp * 1.0.11 2023-07-06 [1] CRAN (R 3.6.0)
RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 3.6.0)
RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 3.6.0)
rematch2 2.1.2 2020-05-01 [1] CRAN (R 3.6.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 3.6.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 3.6.0)
rmarkdown 2.5 2020-10-21 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 3.6.0)
rstan * 2.21.2 2020-07-27 [1] CRAN (R 3.6.0)
rstantools 2.1.1 2020-07-06 [1] CRAN (R 3.6.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 3.6.0)
scales 1.3.0 2023-11-28 [1] CRAN (R 3.6.0)
shiny 1.5.0 2020-06-23 [1] CRAN (R 3.6.0)
shinyjs 2.0.0 2020-09-09 [1] CRAN (R 3.6.0)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 3.6.0)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 3.6.0)
sourcetools 0.1.7 2018-04-25 [1] CRAN (R 3.6.0)
StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 3.6.0)
stringi 1.5.3 2020-09-09 [1] CRAN (R 3.6.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 3.6.0)
sys 3.4 2020-07-23 [1] CRAN (R 3.6.0)
testthat 3.0.0 2020-10-31 [1] CRAN (R 3.6.0)
threejs 0.3.3 2020-01-21 [1] CRAN (R 3.6.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 3.6.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 3.6.0)
tinytex 0.27 2020-11-01 [1] CRAN (R 3.6.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0)
V8 4.4.2 2024-02-15 [1] CRAN (R 3.6.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 3.6.0)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0)
waldo 0.2.3 2020-11-09 [1] CRAN (R 3.6.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 3.6.0)
xfun 0.43 2024-03-25 [1] CRAN (R 3.6.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0)
xts 0.12.1 2020-09-09 [1] CRAN (R 3.6.0)
yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.0)
zoo 1.8-8 2020-05-02 [1] CRAN (R 3.6.0)