Storage Overview & Usage Guidelines
The HPC is a little different that your desktop at home when it comes to storage, not just computing power. It’s a shared resource, so we cant store everybody’s data for all time - there just isn’t enough space. So, before we start putting files onto the HPC, its best you know where to put them in the first place.
On DeepThought, are three main storage tiers. Firstly our bulk storage is the ‘Scratch’ area - and is slower, spinning Hard-Disk Drives (HDD’s). The next storage tier is the ‘Cluster’ parallel filesystem. For distributed jobs, or jobs that required lots of staged files, this filesystem is the standard high-speed and low-latency HPC filesystem. Be aware that it is smaller that /scratch, and as such, is a transient filesystem. Finally, there are hyper-fast NVMe Solid-State Drives (SSD’s) located at /local. For the exact specifications and capacities, see the System Specifications.
We also integrate into R-Drive to allow you access to your Research Data Storage allocations. This is an automatic process for any shares you have access to.
There is a critical differences between these three locations, so please read this page carefully.
The HPC Job & Data Workflow, along with links to the new Data-Workflow Management Portal are under construction and will be linked here when completed.
Storage Accessibility Overview
As general guide, the following table presents the overall storage for the HPC.
Individual Compute Nodes
~1TB (400GB on Node019)
Head Node | Share Dependant
Due to an Upstream Kernel Bug, R-Drive integration is currently unavailable. Please use your file transfer program of choice from a wired desktop to move files from the HPC to R-Drive in a single operation. The HPC Team is activly working on rebuilding the integration.
The HPC is classed as volatile storage. Your research data and datasets that you wanted backed up MUST be moved to /RDrive, or off the HPC.
The following sections will go over the individual storage location/mounts along with some general guidelines of what should be stored where.
Scratch is your working space and ‘Large Dataset Storage’ As you can see from the table above it have far more storage capacity than /home. If you need to store a large data-set, then it should live in here.
What to store in /scratch
Here is a rough guide as to what should live in your /scratch/$FAN directory. In general, anything large, bulky and only needed for a little while should go here.
Job Working Data-sets
Large Intermediate Files
Cluster is the new, high speed parallel filesystem for DeepThought, deployed using BeeGFS. It is highly recommended that you take advantage of high speeds available to reduce the I/O times associated with /scratch - so please read this section carefully.
When performing parallel jobs, to prevent congestion, its best to have a random back-off to your job-scripts. This will take you stage-in times down from up to 30 minutes to less than 3 minutes. An example of this random backoff is below:
sleep $(echo $RANDOM%30 | bc)
The directories you can write to in /cluster are controlled by SLURM. When your job starts, SLURM sets multiple environment variables and creates directories for you to use on this filesystem. See the environment variables sections of the SLURM Guide for more information.
Once you job completes, is cancelled, or errors out, SLURM removes then entire directory of your job. That means, if you do not move your data from the /cluster filesystem, you will lose all of it. This is by design, and the HPC Team cannot recover any data lost this way.
When this quota is exceeded, files can still be written, but the HPC Team is notified of the user and their associated usage.
What to store in /cluster?
Your working data sets
Temporary job files
Results, before you copy them back to /scratch
Your ‘home’ directories. This is a small amount of storage to store your small bits and pieces. This is the analogous to the Windows ‘Documents’ folder. At a command prompt, your home directory will be shortened to ~/.
What to store in /home
Here is a rough guide as to what should live in your /home/$FAN directory. In general, you want small, little things is here.
‘Small’ Results from Jobs
‘Small’ Data-Sets (<5GB)
Local is the per-node, high speed flash storage that is specific to each node.
What to Store in /local
Only transient files should live on /local. Anything that your job is currently working on can be on /local. Once your job has finished with these files, they should be copied (or moved) to /scratch. The directory you were working in on /local should then cleaned, removing all files from your job - is you use the automatic SLURM created directories, then this is done for you.