CommunityData:Hyak software installation

You will often find that Hyak is missing software that you need to do you work. This page includes documentation on building those:

R packages

To install a R package that's not available globally, you can check out a build node, and install the package locally. Here's how to do it:

$ build_machine
$ R

This will start R, where you can install a package in the usual way. The build node has access to the Internet, so it will be able to download the required source packages, etc.

> install.packages('lme4')

Python Packages

Our setup on Mox provides the Anaconda python distribution.

Using an anaconda python distribution has important implications for how you install packages. While in normal python, you would install python packages using `pip`, when you use an anaconda distribution you should use `conda` to install packages. Conda also has some fancy features like virtual environments for using different versions of python or different versions of packages in different projects. The problem with using conda is that it does not include all the packages you might want to use. If you want to install a python package that is missing from conda, you can use pip.

Importantly, you should prefer to install software using conda over pip.

Conda Documentation Pip Documentation

It's often a good idea to create new environments for installing software you will use in each project. This way you can use the latest and greatest versions of packages, but you'll still be able to run code in your old projects. To create a new conda environment:

   conda create -n my_root

Then add the following to your .bashrc to use this environment automatically by default.

   if [ -z $(conda info --env | grep my_root | grep \*) ]; then
       source activate my_root
   fi

Conda doesn't like it when you try to activate an environment that is already active.

Conda modifies your prompt in a possibly annoying way. To disable this behavior run the command:

   $ conda config --set changeps1 False

Custom modules

Software on Hyak can be outdated, or in some cases, not available at all. In some of these situations, it may be possible to use environment modules to install and run software without necessitating administrative (root) privileges. For example, it is possible to have and run the newest version of R that is installed in a central, shared directory, and it is even possible to have multiple versions of R available in parallel. The following subsection shows how to do this. Ordinarily, this should not be necessary on a day-to-day basis.

Installing and making available a custom module

 Note: If you are using screen to run and manage your builds, keep in mind that screen drops a few environment variables such as LD_LIBRARY_PATH, which may mess up your build process. You should check that all the relevant environment variables are set before starting your build.

The first step toward installing and making available a custom module (in this case, R 3.5.0) is to spin up the build node, download R, compile it with a specific prefix, and install it.

$ build_machine
$ module load contrib/texlive/2017  # loads the texlive module that is helpful for generating R documentation
$ module load contrib/openblas/0.2.20  # loads the openblas library, which speeds up some R operations significantly
$ wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
$ tar xzvf R-3.5.0.tar.gz
$ cd R-3.5.0
$ ./configure --prefix=/gscratch/comdata/modules/sw/R/3.5.0  --without-x --enable-R-shlib --with-lapack --with-blas="-L/sw/contrib/openblas/0.2.20/lib -lopenblas"
$ make
$ make install

The --prefix option to ./configure tells the build scripts that R is going to be installed in /gscratch/comdata/modules/sw/R/3.5.0. This follows a convention that we picked—software in modules should go into /gscratch/comdata/modules/sw/{SOFTWARE_NAME}/{SOFTWARE_VERSION}. The --prefix option is the most important flag for ./configure—any other flag or option will be specific to the software being installed.

The second step is to write a modulefile. This contains the metadata about our module. Edit the file /gscratch/comdata/modules/modulefiles/R/3.5.0 to contain the following

#%Module1.0####################################################################
##
proc ModulesHelp { } {
        puts stderr "\tModule providing R 3.5.0."
}

module-whatis "Module providing R 3.5.0."

module load contrib/openblas/0.2.20 # this loads any module dependencies
prepend-path    PATH            /gscratch/comdata/modules/sw/R/3.5.0/bin
prepend-path    MANPATH         /gscratch/comdata/modules/sw/R/3.5.0/share/man

Note that the filename follows a similar convention as --prefix earlier (/gscratch/comdata/modules/modulefiles/{SOFTWARE_NAME}/{SOFTWARE_VERSION}). This file sets up the PATH and MANPATH environment variables appropriately so that the specified version of R can be accessed and run as needed. There are many more directives that can go into the modulefile—see man modulefile for details on those directives.

Once this file is written out, the module avail command should list R/3.5.0 as an available module. This is because the module system is set up to look inside /gscratch/comdata/modules/modulefiles for module files, thanks to the MODULEPATH variable that is set through .bashrc. The command module load R/3.5.0 should make R available and ready for use. To avoid running module load R/3.5.0 whenever you log in, you can add the command at the end of your .bashrc file (after the section that sets MODULEPATH).