Warning
Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
To have a cross-platform engine for the BUGS language
To be extensible, allowing users to write their own functions, distributions and samplers.
To be a platform for experimentation with ideas in Bayesian modeling
After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx or qrsh command. To make JAGS available in this session, run one of the following module commands
module load apps/gcc/4.8.2/JAGS/4.2
module load apps/gcc/4.8.2/JAGS/3.4
module load apps/gcc/4.8.2/JAGS/3.1
You can now run the jags command
jags
Welcome to JAGS 4.2.0 on Thu Jun 30 09:21:17 2016
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
.
rjags and runjags are CRAN packages that provide an R interface to jags. They are not installed in R by default.
After connecting to iceberg (see Establishing a SSH connection), start an interactive session with the qrshx command. Run the following module commands
module load compilers/gcc/4.8.2
module load apps/gcc/4.8.2/JAGS/4.2
module load apps/R/3.3.0
Launch R by typing R and pressing return. Within R, execute the following commands
install.packages('rjags')
install.packages('runjags')
and follow the on-screen inctructions. Answer y to any questions about the creation of a personal library should they be asked.
The packages will be stored in a directory called R within your home directory.
You should only need to run the install.packages commands once. When you log into the system in future, you will only need to run the module commands above to make JAGS available to the system.
You load the rjags packages the same as you would any other R package
library('rjags')
library('runjags')
If you received an error message such as
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/te1st/R/x86_64-unknown-linux-gnu-library/3.2/rjags/libs/rjags.so':
libjags.so.3: cannot open shared object file: No such file or directory
Error: package or namespace load failed for 'rjags'
the most likely cause is that you forget to load the necessary modules before starting R.
JAGS 4.2 was built with gcc 4.8.2
Installed using install.sh
This module file was installed as /usr/local/modulefiles/apps/gcc/4.8.2/JAGS/4.2
JAGS 3.4 was built with gcc 4.8.2
module load compilers/gcc/4.8.2
tar -xvzf ./JAGS-3.4.0.tar.gz
cd JAGS-3.4.0
mkdir -p /usr/local/packages6/apps/gcc/4.8.2/JAGS/3.4
./configure --prefix=/usr/local/packages6/apps/gcc/4.8.2/JAGS/3.4
make
make install
JAGS 3.1 was built with gcc 4.8.2
module load compilers/gcc/4.8.2
tar -xvzf ./JAGS-3.1.0.tar.gz
cd JAGS-3.1.0
mkdir -p /usr/local/packages6/apps/gcc/4.8.2/JAGS/3.1
./configure --prefix=/usr/local/packages6/apps/gcc/4.8.2/JAGS/3.1
make
make install