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--- software:r:farber [2017-10-23 18:05] – created sraskar
+++ software:r:farber [2019-08-30 15:11] – anita
@@ Line 27: / Line 27: @@
 for use.
-^r-cran         |All CRAN modules in CRAN which compile and install cleanly   \
+^r-cran         |All CRAN modules in CRAN which compile and install cleanly without any additional dependencies.  N.B. all below library packs require this CRAN modle as a base.|
-                 without any additional dependencies.  N.B. all below library \
+^r-bioconductor |The full suite of[[http://www.bioconductor.org/|Bioconductor]] modules. |
-			  packs require this CRAN modle as a base.                      |
+^r-fftw         |CRAN modules which need FFTW |
-^r-bioconductor |The full suite of                                            \
+^r-gsl          |CRAN modules which need GSL(GNU Scientific Library), GLPK(GNU Linear Programming Kit), or MPFR(GNU MPFR Library)  |
-                 [[http://www.bioconductor.org/|Bioconductor]] modules.        |
+^r-gdal         |CRAN modules which need GDAL(Geospatial Data Abstraction Library) and GEOS(Geometry Engine, Open Source)  |
-^r-fftw         |CRAN modules which need FFTW                                  |
+^r-jags         |CRAN modules which need JAGS(Just Another Gibbs Sampler) and the r-gsl library mentioned above. |
-^r-gsl          |CRAN modules which need GSL(GNU Scientific Library),         \
+^r-mpi          |CRAN modules which need the OpenMPI libraries for parallel computing.  |
-                 GLPK(GNU Linear Programming Kit), or MPFR(GNU MPFR Library)   |
+^r-netcdf       |CRAN modules which need NetCDF, HDF4, HDF5, and UDUNITS libraries. |
-^r-gdal         |CRAN modules which need GDAL(Geospatial Data Abstraction     \
+^r-all          |In addition to loading all the previously mentioned bundles, and CRAN module with multiple dependencies from the above list is also included. |
-                 Library) and GEOS(Geometry Engine, Open Source)               |
+^r-cuda         |Not currently available. |
-^r-jags         |CRAN modules which need JAGS(Just Another Gibbs Sampler) and \
-                 the r-gsl library mentioned above.                            |
-^r-mpi          |CRAN modules which need the OpenMPI libraries for parallel   \
-                 computing.                                                    |
-^r-netcdf       |CRAN modules which need NetCDF, HDF4, HDF5, and UDUNITS      \
-                 libraries.                                                    |
-^r-all          |In addition to loading all the previously mentioned bundles, \
-                 and CRAN module with multiple dependencies from the above    \
-			  list is also included.                                        |
-^r-cuda         |Not currently available.                                      |
 === Searching for modules ===
@@ Line 255: / Line 245: @@
 === Using IT's udbuild environment ===
-IT developed a formalization for installing modules called [[farber:udbuild]]
+IT developed a formalization for installing modules called [[/abstract/farber/install_software|udbuild]]
 which can simplify the installation of modules.  Here is an example ''udbuild''
 script which can be used to install a personal R library.
@@ Line 297: / Line 287: @@
 This script will attempt to build the cuda capable R modules using the
 cuda 6.5 version into ''$WORKDIR/sw/r/add-ons/r3.1.1/testing/default-cuda-6.5''.
+====== R script in batch ======
+==== matmul.R script ====
+Consider the simple R script file to multiply a small 3x3 matrix
+<file R matmul.R>
+# Calculate and print small matrix AA'
+a <- matrix(1:12,3,4);
+a%*%t(a)
+</file>
+Let's test this R script using ''Rscript'' from the command line on a compute node.  Don't forget to set your [[general/userguide/04_compute_environ?&#using-workgroup-and-directories|workgroup]] to define your cluster group or //investing-entity// compute nodes before you use ''qlogin'' to get on a compute node. For example,
+<code bash>
+workgroup -g it_css
+qlogin
+vpkg_require r/3
+Rscript matmul.R
+</code>
+The output to the screen:
+<code>
+     [,1] [,2] [,3]
+[1,]  166  188  210
+[2,]  188  214  240
+[3,]  210  240  270
+</code>
+To return to the head node, type
+<code bash>
+exit
+</code>
+==== matmul.qs file ====
+To run a R script in batch instead of on the command line has nearly the same steps.
+Consider the queue submission script file:
+<file matmul.qs>
+#$ -N matmultiply
+# Add vpkg_require commands after this line:
+vpkg_require r/3
+# Syntax: Rscript [options] filename.R [arguments]
+Rscript matmul.R
+</file>
+Now to run the R script simply submit the job from the head node with the
+''qsub'' command.
+<code>
+qsub matmul.qs
+</code>
+You should see a notification that your job was submitted.  Something like this
+<code bash>
+Your job 2283886 ("matmultiply") has been submitted
+</code>
+After the code completes the output of the script will appear in the file
+''matmultiply.o2283886'' because ''-N matmultiply'' defines the name of the job in ''matmul.qs'' and appears in the notification above as ''("matmultiply")'' with ''2283886'' assigned as the job ID. Type
+<code>
+more matmultiply.o2283886
+</code>
+to display the contents of the output file on the screen.  For example,
+<code>
+Adding dependency `x11/RHEL6.1` to your environment
+Adding package `r/3.0.2` to your environment
+     [,1] [,2] [,3]
+[1,]  166  188  210
+[2,]  188  214  240
+[3,]  210  240  270
+</code>