RStan is an R interface to Stan. Stan is a platform for modeling.
RStan is installed as an R package and there is nothing too special about it.
First, load the R module you need to use. There are different
options, using different compilers. Do not use an
version, because it requires the intel compilers to work on the nodes
to compile every time you run, and they aren’t available there. If
you load a
goolf R version, it will work (you could work around
this by pre-compiling models, if you wanted):
$ module spider R ... R/3.4.1-goolf-triton-2017a R/3.4.1-iomkl-triton-2017a $ module load R/3.4.1-goolf-triton-2017a
If you change R versions (from intel to gcc) or get errors about
loading libraries, you may have installed incompatible libraries.
~/R directory and reinstalling all of your libraries
is a good first place to start.
You should detect the number of cores with:
Common Rstan problems¶
Models must be compiled on the machine that is running them, Triton or other workstations. The compiled model files aren’t necessarily portable, since they depend on the libraries available when build. One symptom of this problem is error messages which talk about loading libraries and
GLIBC_2.23or some such.
In order to compile models, you must have the compiler available on the nodes. Thus, the Intel compilers (
iomkl) won’t work. It also won’t work if the Intel compiler license servers are down. Using the GNU compiler toolchains are more reliable.