Software

Core Software and Libraries

The Campus Cluster maintains a variety of core software and libraries to support computing activities. Software can be added to a user’s environment using modules.

Campus Cluster core software and libraries list (click to expand/collapse)

Campus Cluster core software and libraries
Software	Version
Anaconda	5.2.0 anaconda/2 (python 2.7.15) anaconda/3 (python 3.6.5)
	2018.12 anaconda/2018-Dec/2 (python 2.7.15) anaconda/2018-Dec/3 (python 3.6.8)
	2019.10 anaconda/2019-Oct/2 (python 2.7.16) anaconda/2019-Oct/3 (python 3.7.4)
	2020.07 anaconda/2020-Jul/3 (python 3.8.3)
	2021.05 anaconda/2021-May/3 (python 3.8.8)
	2022.05 anaconda/2022-May/3 (python 3.9.12)
	2023.03 anaconda/2023-Mar/3 (python 3.10.9)
Boost	1.68.0 1.71.0
CMake	3.12.0 3.18.4
Cuda	9.2 10.0 11.6
Emacs	26.1 27.1
FFTW	3.3.8 (Intel MPI, MVAPICH2, OpenMPI)
FFTW	3.3.9 (Intel MPI, MVAPICH2, OpenMPI)
GCC	7.2.0 (default) 8.2.0 9.2.0 11.2.0 12.2.0
Git	2.19.0
GSL	2.5
Intel compilers	18.0 19.0 20.4
Intel MKL	2018 (Intel 18 compilers) 2019 (Intel 19 compilers) 2020 (Intel 20 compilers)
Intel MPI	2018 (Intel 18 compilers) 2019 (Intel 19 compilers) 2020 (Intel 20 compilers)
JDK (Oracle/Sun)	1.8 (default) 9 10 11 12 13
Mathematica	11 12
MATLAB	9.4 9.5 9.7
MVAPICH2	2.3 2.3.4
OpenBLAS	0.2.20 0.3.7 0.3.12
OpenMPI	3.1.1 4.0.5 4.1.0 4.1.1 4.1.4
PAPI	5.6.0
PETSc	3.10.0 3.11.1 3.15.4
Python	2.7.15 (python/2) 3.7.0 (python/3) 3.9.16 (python/3.9.16)
R	3.5.1 3.6.2 4.0.1 4.0.2 4.0.3 4.1.1 4.2.2
Singularity	3.2.0 3.8.5
SVN	1.10.3
Valgrind	3.13.0
VIM	8.1

Managing Your Environment (Modules)

The module command is a user interface to the Modules package. The Modules package provides for the dynamic modification of the user’s environment via modulefiles. A modulefile contains the information needed to configure the shell for an application. Modules are independent of the user’s shell, so both tcsh and bash users can use the same commands to change the environment.

Useful module commands
Command	Description
`module avail`	lists all available modulefiles
`module list`	lists currently loaded modulefiles
`module help modulefile`	help on module modulefile
`module display modulefile`	display information about modulefile
`module load modulefile`	load modulefile into current shell environment
`module unload modulefile`	remove modulefile from current shell environment
`module swap modulefile1 modulefile2`	unload modulefile1 and load modulefile2

To include particular software in the environment for all new shells, edit your shell configuration file ($HOME/.bashrc for bash users and $HOME/.cshrc for tcsh users) by adding the module commands to load the software that you want to be a part of your environment. After saving your changes, you can source your shell configuration file or log out and then log back in for the changes to take effect.

Note: Order is important. With each module load, the changes are prepended to your current environment paths.

For additional information on Modules, see the module and modulefile man pages or visit the Modules SourceForge page.

R on the Campus Cluster

Introduction

R is a programming language and software environment for statistical computing and graphics. R and its libraries implement a wide variety of statistical and graphical techniques, including linear and non-linear modelling, classical statistical tests, time-series analysis, classification, clustering, and others. R is easily extensible through functions and extensions, and the R community is noted for its active contributions in terms of packages. R is also an interpreted language in which users typically access it through a command line interpreter.

R and R packages are available via the Comprehensive R Archive Network (CRAN), a collection of sites which carry identical material, consisting of the R distribution(s), the contributed extensions, documentation for R, and binaries.

Versions

See the Core Software and Libraries for the versions of R installed on the Campus Cluster.

Adding R to Your Environment

Each R installation on the Campus Cluster has a modulefile that you can use to load a specific version of R into your user environment. You can see the available versions of R by typing module avail R on the command line.

