Building your own software¶

CCR maintains a global suite of software available to all users via Modules. If you need a particular software package or library that's not available as a module or a container you can ask us to build it or attempt to build yourself. This document provides some pointers on building custom modules for your group or personal use.

Software build requests¶

Users can request software be installed by CCR staff by submitting a new issue on GitHub, where you'll be asked to fill out a form and provide information about your research group and the software you'd like to use. We ask that you first search CCR's GitHub software issues to see if another user has already submitted a request. Users are strongly encourage to vote on which software is to be installed by adding a "like" or "thumbs up" on the issue. Due to limited staffing we'll be installing more popular software requests first so it's important you vote. Please refer to our software installation policy prior to submitting a build request.

About EasyBuild¶

CCR uses EasyBuild for building software. EasyBuild is a software build and installation framework that helps manage software on High Performance Computing (HPC) systems in an efficient and reproducible way.

EasyBuild is written in python and uses simple human readable build recipes. EasyBuild provides a vast repository of build recipes for all kinds of software shared with the greater HPC community. There's a good chance that the software you're looking for already has an EasyBuild recipe.

EasyBuild recipes, called easyconfigs, are text files (python syntax) used to instruct EasyBuild how to build software. You can browse the community supported recipes on EasyBuild's GitHub repository.

The standard EasyBuild recipe filename format is:

<software name>-<version>-<compiler>-<compiler version>.eb

Example:

  SAMtools-1.16.1-GCC-11.2.0.eb

   Software Name: SAMtools
         Version: 1.16.1
        Compiler: GCC
Compiler Version: 11.2.0

When building software with EasyBuild, it's very important to pay attention to the compiler and compiler version as it will be much easier to build software for a compiler CCR already supports.

Easybuild provides more information on the EasyBuild website.

EasyBuild will take care of compiling, installing, and creating a Modulefile for you. CCR provides EasyBuild as it's own module and has pre-configured EasyBuild with the appropriate settings for CCR's environment. To load CCR's "easybuild" module simply run this:

$ module load easybuild

Building a new software module¶

If you can't find the software you're looking for from the available software provided by CCR, you can attempt to build it yourself. You can use easybuild to search for recipes to build. For example:

$ module load easybuild
$ eb -S some_package_name

# For example
$ eb -S samtools
 * $CFGS1/s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb
 * $CFGS1/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb
 * $CFGS1/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb
 * $CFGS1/s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb
 * $CFGS1/s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb
 * $CFGS1/s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb

Select the recipe, be sure to select the one for a supported compiler toolchain if necessary and build the software by running the following command:

# Check what are the dependencies
$ eb SAMtools-X.X.X-GCC-Y.Y.Y.eb -M

# Build the the software and all the dependencies at once
$ eb SAMtools-X.X.X-GCC-Y.Y.Y.eb --robot

# Build only the software (no deps)
$ eb SAMtools-X.X.X-GCC-Y.Y.Y.eb

Once the above command is complete you should see your new module when you run module avail under the Your Modules section:

$ module avail
----- Your personal Compiler-dependent avx512 modules ---------
   samtools/X.X.X (bio)

There is an excellent tutorial on how to build software with EasyBuild on the EasyBuild website.

Building modules for your group¶

By default, easybuild modules are stored in $HOME/.local/easybuild/$CCR_VERSION. This should be fine for small software libraries and personal use. However, the downsides are your group members will not be able to see your modules and you can easily fill up your home directory quota. To build software modules in your projects space, simply set the CCR_BUILD_PREFIX env variable to your desired location before running easybuild. For example:

$ module load easybuild
$ export CCR_BUILD_PREFIX=/projects/academic/[YourGroupName]/easybuild
# verify the install path. Note CCR_VERSION will always be appended to the path
$ eb --show-config | grep installpath
installpath             (E) = /projects/academic/[YourGroupName]/easybuild/2023.01

To ensure your new custom modules show up in module avail, you can set the CCR_CUSTOM_BUILD_PATHS env variable. Note: this only has to be done once.

# Also set the env variable so new modules get picked up in the menu
$ export CCR_CUSTOM_BUILD_PATHS=$CCR_BUILD_PREFIX

# To ensure this path gets picked up on login
$ mkdir -p $HOME/.ccr
$ echo $CCR_CUSTOM_BUILD_PATHS > ~/.ccr/modulepaths