Work Areas
Applications
- Alpine3D/POP-C++
- ATLAS
- CATS
- NAMD
- crypto
- geotop
- GROMACS
- GAMESS
- JOpera/SwissPIT
- ROSETTA
- gpremium
- gmhc_coev
- george
- GFIT_ABC_workflow
- MedGift
- MetaPIGA
- MPI RTE Definition
- R scripts
- Selectome
- Apply with new Application
- New App Testing
- AppPot/UML
- OpenFoam
Data Management
VO
Middleware
Security
Support
Monitoring
Management

Generic R script language support

R script is suported on the SMSCG infrastructure throught the use of a dedicated apppot Virtual image

The base apppot VM privdes the following R packages:

r-base
r-base-dev

End users can download the base apppot image from

run it locally and install all additional packages required

How to create a custimized R apppot image

1. download the apppot base R image

# arccp srm://dpm.lhep.unibe.ch/dpm/lhep.unibe.ch/home/smscg/apppot-0.26.disk_R.img ./apppot-0.26.disk_R.img

2. Start apppot locally for customization ( for additional information on how to start apppot image on local machines please consult http://code.google.com/p/apppot/ )

# apppot-start --apppot ./apppot-0.26.disk_R.im

3. Once logged into the started VM, install all required R packages

4. create an apppot snap-shot

# apppot-snap changes

# change file will be available on host machine

5. prepare the SMSCG job r_script.xrsl

&(executable="/$APPPOT_STARTUP")
( arguments = "--apppot" "apppot.cow,$APPPOT_IMAGE" "--linux" "$APPPOT_KERNEL" "--changes" "changes.tgz" )
( inputfiles = ( "changes.tgz" "./apppot.2011-12-22.changes.tar.gz" ) ("apppot-run" "./_apppot-run"))
( executables = "changes.tgz" "apppot-run")
( stdout = "appot.out" )
( join = "yes" )
( runtimeenvironment = "ENV/APPPOT-0.26" )
( cache = "yes" )
( count = "1" )
( architecture = "x86_64" )
( memory = "2000" )

# where

./apppot.2011-12-22.changes.tar.gz

and

./_apppot-run

are respectively the change file created with apppot-snap and the R driver script to be executed

6. Submit the SMSCG job

# arcsub -d DEBUG -f r_script.xrsl