R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MAC OS/X.
Version and Availability
Softenv Keys for R on qb
▶ Display Softenv Keys for R all clusters
▶ Softenv FAQ?
The information here is applicable to LSU HPC and LONI systems.
SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.
System Default Path
When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.
SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.
Viewing Available Packages
Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.
$ softenv These are the macros available: * @default These are the keywords explicitly available: +amber-8 Applications: 'Amber', version: 8 Amber is a +apache-ant-1.6.5 Ant, Java based XML make system version: 1.6. +charm-5.9 Applications: 'Charm++', version: 5.9 Charm++ +default this is the default environment...nukes /etc/ +essl-4.2 Libraries: 'ESSL', version: 4.2 ESSL is a sta +gaussian-03 Applications: 'Gaussian', version: 03 Gaussia ....
Listing of Available Packages
For a more accurate, up to date list, use the softenv command.
Currently there are some caveats to using this tool.
- packages might be out of sync between what is listed and what is actually available
- resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..
This information can be viewed using the softenv command:
Managing Environment with SoftEnv
The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:
To update the environment after modifying this file, one simply uses the resoft command:
R may be run either interactively or as a batch process reading commands from a script file. An interactive command would look like:
$ R [options] [< infile] [> outfile]
A line to run R in a shell script would look like:
R CMD BATCH "--args arg1 arg2" script.R
where script.R is the name of a file containing R commands, and --args gives two arguments that are passed to the script.
The number of possible options is quite large. Please see the online documentation in the Resources section below for all the details on the command line options, and the R scripting language itself.
Last modified: March 25 2014 14:23:08.