Software and package installation

Install software yourself

Build from source

• To build from source use a compiler module
• We have several compiler versions from GNU and INTEL
• check with: $ ml avail gcc and $ ml avail intel
• Guide for compiling serial programs
• Guide for compiling parallel programs
• Available combinations of compilers and parallel libraries

Packages and libraries to scripting programs

• Python, R and Julia all have some centrally installed packages that are available from the modules.
• R has a special module called R_packages, and some Machine Learning python packages are included in the python_ML_packages module.
• If not found there you can try to install those by yourself.

Tip Python packages

• Try Conda first directly on Bianca and PyPI on Rackham.
• We have mirrored all major Conda repositories directly on UPPMAX, on both Rackham and Bianca. These are updated every third day.
• If you want to keep number of files down, use PyPI (pip).
• Also it is easier to get conflicting environments if using both Python module and Conda in parallel.

Conda

• We have mirrored all major Conda repositories directly on UPPMAX, on both Rackham and Bianca. These are updated every third day.

Available Conda channels

• bioconda
• biocore
• conda-forge
• dranew
• free
• main
• pro
• qiime2
• r
• r2018.11
• scilifelab-lts

• Conda user guide

Python packages with pip

• Installing with pip

R packages

• On UPPMAX the module R_packages is an omnibus package library containing almost all packages in the CRAN and BioConductor repositories.
• As of 2023-05-31, there were a total of 23100 R packages installed in R_packages/4.2.1.
• A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in R_packages/4.2.1

• The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere.

• Installing R packages

Julia packages

• At UPPMAX there is a central library with installed packages.
• This is good, especially when working on Bianca, since you then do not need to install via the wharf.

• A selection of the Julia packages and libraries installed on UPPMAX are:

  CSV
  CUDA
  MPI
  Distributed
  IJulia
  Plots
  PyPlot
  DataFrames
  

• Installing julia packages

Containers

Info

• Containers let you install programs without needing to think about the computer environment, like
  • operative system
  • dependencies (libraries and other programs) with correct versions
• Everything is included
• Draw-backs
  • you install also things that may be already installed
  • therefore, probably more disk space is needed

Singularity

See the UPPMAX Singularity user guide

Docker

Docker will unfortunately not work on the clusters, since it requires root permission.

More info

• Singularity user guide
• Part from Bianca course but applicable also on Rackham

Spack

• The UPPMAX staff has already other ways to install most software applications.
• Please use Spack only if other ways to install your tool is not possible or very difficult, e.g. requiring very many dependencies and it is not available through, e.g. Easybuild.
• UPPMAX Spack user guide

Own development

• You may have your own code that you want to run on UPPMAX.
• Guide for compiling serial programs
• Guide for compiling parallel programs
• Available combinations of compilers and parallel libraries
• User guide for debuggers
• User guide for profilers

Run own scripts or programs

Unless your script or program is in the active path, you run it by the full path or ./<file> if you are in the present directory.

Summary

Keypoints

• You have got an overview of the procedures to install packages/libraries and tools on Bianca through the wharf
• If you feel uncomfortable or think that many users would benefit from the software, ask the support to install it.