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ULHPC User Environment

Your typical journey on the ULHPC facility is illustrated in the below figure.

Typical workflow on UL HPC resources

You daily interaction with the ULHPC facility includes the following actions:

Preliminary setup

  1. Connect to the access/login servers
    • This can be done either by ssh (recommended) or via the ULHPC OOD portal
    • (advanced users) at this point, you probably want to create (or reattach) to a screen or tmux session
  2. Synchronize you code and/or transfer your input data using rsync/svn/git typically
  3. Reserve a few interactive resources with salloc -p interactive [...]
    • recall that the module command (used to load the ULHPC User software) is only available on the compute nodes
    • (eventually) build your program, typically using gcc/icc/mpicc/nvcc..
    • Test your workflow / HPC analysis on a small size problem (srun/python/sh...)
    • Prepare a launcher script <launcher>.{sh|py}

Then you can proceed with your Real Experiments:

  1. Reserve passive resources: sbatch [...] <launcher>
  2. Grab the results and (eventually) transfer back your output results using rsync/svn/git

For more information:

'-bash: module: command not found' on access/login servers

Recall that by default, the module command is (on purpose) NOT available on the access/login servers. You HAVE to be on a computing node (within a slurm job)

Home and Directories Layout

All ULHPC systems use global home directories. You also have access to several other pre-defined directories setup over several different File Systems which co-exist on the ULHPC facility and are configured for different purposes. They are listed below:

Directory Env. file system backup
/home/users/<login> $HOME GPFS/Spectrumscale no
/work/projects/<name> - GPFS/Spectrumscale yes (partial, backup subdirectory)
/scratch/users/<login> $SCRATCH Lustre no
/mnt/isilon/projects/<name> - OneFS yes (live sync and snapshots)

Shell and Dotfiles

The default login shell is bash -- see /etc/shells for supported shells.

ULHPC dotfiles vs. default dotfiles

The ULHPC team DOES NOT populate shell initialization files (also known as dotfiles) on users' home directories - the default system ones are used in your home -- you can check them in /etc/skel/.* on the access/login servers. However, you may want to install the ULHPC/dotfiles available as a Github repository. See installation notes. A working copy of that repository exists in /etc/dotfiles.d on the access/login servers. You can thus use it: 

$ /etc/dotfiles.d/install.sh -h
# Example to install ULHPC GNU screen configuration file
$ /etc/dotfiles.d/install.sh -d /etc/dotfiles.d/ --screen -n   # Dry-run
$ /etc/dotfiles.d/install.sh -d /etc/dotfiles.d/ --screen      # real install

Changing Default Login Shell (or NOT)

If you want to change your your default login shell, you should set that up using the ULHPC IPA portal (change the Login Shell attribute). Note however that we STRONGLY discourage you to do so. You may hit unexpected issues with system profile scripts expecting bash as running shell.

System Profile

/etc/profile contains Linux system wide environment and startup programs. Specific scripts are set to improve your ULHPC experience, in particular those set in the ULHPC/tools repository, for instance:

Customizing Shell Environment

You can create dotfiles (e.g., .bashrc, .bash_profile, or .profile, etc) in your $HOME directory to put your personal shell modifications.

Custom Bash Initialisation Files

On ULHPC system ~/.bash_profile and ~/.profile are sourced by login shells, while ~/.bashrc is sourced by most of the shell invocations including the login shells. In general you can put the environment variables, such as PATH, which are inheritable to subshells in ~/.bash_profile or ~/.profile and functions and aliases in the ~/.bashrc file in order to make them available in subshells. ULHPC/dotfiles bash configuration even source the following files for that specific purpose:

  • ~/.bash_private: custom private functions
  • ~/.bash_aliases: custom private aliases.
Understanding Bash Startup Files order

See reference documentation. That's somehow hard to understand. Some tried to explicit it under the form of a "simple" graph -- credits for the one below to Ian Miell (another one)

This explains why normally all ULHPC launcher scripts start with the following sha-bang (#!) header

#!/bin/bash -l
#
#SBATCH [...]
[...]
That's indeed the only way (i.e. using /bin/bash -l instead of the classical /bin/bash) to ensure that /etc/profile is sourced natively, and thus that all ULHPC environments variables and modules are loaded. If you don't proceed that way (i.e. following the classical approach), you MUST then use the following template you may see from other HPC centers: 
#!/bin/bash
#
#SBATCH [...]
[...]
# Load ULHPC Profile
if [ -f  /etc/profile ]; then
   .  /etc/profile
fi

