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software:r:farber [2018-04-26 13:23] – [personal/program specific R libraries and extensions] sraskar | software:r:farber [2019-08-30 15:11] – anita | ||
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This script will attempt to build the cuda capable R modules using the | This script will attempt to build the cuda capable R modules using the | ||
cuda 6.5 version into '' | cuda 6.5 version into '' | ||
+ | |||
+ | ====== R script in batch ====== | ||
+ | |||
+ | ==== matmul.R script ==== | ||
+ | |||
+ | Consider the simple R script file to multiply a small 3x3 matrix | ||
+ | |||
+ | <file R matmul.R> | ||
+ | # Calculate and print small matrix AA' | ||
+ | a <- matrix(1: | ||
+ | a%*%t(a) | ||
+ | </ | ||
+ | |||
+ | Let's test this R script using '' | ||
+ | |||
+ | <code bash> | ||
+ | workgroup -g it_css | ||
+ | qlogin | ||
+ | vpkg_require r/3 | ||
+ | Rscript matmul.R | ||
+ | </ | ||
+ | |||
+ | The output to the screen: | ||
+ | |||
+ | < | ||
+ | [,1] [,2] [,3] | ||
+ | [1,] 166 188 210 | ||
+ | [2,] 188 214 240 | ||
+ | [3,] 210 240 270 | ||
+ | </ | ||
+ | |||
+ | To return to the head node, type | ||
+ | <code bash> | ||
+ | exit | ||
+ | </ | ||
+ | |||
+ | ==== matmul.qs file ==== | ||
+ | |||
+ | To run a R script in batch instead of on the command line has nearly the same steps. | ||
+ | Consider the queue submission script file: | ||
+ | |||
+ | <file matmul.qs> | ||
+ | #$ -N matmultiply | ||
+ | |||
+ | # Add vpkg_require commands after this line: | ||
+ | vpkg_require r/3 | ||
+ | |||
+ | # Syntax: Rscript [options] filename.R [arguments] | ||
+ | Rscript matmul.R | ||
+ | </ | ||
+ | |||
+ | Now to run the R script simply submit the job from the head node with the | ||
+ | '' | ||
+ | |||
+ | < | ||
+ | qsub matmul.qs | ||
+ | </ | ||
+ | |||
+ | You should see a notification that your job was submitted. | ||
+ | |||
+ | <code bash> | ||
+ | Your job 2283886 (" | ||
+ | </ | ||
+ | |||
+ | After the code completes the output of the script will appear in the file | ||
+ | '' | ||
+ | |||
+ | < | ||
+ | more matmultiply.o2283886 | ||
+ | </ | ||
+ | |||
+ | to display the contents of the output file on the screen. | ||
+ | |||
+ | < | ||
+ | Adding dependency `x11/ | ||
+ | Adding package `r/3.0.2` to your environment | ||
+ | [,1] [,2] [,3] | ||
+ | [1,] 166 188 210 | ||
+ | [2,] 188 214 240 | ||
+ | [3,] 210 240 270 | ||
+ | </ | ||