Common Steps Before Installing Software

Before you proceed to installing software on HPC, check HPC Software Guide which lists the Software already installed in HPC. Follow these steps if it is not installed:

Reserve a Node

Reserve either a compute node or a GPU node

• If your software does not require a GPU, then reserve a compute node

  • srun -N 1 -n 1 --mem=4gb --pty /bin/bash

• Some packages allow compilation in parallel. To compile in parallel you will need more tasks. Choose a different value for the flag -n. These will be the number of threads that you can specify at compilation. 

If your software requires a GPU, then check what GPU node you will need and reserve it. For example, if your software requires a GPU K40, then you would allocate it like this:

• 1. srun -p gpu -C gpuk40 --gres=gpu:1 -N 1 -n 1 --mem=4gb --pty /bin/bash

Choose a hierarchy

Choosing a hierarchy is really important as it determines which compiler you will be using: 

• MPI for Intel: this is the default setting. If all the dependencies you need are in the Intel + MPI hierarchy, this is your setting. 

• MPI for GCC: if your software requires MPI and you want to use a GCC compiler, or your dependencies are in this hierarchy. From the default setting run:

  • module swap intel gcc

• This will change the hierarchy 

  • Intel: If your software and its dependencies do not require MPI and you want to use an Intel Compiler.

  • To set up just the Intel compiler from any hierarchy, run: 

    • module purge 

    • module load intel

  • GCC: If your software and its dependencies do not require MPI and they are all under the GCC hierarchy.

  • To set up just the GCC compiler from any hierarchy, run: 

    • module purge 

    • module load gcc

Will You Need the Base Module?

Deciding if you need the base module or not is quite important. If one of your dependencies is a more recent version of a RHEL7 package, then you will need base. It may be that the base module will be loaded as a dependency of one of the dependencies of your software.

We recommend using the system libraries as much as possible.

NOTE: Compiling with base can bring some compilation errors. Please read carefully the page about Working With the Base Module.

Load the Dependencies

Before you attempt to compile software, make sure that all the dependencies are loaded.

For more information, visit HPC Software Installation Guide.