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:
[alces@login1(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:
[alces@login1(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:
[alces@login1(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:
[alces@login1(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
[alces@login1(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
[alces@login1(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:
[alces@login1(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)
[alces@login1(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
[alces@login1(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
[alces@login1(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:
[root@login1(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:
[barney@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
[barney@login1(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:
[barney@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 ... SKIPPED (already loaded)
|
OK
[barney@login1(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:
[alces@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
[alces@login1(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’