...
For important information and announcements, please follow this page and the messages displayed in the login message.
Access to Helios
We strongly suggest using SSH keys to access the machine! SSH key management can be done through the PLGrid portal. Password access will be disabled in the near future.
Computing resources on Helios are assigned based on PLGrid computing grants. To perform computations on Helios, you must obtain a computing grant through the PLGrid Portal (https://portal.plgrid.pl/) and apply for Helios access.
...
Note that Helios uses PLGrid accounts and grants. Make sure to request the "Helios access" access service in the PLGrid portal.
Helios is using the node job-exclusive policy. This means that nodes are allocated for a dedicated, single job which is using the resources. This also impacts the accounting where the minimum amount of resources used equals to one node.
Helios is built with Slingshot interconnect and nodes of the following specificationis a hybrid cluster. CPU nodes use x86_64 CPUs, while the GPU partition is based on GH200 superchips, which include an Nvidia Grace - ARM CPU and Nvidia Hopper GPU. HPE Slingshot is used as an interconnect. The login01 node uses an x86_64 CPU and RHEL 8. Please keep this in mind when compiling software, etc. Knowing the destination CPU architecture and operating system is important for selecting the proper modules and software. Each architecture has its own set of modules, in order to see the complete list of modules you need to run module avail on a node of a chosen type. Node specification can be found below:
| Partition | Number of nodes | Operating system | CPU | RAM | Proportional RAM for one CPU | Proportional RAM for one GPU | Proportional CPU for one GPU | Accelerator |
|---|---|---|---|---|---|---|---|---|
| plgrid (includes plgrid-long) | 272 | RHEL 8 | 192 cores, x86_64, 2x AMD EPYC 9654 96-Core Processor @ 2.4 GHz | |||||
| 384GB | ||||||||
| 2000MB | n/a | n/a | ||||||
| plgrid-bigmem | 120 | RHEL 8 | 192 cores, x86_64, 2x AMD EPYC 9654 96-Core Processor @ 2.4 GHz | |||||
| 768GB | ||||||||
| 4000MB | n/a | n/a | ||||||
| plgrid-gpu-gh200 | 110 | CrayOS (SLES 15sp5) | 288 cores | |||||
| , aarch64, 4x NVIDIA Grace CPU 72-Core @ 3.1 GHz | 480GB | n/a | ||||||
| 120GB | 72 | 4x NVIDIA GH200 96GB |
Note that Helios will soon be upgraded to RHEL 9. This change will be applied to all CPU and GPU nodes.
Job submission
Helios is using Slurm resource manager, jobs should be submitted to the following partitions:
| Name | Timelimit | Resource type (account suffix) | Access requirements | Description |
|---|---|---|---|---|
| plgrid | 72h | -cpu | Generally available. | Standard partition. |
| plgrid-long | 168h | -cpu | Requires a grant with a maximum job runtime of 168h. | Used for jobs with extended runtime. |
| plgrid-gpu-gh200 | 48h | -gpu-gh200 | Requires a grant with GPGPU resources. | GPU partition. |
If you are unsure of how to properly configure your job on Helios please consult this guide: Job configuration
...
Helios uses a new naming scheme for CPU and GPU computing accounts, which are supplied by the -A parameter in sbatch command. Currently, accounts are named in the following manner:
| Resource | account name |
|---|---|
| CPU | grantname-cpu |
| GPU | grantname-gpu-gh200 |
Please mind that sbatch -A grantname won't work on its own. You need to add the -cpu, -cpu-bigmem, or -gpu-gh200 suffix! Available computing grants, with respective account names (allocations), can be viewed using the hpc-grants command.
...
Available storage spaces are described in the following table:
| Location | Location in the filesystem | Purpose |
|---|---|---|
| $HOME | /net/home/plgrid/<login> | Storing own applications, and configuration files. Limited to 10GB. |
| $SCRATCH | /net/scratch/hscra/plgrid/<login> | High-speed storage for short-lived data used in computations. Data older than 30 days can be deleted without notice. It is best to rely on the $SCRATCH environment variable. |
| $PLG_GROUPS_STORAGE/<group name> | /net/storage/pr3/plgrid/<group name> | Long-term storage for data living for the period of computing grant. Should be used for storing significant amounts of data. |
Current usage, capacity and other storage attributes can be checked by issuing the hpc-fs command.
...
Applications and libraries are available through the modules system. Please note that the module structure was flattened, and module paths have changed compared to Prometheus Modules for ARM and x86 CPUs are not interchangeable, and selecting the right module for the destined architecture is critical for getting software to work! Please load the proper modules on the node, inside of the job script! The list of available modules can be obtained by issuing the command:
module avail
This command should be run on a compute node to get a full list of modules available on the given architecture (node type)! The list is searchable by using the '/' key. The specific module can be loaded by the add command:
...
and the environment can be purged by:
module purge
Modules' names on Helios are case sensitive.
Sample job scripts
Example job scripts are available on this page: Sample scripts
...