December 18, 2020


  • Filesystem
    • Paths
    • Quotas
    • Usage
  • Software
    • Module System
    • Installs
    • Management
  • Job Scheduling
    • Node
    • Partition
    • Limits
    • Jobs

Filesystem: Paths


Filesystem: Paths

  • Symlink ( dotted lines) - A shortcut to another directory or file

  • Mount ( Local/ Shared) - An entry point to a disk or storage device (ie. 'C:/' or Google Drive)

Filesystem: Paths

Case sensitive

All paths and commands are case sensitive, an uppercase letter is not the same as a lowercase letter.

Path Types

  • Absolute path - Full path from root to current working directory
  • Relative path - Partial path or non-absolute path (current directory implied)

Filesystem: Quotas

All storage has limits.

  • Local Storage (ie. laptop hard drive)

    Only exists on a single machine (node) and is limited by disk size.

  • Shared Storage (ie. Google Drive)

    Exists accross all machines (nodes) and is limited by a quota.

Filesystem: Usage

Make workshop directory, if it does not already exist:

mkdir -p ~/workshop_dir

Check directory size:

du -hs ~/workshop_dir

Check local node storage:

df -h /tmp
df -h /scratch

Filesystem: Usage

Software: Module System

This system allows multiple versions of software to be loaded and unloaded.

To view software that is available:

module avail

To search for a specific software:

module avail samtools
# OR
hpcc-software samtools

Software: Module System

Software: Installs


For a basic Python package (pypi) you can use pip to install it:

pip install PKGNAME --user

For example, here is how you would install the camelcase package:

pip install camelcase --user

Software: Installs

Software: Management

  • Conda - A software management system that allows you to install thousands of software packages and tools, including R and Python languages.

Full instructions regarding conda setup can be found here.

  • Singularity - A Linux container system (similar to Docker) which allows users to prepare a Linux environment from scratch.

Some singularity examples can be found here.

A previous workshop regarding custom software installs utilizing the above technologies can be found here.

Software: Management


List current conda virtual environments:

conda env list

Create a Python 3 environment named python3:

conda create -n python3 python=3

Install Python package with conda:

conda install -n python3 numpy

Note: If package fails to be found, search on the Anaconda Website. After searching click on one of the results and the command for installing will be provided. Remember to add your -n python3 environment name.

Software: Management


After the conda environment is setup and numpy is installed, we can test it with the following:

conda activate python3
python -c 'import numpy as np; a = np.arange(15).reshape(3, 5); print(a)'

Software: Management


Warning: This is a demo, should be used for advanced projects

You may need a singularity image if…

  • You may want to build/control your own Linux environment
  • Your software requires older, or newer, libraries
  • Installation instructions are for Ubuntu

Software: Management


First you must get your own Linux machine, and install Singularity. Perhaps the easiest way to do this is mentioned here.

After this you can use pre-built images or try to build a custom singularity image:


singularity exec docker://ubuntu:latest echo "Hello Dinosaur!"


  1. Create a Singularity definition file
  2. Build container image based on definition file
  3. Run shell inside image to test

Software Management

Definition File

Make file myLinuxEnv.def with the following content:

bootstrap: docker
From: ubuntu:latest

  apt update
  apt install httpd

Software Management

Build Container Image

Run the following command using defenition file:

singularity build myLinuxEnv.sing myLinuxEnv.def

Software Management


Test the image buy going inside it:

singularity shell myLinuxEnv.sing

Once the Singularity image is tested, transfer it to the cluster (SCP/SFTP), and execute it within a job like so:

module load singularity
singularity exec myLinuxEnv.sing 'cat /etc/lsb-release'

Job Scheduling: Slurm

Job Scheduling: Node

Job Scheduling: Partitions

Job Scheduling: Partitions

  • Default?

    Fallback to this value if not explicitly provided.

  • Maximum?

    Upper limit of what can be requested.

For more details regarding our partitions, please review our Cluster Jobs: Partitions manual page.

Job Scheduling: Status

List all jobs owned by you and status:

squeue -u $USER

List all group jobs and status:

squeue -A $GROUP

Job Scheduling: Limits

List current Slurm limits:


List CPUs currently used by you:


List CPUs currently used by entire group (primary):


Job Scheduling: Jobs


Move into workshop directory:

cd ~/workshop_dir

Download example job submission script:

# Non-Stats
wget -O

# Stats Department
wget -O

Check job submission script contents (use arrow keys to navigate and ctrl+x to quit):


Job Scheduling: Jobs


Submit as non-interactive job:


Submit interactive job:

srun -p short --pty bash -l

# OR

srun -p statsdept --pty bash -l

Job Scheduling: Jobs