Preliminary access essentials

Content

Support

Please contact the PLGrid Helpdesk: https://helpdesk.plgrid.pl/ regarding any difficulties in using the cluster.

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.

If your grant is active, and you have applied for the service access, the request should be accepted in about half an hour. Please report any issues through the helpdesk.

Machine description

Available login nodes:

• ssh <login>@login01.helios.cyfronet.pl

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 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. Node specification can be found below:

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:

If you are unsure of how to properly configure your job on Helios please consult this guide: Job configuration

Accounts and computing grants

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:

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.

Resource allocated on Helios doesn't use normalization, which was used on Prometheus and previous clusters. 1 hour of CPU time equals 1 hour spent on a computing core with a proportional amount of memory (consult the table above). The billing system accounts for jobs with more memory than the proportional amount. If the job uses more memory for each allocated CPU than the proportional amount, it will be billed as it would have used more CPUs. The billed amount can be calculated by dividing the used memory by the proportional memory per core and rounding the result to the closest and larger integer. Jobs on CPU partitions are always billed in CPU hours.

The same principle was applied to GPU resources, where the GPU-hour is a billing unit, and there are proportional memory per GPU and proportional CPUs per GPU defined (consult the table above).

The cost can be expressed as a simple algorithm:

cost_cpu    = job_cpus_used * job_duration
cost_memory = ceil(job_memory_used/memory_per_cpu) * job_duration
final_cost  = max(cost_cpu, cost_memory)

and for GPUs, where a GPU has the respective amount of memory per GPU and CPUs per GPU, respectively:

cost_gpu    = job_gpus_used * job_duration
cost_cpu    = ceil(job_cpus_used/cpus_per_gpu) * job_duration
cost_memory = ceil(job_memory_used/memory_per_gpu) * job_duration
final_cost  = max(cost_gpu, cost_cpu, cost_memory)

Storage

Available storage spaces are described in the following table:

Current usage, capacity and other storage attributes can be checked by issuing the hpc-fs command.

System Utilities

Please use the following commands to interact with the account and storage management system:

• hpc-grants - shows available grants, resource allocations, consumed resourced
• hpc-fs - shows available storage
• hpc-jobs - shows currently pending/running jobs
• hpc-jobs-history - shows information about past jobs

Software

Applications and libraries are available through the modules system. 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:

module add openmpi/4.1.1-gcc-11.2.0

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

More information

Helios is following Prometheus' configuration and usage patterns. Prometheus documentation can be found here: https://kdm.cyfronet.pl/portal/Prometheus:Basics