Working with Gridware Applications: R

The following guide will detail the installation of R, along with some of the advanced features of Alces Gridware when working with the R Gridware package.

R Installation

Many different versions of R are available through the Alces Gridware utility - you can see the list of available packages with the alces gridware list function, for example:

[[email protected](hpc1) ~]$ alces gridware list R
base/apps/R/2.15.0  base/apps/R/2.15.1  base/apps/R/2.15.2  base/apps/R/2.15.3
base/apps/R/3.0.0   base/apps/R/3.0.1   base/apps/R/3.1.1   base/apps/R/3.1.2
base/apps/R/3.2.0   base/apps/R/3.2.1   base/apps/R/3.2.2

To install, for example - R version 3.2.2; run the following command:

[[email protected](hpc1) ~]$ alces gridware install R/3.2.2
Installing base/apps/R/3.2.2
ERROR: Unable to satisfy compilation requirements: libs/lapack, libs/blas

The Alces Gridware tool automatically checks dependencies for you - in this case, we do not have some of the required libraries needed to compile the R application. First - install the libs/lapack and libs/blas Gridware packages, you will then be able to proceed with the R 3.2.2 installation:

[[email protected](hpc1) ~]$ alces gridware install R/3.2.2
Installing base/apps/R/3.2.2
 > Preparing package sources
        Download --> R-3.2.2.tar.gz ... SKIP (Existing source file detected)
          Verify --> R-3.2.2.tar.gz ... OK
        Packaged --> Rprofile       ... OK

 > Preparing for installation
           Mkdir ... OK (/var/cache/gridware/src/apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419)
         Extract ... OK

 > Proceeding with installation
         Compile ... OK
           Mkdir ... OK
(/opt/gridware/depots/2b8a9f1c/el7/pkg/apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419)
         Install ... OK
          Module ... OK

Installation complete.

Once the compilation has finished - the R 3.2.2 Gridware package will be available for use, check its availability and load using:

[[email protected](hpc1) ~]$ module avail
---  /opt/gridware/local/el7/etc/modules  ---
  apps/perl/5.18.0/gcc-4.8.5
  apps/perl/5.20.2/gcc-4.8.5
  apps/python/2.7.5/gcc-4.8.5
  apps/python/2.7.8/gcc-4.8.5
  apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
  compilers/gcc/system
  libs/blas/20110419/gcc-4.8.5
  libs/gcc/system
  libs/lapack/3.5.0/gcc-4.8.5
  null
---  /opt/clusterware/etc/modules  ---
  null
  services/gridscheduler
[[email protected](hpc1) ~]$ module load apps/R
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system ... SKIPPED (already loaded)
 |
 OK
[[email protected](hpc1) ~]$ R --version
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

Multiple versions of a package can exist at one time, however only one version of a particular application can be loaded at any one time - to load a different version of R:

[[email protected](hpc1) ~]$ alces module load apps/R/3.1.2
apps/R/3.1.2/gcc-4.8.5+lapack-3.5.0+blas-20110419 ... VARIANT (have alternative: apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419)
[[email protected](hpc1) ~]$ alces module unload apps/R/3.2.2
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419 ...
                                             UNLOADING --> OK
[[email protected](hpc1) ~]$ alces module load apps/R/3.1.2
apps/R/3.1.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system ... SKIPPED (already loaded)
 |
 OK
[[email protected](hpc1) ~]$ R --version
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"

Installation of language libraries

Through the Alces Gridware utility, installation of lanaguage libraries is possible both on a system-wide level, and also on a per-user basis. The following section details both system-wide language library installation, as well as user-level language library installation.

System-wide language libraries: R

As the alces administrator user, or any other sudo enabled user that can switch to root - change to the root user account.

To add R packages, first load the version of R you wish to install packages to - for example apps/R/3.2.2:

[root@login1(hpc1) ~]# module load apps/R/3.2.2
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system
 |    * --> OK
 |
 OK

Next, load the R application - and use the install.packages command to install your desired system-wide packages:

[[email protected](hpc1) ~]# R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> install.packages("randomForest", repos="http://cran.cnr.berkeley.edu")
Installing package into ‘/opt/gridware/share/R/3.2.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.cnr.berkeley.edu/src/contrib/randomForest_4.6-12.tar.gz'
<-- snip -->
> library(randomForest)
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

Once the installation is complete and you have verified the package works as intended, yo ucan check the package is available to other users on the system:

[[email protected](hpc1) ~]$ module load apps/R/3.2.2
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system
 |    * --> OK
 |
 OK
[[email protected](hpc1) ~]$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
<-- snip -->
> library(randomForest)
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

User-specific language libraries: R

Users may also wish to install their own language libraries, these will be unavailable to other users of the environment.

As the user you wish to install an R package for, load the version of R you wish to install the packages for (e.g. apps/R/3.2.2).

After the R application is loaded, use the install.packages("packagename") function to install packages you require - for example:

[[email protected](hpc1) ~]$ module load apps/R/3.2.2
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system ... SKIPPED (already loaded)
 |
 OK
[[email protected](hpc1) ~]$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
<-- snip -->
> install.packages("snow")
Installing package into ‘/home/barney/gridware/share/R/3.2.2’
(as ‘lib’ is unspecified)
<-- snip -->
> library(snow)
> packageVersion("snow")
[1] ‘0.4.1’

The snow package installation was successful - and we can now use it as the barney user. Switching to another user will confirm the user-level installation success, the alces user will not be able to use the snow R package:

[[email protected](hpc1) ~]$ module load apps/R/3.2.2
apps/R/3.2.2/gcc-4.8.5+lapack-3.5.0+blas-20110419
 | -- libs/gcc/system
 |    * --> OK
 |
 OK
[alc[email protected](hpc1) ~]$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
<-- snip -->
> library(snow)
Error in library(snow) : there is no package called ‘snow’