The latest version of R available on the Campus Cluster can be loaded into your environment by typing module load R.

To load a specific version, you will need to load the corresponding modulefile. See Managing Your Environment (Modules), for more information about modules.

Installing Add-on Packages (in user specified locations)

Any R add-on package not available in the system installation (see Viewing Installed R Packages for information on viewing the list) can be installed from the CRAN in a user specified location that you have write access to with just a few easy steps.

Generally, when installing any software there are a few things to consider:

Home directory disk usage quotas (see Storage Areas).
Will the software be used by multiple users in my group?
Project space is the recommended location to install software (see Investor-Specific Software Installation).
Does the desired software have dependencies/requirements?
Is the prerequisite software already installed?

Installation Command Syntax

Note

The install.packages() command is run within R. You need to load (module load r) and run (r) R prior to using install.packages().

R package installations, for the most part, are straight forward. Minimally, all that is needed is the name of the package that is to be installed, but installation location and the repository can also be specified.

Command (“Package Name”, “Location”, “Repository”)

install.packages('package_name', '/path/to/r_libraries', 'Repository URL')
Behavior: Installs the package downloaded from the specified repository in the specified location.

Command (“Local Filename”, “Location”, “Repository”)

install.packages('package_name.tar.gz', '/path/to/r_libraries', repos = NULL)
Behavior: Installs the local package(file) in the specified location specifying no repository(NULL)

When the installation location and the repository URL are not specified, R packages are installed in a default location and the R installation process prompts to choose from a list of repositories.

R packages downloaded manually from the CRAN can be installed by specifying the local filename and omitting the repository URL (specifying NULL).

Using Rscript

To run R commands without starting an R session the command Rscript can be used (as we show in the examples on this page).

As a scripting front end for R, Rscript enables the use of R via shell scripts and scripting applications.

Installation Steps

Below are steps with examples of the actual commands that can be run on the Campus Cluster. In these steps ~/Rlibs is used for the location to install user specific add-on packages (The tilde “~” means the user’s home directory—i.e., $HOME).

Note

It is assumed that these steps are being run under the default BASH shell. When using a different shell, the syntax for that shell should be used where appropriate.

Create a directory for your R packages:
```
mkdir ~/Rlibs
```
Load the R modulefile:
```
module load R/4.2.2_sandybridge
```
Set the R library environment variable (R_LIBS) to include your R package directory:
```
export R_LIBS=~/Rlibs:${R_LIBS}
```

Use the install.packages function to install your R package:

Rscript -e "install.packages('RCurl', '~/Rlibs', 'https://cran.r-project.org')"

If the environment variable R_LIBS is not set and a directory is not specified with the install.packages command, then R packages will be installed under ~/R/x86_64-unknown-linux-gnu-library by default. This R subdirectory structure is created automatically.

The R_LIBS environment variable will need to be set every time when logging in to the Campus Cluster if the user’s R package location is to be visible to an R session. The following can be added to a user’s ~/.bashrc file to remove the need to set the R_LIBS environment variable with every login session to the Campus Cluster:

if [ -n $R_LIBS ]; then
      export R_LIBS=~/Rlibs:$R_LIBS
else
      export R_LIBS=~/Rlibs
fi

Warnings and Error Messages

R packages that are not available in the current CRAN (Comprehensive R Archive Network) or if the name of the package is misspelled, tend to generate a message similar to the following:

[golubh1 ~]$ Rscript -e "install.packages('phybase','~/Rlibs', 'https://cran.r-project.org')"
Warning message:
package 'phybase' is not available (for R version 3.2.2)

Searching the CRAN site for your desired R package may provide links to archived versions that are not available in the current CRAN. In this case the specific archived R package can be downloaded and installed from the local file using the same command but omitting the repository URL (specifying NULL).

Some R packages have dependencies and require them to be installed first and will generate an error message similar to the following:

[golubh1 ~]$ Rscript -e "install.packages('phybase_1.1.tar.gz', '~/Rlibs',  repos = NULL)"
ERROR: dependency 'ape' is not available for package 'phybase'
* removing '/home/jdoe/Rlibs/phybase'
Warning message:
In install.packages("phybase_1.1.tar.gz", repos = NULL) :
installation of package 'phybase_1.1.tar.gz' had non-zero exit status

Installing the required R package first, then the desired R package resolves this issue.

Viewing Installed R Packages

The library() command can be used to view all user and system installed R packages (user installed packages are only visible to R when the $R_LIBS environment variable is set).

