Workspaces Introduction

HPC data typically is shared data. This could be between students and supervisors, between researchers of a research group, or even between researchers of different institutes. These data needs to be accessible even if people leave the team. Furthermore, these data is usually processed with a set of custom software tools, which need to be easy accessible, share, between the collaborators.

Register new HPC Workspace

Primary Investigators (PIs) can apply for a HPC Worksspace by requesting a new Research Storage share using the following link. Indicate that you will need “Access from UBELIX” and decide if you need addtional “Access via SMB”.

Workspaces provide a group shared environment, including storage with user-defined access, SLURM accounting, and tools. They provide a collaborative environment with user defined access groups:

a primary group with read/write access and
a secondary group with read only access

Each Workspace provides:

group based storage access (data and software)
permanent group storage
temporary group storage with less restricted quota
high bandwidth storage and backup
user-friendly access to a custom software repositories and monitoring tools and
SLURM accounting to that Workspace. Fair share between all accounts

Attention

Please always load the Workspace module, even if only just copying files into it. The module corrects the umask and therewith the created file and directory permissions.

Furthermore, it is good practice to use $WORKSPACE/file1 instead of absolute path /path/to/Workspace/file1

Workspace Software

Workspace modules provide support for user-friendly file system access and custom software stacks in HPC Workspaces The module can also be used to set up HOME for a custom software stack.

Workspace module

The Workspace module adjust the environment to work in a specific HPC Workspace.

module load Workspace

sets the following environment variables (Shortcuts) and Software stacks

There are the following possibilities:

you belong to no Workspace: load module load Workspace_Home to use your software stack in your HOME directory and set $WORKSPACE and $SCRATCH variables to your private directories.
you belong to one Workspace: this Workspace gets loaded when module load Workspace
you belong to multiple Workspaces: you need to specify the Workspace to load using the variable $HPC_WORKSPACE. If not specified, the module presents the possible options, e.g.:
```
$ module load Workspace
Workspaces are available:
    HPC_SW_test, hpc_training, 
Please select and load ONE of the following:
    HPC_WORKSPACE=HPC_SW_test module load Workspace
    HPC_WORKSPACE=hpc_training module load Workspace
```
- Thus you load a specific Workspace using:
```
HPC_WORKSPACE=<WorkspaceName> module load Workspace
```
  There are also ways to load an additional Workspace for an additional software stack, see Additional Software Stacks below.

Shortcuts

The workspace module provides the following variables:

Variable	Function
`$WORKSPACE`	full path to the Workspace. Thus, you can access the workspace using: `cd $WORKSPACE`
`$SCRATCH`	full path to the Workspace SCRATCH directory. Thus you can access it using: `cd $SCRATCH`

Additional Settings

The module provides the following settings for a more user-friendly usage of applications. You may not need to use them directly, but tools like SLURM, Apptainer, Python, and R will use them.

Variable	Function
`$APPTAINER_BINDPATH`	using singularity, the Workspace directory will be bind into the container without manual specification. The `WORKSPACE` variable as well as the `SCRATCH` variable will also be ported into the container. Thus, you can specify locations with `$WORKSPACE` or `$SCRATCH` within the container.
`$PYTHONPATH`	if `Python` or `Anaconda` is loaded beforehand, it is set to: `$WORKSPACE/PyPackages/lib/pythonXXX/site-packages` where `XXX` is the Python major and minor version. And also add the `bin` directory to `$PATH`.
`$PYTHONPACKAGEPATH`	if `Python` or `Anaconda` is loaded beforehand, it is set to: `$WORKSPACE/PyPackages`. This can be used for e.g. `pip install --prefix $PYTHONPACKAGEPATH`
`$CONDA_ENVS_PATH`	therewith conda environments can be created and shared within the Workspace
`$R_LIBS`	therewith additional R packages can be installed and searched in the shared Workspace. The directory need to be created first. See R page

Software stacks

Beside, a set of software packages we provide for our different CPU architecture, the Workspace module provides tools to install custom software stacks within your Workspace. Especially with EasyBuild shortcuts are provided to install and use custom software stacks easily build for all architectures.

For installing packages with EasyBuild, see EasyBuild description. Manual package can also be installed in the similar manner. Adding a Modulefile provides the users to load packages as used to. Please see Installing Custom Software.

As a result all users of the Workspace can use the software packages by loading the Workspace module and the software product module.

Python packages

The Workspace module provides support to install and use Python packages in a shared manner, by installing them into the Workspace.

First load Python/Anaconda3

Python or Anaconda3 module need to be loaded before loading the Workspace module, since variables to be set depend on Python version. Workspace module can also be reloaded, e.g.:

HPC_WORKSPACE=HPC_SW_test module load Workspace
module load Anaconda3
module load Workspace

Conda environments

The Workspace module provides support for creating and using conda environments in the shared Workspace. See Anaconda Conda environments.

R packages

The Workspace module provides support for installing and using additional R packages in the shared Workspace. Thus a package once installed by one user can be used by all Workspace members. See R installing packages.

UMASK

The Workspace module sets the umask to 002. Thus files and directories get group-writeable, e.g.:

-rw-rw-r-- 1 user group 0 Mar 15 15:15 /path/to/file

Additional Software Stacks

The module Workspace_SW_only provide the access to a software stack of an HPC Workspace B while working in an HPC Workspace A.

This could be that a common software stack is provided for multiple (data) Workspaces or that you are trying software packages in your HOME

As an example you could load:

HPC_WORKSPACE=A module load Workspace
HPC_WORKSPACE=B module load Workspace_SW_only

When you want to load packages from your HOME while working in A, you can

HPC_WORKSPACE=$HOME module load Workspace_SW_only
HPC_WORKSPACE=A module load Workspace

Note that the variable HPC_WORKSPACE is cleared after each loading of a Workspace*module. The currently loaded Workspace names are stored in $HPC_WORKSPACE_LOADED for the Workspace module and $HPC_WORKSPACE_SW_ONLY for the Workspace_SW_only module.

Backup

All data in the permanent space (/storage/workspaces/) is protected using daily snapshots and backups.

Scratch will not be protected by snapshots or backups.

Quota

For default and actual quota information use quota tool. More details see File System Quota.

SLURM

Computational work is accounted to a Workspace account. All available resources are equally distributed between workspaces.