{"id":353,"date":"2014-02-28T13:17:22","date_gmt":"2014-02-28T13:17:22","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=353"},"modified":"2014-02-28T13:22:44","modified_gmt":"2014-02-28T13:22:44","slug":"hpc-lampredi-software-update-jags-v3-4-0","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=353","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 JAGS v3.4.0"},"content":{"rendered":"

JAGS 3.4.0,\u00a0\u00a0Just Another Gibbs Sampler.\u00a0 It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation\u00a0 not wholly unlike\u00a0BUGS<\/a>.<\/p>\n

http:\/\/mcmc-jags.sourceforge.net\/<\/a><\/p>\n

 <\/p>\n

---------------------------------------------------------------------------------<\/code><\/p>\n

\n

$ module load apps\/jags<\/p>\n

apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

| — libs\/gcc\/system<\/p>\n

|\u00a0 \u00a0 * –> OK<\/p>\n

|<\/p>\n

OK<\/p>\n

$ ls $JAGSDIR<\/p>\n

bin\u00a0 include\u00a0 lib\u00a0 libexec\u00a0 share<\/p>\n

 <\/p>\n

$ ls $JAGSBIN<\/p>\n

jags<\/p>\n

 <\/p>\n

$ jags<\/p>\n

Welcome to JAGS 3.4.0 on Fri Feb 28 13:13:48 2014<\/p>\n

JAGS is free software and comes with ABSOLUTELY NO WARRANTY<\/p>\n

Loading module: basemod: ok<\/p>\n

Loading module: bugs: ok<\/p>\n

 <\/p>\n

---------------------------------------------------------------------------------<\/code><\/p>\n

\n

$ module whatis apps\/jags<\/p>\n

apps\/jags\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 :<\/p>\n

Title: JAGS<\/p>\n

Summary: Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation<\/p>\n

License: GPLv2<\/p>\n

Group: Bioinformatics<\/p>\n

URL: http:\/\/mcmc-jags.sourceforge.net\/<\/p>\n

 <\/p>\n

Name: jags<\/p>\n

Version: 3.4.0<\/p>\n

Module: apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

Module path: \/opt\/gridware\/etc\/modules\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

Package path: \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

 <\/p>\n

Repository: file:\/opt\/gridware\/etc\/repos\/local<\/p>\n

Package: apps\/jags\/3.4.0@08f607cc<\/p>\n

Last update: 2014-02-28<\/p>\n

 <\/p>\n

Builder: root@headnode1.lampredi.cluster.local<\/p>\n

Build date: 2014-02-28T11:48:10<\/p>\n

Build modules: libs\/atlas\/3.10.0\/gcc-4.4.6<\/p>\n

Compiler: compilers\/gcc\/system<\/p>\n

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n

Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n

 <\/p>\n

For further information, execute:<\/p>\n

 <\/p>\n

module help apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

---------------------------------------------------------------------------------<\/code><\/p>\n

\n

$ module help apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

 <\/p>\n

———– Module Specific Help for ‘apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0’ —————————<\/p>\n

======== JAGS ========<\/p>\n

Analysis of Bayesian hierarchical models using Markov Chain<\/p>\n

Monte Carlo simulation<\/p>\n

=====================<\/p>\n

This module sets up your environment for the use of the ‘jags’<\/p>\n

application. This module sets up version ‘3.4.0’ of the<\/p>\n

application.<\/p>\n

 <\/p>\n

>> SYNOPSIS <<<\/p>\n

JAGS is Just Another Gibbs Sampler.\u00a0 It is a program for analysis of<\/p>\n

Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)<\/p>\n

simulation not wholly unlike BUGS.\u00a0 JAGS was written with three aims<\/p>\n

in mind:<\/p>\n

* To have a cross-platform engine for the BUGS language.<\/p>\n

* To be extensible, allowing users to write their own functions,<\/p>\n

distributions and samplers.<\/p>\n

* To be a plaftorm for experimentation with ideas in Bayesian<\/p>\n

modelling.<\/p>\n

 <\/p>\n

>> LICENSING <<<\/p>\n

This package is made available subject to the following license(s):<\/p>\n

GPLv2<\/p>\n

Please refer to the website for further details regarding licensing.<\/p>\n

 <\/p>\n

>> FURTHER INFORMATION <<<\/p>\n

More information about this software can be found at the website:<\/p>\n

http:\/\/mcmc-jags.sourceforge.net\/<\/a><\/p>\n

For further details regarding this module, including the environment<\/p>\n

modifications it will apply, execute:<\/p>\n

 <\/p>\n

module show apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

>> GET STARTED <<<\/p>\n

Please refer to the website for further details on usage of this<\/p>\n

package.<\/p>\n

---------------------------------------------------------------------------------<\/code><\/p>\n

\n

$ module show apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

——————————————————————-<\/p>\n

\/opt\/gridware\/etc\/modules\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0:<\/p>\n

module-whatis<\/p>\n

Title: JAGS<\/p>\n

Summary: Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation<\/p>\n

License: GPLv2<\/p>\n

Group: Bioinformatics<\/p>\n

URL: http:\/\/mcmc-jags.sourceforge.net\/<\/p>\n

 <\/p>\n

Name: jags<\/p>\n

Version: 3.4.0<\/p>\n

Module: apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

Module path: \/opt\/gridware\/etc\/modules\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

Package path: \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

 <\/p>\n

Repository: file:\/opt\/gridware\/etc\/repos\/local<\/p>\n

Package: apps\/jags\/3.4.0@08f607cc<\/p>\n

Last update: 2014-02-28<\/p>\n

 <\/p>\n

Builder: root@headnode1.lampredi.cluster.local<\/p>\n

Build date: 2014-02-28T11:48:10<\/p>\n

Build modules: libs\/atlas\/3.10.0\/gcc-4.4.6<\/p>\n

Compiler: compilers\/gcc\/system<\/p>\n

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n

Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n

 <\/p>\n

For further information, execute:<\/p>\n

module help apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

module-prereq libs\/gcc\/system<\/p>\n

module-conflict apps\/jags<\/p>\n

setenv JAGSDIR \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0<\/p>\n

setenv JAGSBIN \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/bin<\/p>\n

setenv JAGSLIB \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/lib<\/p>\n

setenv JAGSINCLUDE \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/include<\/p>\n

prepend-path LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/lib<\/p>\n

prepend-path MANPATH \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/share\/man<\/p>\n

prepend-path PKG_CONFIG_PATH \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/lib\/pkgconfig<\/p>\n

prepend-path PATH \/opt\/gridware\/pkg\/apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0\/bin<\/p>\n

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014<\/p>\n

\n

Lampredi HPC
\nigm-lampredi-users@ncl.ac.uk<\/p>\n

IGM IT
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

JAGS 3.4.0,\u00a0\u00a0Just Another Gibbs Sampler.\u00a0 It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation\u00a0 not wholly unlike\u00a0BUGS. http:\/\/mcmc-jags.sourceforge.net\/   ——————————————————————————— $ module load apps\/jags apps\/jags\/3.4.0\/gcc-4.4.6+atlas-3.10.0 | — libs\/gcc\/system |\u00a0 \u00a0 * –> OK | OK $ ls $JAGSDIR bin\u00a0 include\u00a0 lib\u00a0 libexec\u00a0 share   $ ls $JAGSBIN […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21],"class_list":["post-353","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/353","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=353"}],"version-history":[{"count":5,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/353\/revisions"}],"predecessor-version":[{"id":355,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/353\/revisions\/355"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=353"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=353"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=353"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}