Since all ULHPC systems share the Global HOME filesystem, the same $HOME is available regardless of the platform. To make system specific customizations use the pre-defined environment ULHPC_CLUSTER variable:

Example of cluster specific settings

case $ULHPC_CLUSTER in
    "iris")
        : # Settings for iris
        export MYVARIABLE="value-for-iris"
        ;;
    "aion")
        : # settings for aion
        export MYVARIABLE="value-for-aion"
        ;;
    *)
        : # default value for
        export MYVARIABLE="default-value"
        ;;
esac

CentOS

Operating Systems

RedHat

The ULHPC facility runs RedHat-based Linux Distributions, in particular:

Thus, you are more than encouraged to become familiar - if not yet - with Linux commands. We can recommend the following sites and resources:

Impact of CentOS project shifting focus starting 2021 from CentOS Linux to CentOS Stream

You may have followed the official announcement on Dec 8, 2020 where Red Hat announced that it will discontinue CentOS 8 by the end of 2021 and instead will focus on CentOS Stream going forward. Fortunately CentOS 7 will continue to be updated until 2024 and is therefore not affected by this change.

While CentOS traditionally has been a rebuild of RHEL, CentOS Stream will be more or less a testing ground for changes that will eventually go into RHEL. Unfortunately this means that CentOS Stream will likely become incompatible with RHEL (e.g. binaries compiled on CentOS Stream will not necessarily run on RHEL and vice versa). It is also questionable whether CentOS Stream is a suitable environment for running production systems.

For all these reasons, the migration to CentOS 8 for Iris (initially planned for Q1 2021) has been cancelled. Alternative approaches are under investigation, including an homogeneous setup between Iris and Aion over Redhat 8.

Discovering, visualizing and reserving UL HPC resources

See ULHPC Tutorial / Getting Started

ULHPC User Software Environment

The UL HPC facility provides a large variety of scientific applications to its user community, either domain-specific codes and general purpose development tools which enable research and innovation excellence across a wide set of computational fields. -- see software list.

We use the Environment Modules / LMod framework which provided the module utility on Compute nodes to manage nearly all software.
There are two main advantages of the module approach:

  1. ULHPC can provide many different versions and/or installations of a single software package on a given machine, including a default version as well as several older and newer version.
  2. Users can easily switch to different versions or installations without having to explicitly specify different paths. With modules, the MANPATH and related environment variables are automatically managed.

ULHPC modules are in practice automatically generated by Easybuild.

EasyBuild (EB for short) is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. A large number of scientific software are supported (at least 2175 supported software packages since the 4.3.2 release) - see also What is EasyBuild?.

For several years now, Easybuild is used to manage the ULHPC User Software Set and generate automatically the module files available to you on our computational resources in either prod (default) or devel (early development/testing) environment -- see ULHPC Toolchains and Software Set Versioning. This enables users to easily extend the global Software Set with their own local software builds, either performed within their global home directory or (better) in a shared project directory though Easybuild, which generate automatically module files compliant with the ULHPC module setup.

ULHPC Environment modules Using Easybuild on ULHPC Clusters

Self management of work environments in UL HPC with Conda

Packages provided through the standard channels of modules and containers are optimized for the ULHPC clusters to ensure their performance and stability. However, many packages where performance is not critical and are used by few users are not provided through the standard channels. These packages can still be installed locally by the users through an environment management system such as Conda.

Contact the ULHPC before installing any software with Conda

Prefer binaries provided through modules or containers. Conda installs generic binaries that may be suboptimal for the configuration of the ULHPC clusters. Furthermore, installing packages locally with Conda consumes quotas in your or your project's account in terms of storage space and number of files.

Contact the ULHPC High Level Support Team in the service portal [Home > Research > HPC > Software environment > Request expertise] to discuss possible options before installing any software.

Conda is an open source environment and package management system. With Conda you can create independent environments, where you can install applications such as python and R, together with any packages which will be used by these applications. The environments are independent, with the Conda package manager managing the binaries, resolving dependencies, and ensuring that package used in multiple environments are stored only once. In a typical setting, each user has their own installation of a Conda and a set of personal environments.

Management of work environments with Conda

Last update: November 13, 2024