[golubh1 ~]$ Rscript -e "library()"

Packages in library '/home/jdoe/Rlibs':

R6                      Classes with reference semantics
RCurl                   General network (HTTP/FTP/...) client interface
                        for R
...
stringr                 Simple, Consistent Wrappers for Common String
                        Operations
whisker                 {{mustache}} for R, logicless templating


Packages in library '/usr/local/R/4.2.2/lib64/R/library':

KernSmooth              Functions for kernel smoothing for Wand & Jones
                        (1995)
MASS                    Support Functions and Datasets for Venables and
                        Ripley's MASS
...
tools                   Tools for Package Development
utils                   The R Utils Package

Python on the Campus Cluster

Introduction

Python is an interpreted, high-level, general-purpose programming language.

Python and Python packages are available via the The Python Package Index (PyPI), which hosts thousands of third-party modules for Python. Both Python’s standard library and the community-contributed modules allow for endless possibilities.

Anaconda also provides a Python environment with python packages.

Versions

See the Core Software and Libraries for the versions of Python and Anaconda installed on the Campus Cluster.

Adding Python to Your Environment

Each Python installation on the Campus Cluster has a corresponding modulefile that can be used to load a specific version of Python into your user environment.

You can see the available versions of Python by typing module avail python and/or module avail anaconda on the command line. See Managing Your Environment (Modules) for more information about modules.

Installing Python Packages (in user specified locations)

Generally, any Python package not available in the system installation (see Viewing Installed Python Packages for information on viewing the list) can be installed from the Python Package Index (PyPI) in a user specified location that you have write access to with just a few easy steps.

Generally, when installing any software there are a few things to consider:

Home directory disk usage quotas (see Storage Areas).
Will the software be used by multiple users in my group?
Project space is the recommended location to install software (see Investor-Specific Software Installation).
Does the desired software have dependencies/requirements?
Is the prerequisite software already installed?

Campus Cluster users must install software/libraries into user write-able locations like their home directory, their group’s project space or their scratch space.

Note

The example instructions below use scratch space. Please note that software installed in scratch space is not permanent and may be removed at any time. We recommend that you install in your group’s project space. For a persistent installation, users should replace the path to their scratch space with the path to their project space in the instructions below`

Warning

There is a 5GB quota (disk usage) on all user’s home directories, so we do not recommend that users install software/libraries in their home directories since multiple Python packages (or an Anaconda installation) can push the disk usage over quota very quickly.

Additionally, users should use one of the installation methods listed below (Python or Anaconda). Combining installation methods can cause unexpected behavior/errors.

Installation Command Syntax

Under Python:

To Install a specific python package into a user location, use the pip install command with the -t option.

module load python/3

mkdir -p /home/${USER}/scratch/mypython3

pip install -t /home/${USER}/scratch/mypython3  phonopy

export PYTHONPATH=/home/${USER}/scratch/mypython3:${PYTHONPATH}

Users will have to run the above “export…” command after loading python into their user environment with the module command on future login sessions. This allows the Campus Cluster’s python installation to see the user’s specific python packages.

Alternatively, users can add two commands to their ${HOME}/.bashrc file so that Python is setup for their user environment every time they login to the Campus Cluster.

module load python/3

export PYTHONPATH=/home/${USER}/scratch/mypython3:${PYTHONPATH}

You can run the “pip install -t…” command for each python package/library you want to install.

Under Anaconda:

Note

The following commands will create an anaconda environment in your scratch directory (which is temporary), we recommend that you use your group’s project space to install software/libraries specific to your needs.

To create a minimal anaconda environment with python and any dependencies, type the following. Other packages can be used in place of “python” if you want to base your environment around that specific package, for example, “tensorflow”.

mkdir -p /scratch/users/$USER/my.conda.dir

cd ${HOME}

ln -s /scratch/users/${USER}/my.conda.dir .conda

module load anaconda/2023-Mar/3

conda create -n my.anaconda python

conda info -e

source activate my.anaconda

conda info -e

conda install pytorch

conda list

Use the command source activate environment_name instead of conda init or conda activate environment_name to activate your anaconda environment.

To deactivate the anaconda environment, type:

conda deactivate

To create a complete clone anaconda environment, replace

conda create -n my.anaconda python

with

conda create -n my.anaconda anaconda

Viewing Installed Python Packages

After enabling Python in your user environment by loading a Python or Anaconda modulefile, one can view a list of the Python packages installed under the Python/Anaconda installation (including your own installed packages) by typing pip list if you have loaded a Python modulefile or conda list if you have loaded an Anaconda modulefile.