Known Issues HPC3

Below is a list issues that we're actively working on. We hope to have these resolved soon. This is intended to be a temporary page.

For differences between the new platforms and Mahuika, see the more permanent differences from Mahuika.

Recently fixed

• The nn_ commands are available. eg nn_seff <jobid>.
• Some filesystem snapshots are available.
• We have a stable IP address range for outgoing connections.
• --gres=ssd works as it did on Mahuika.

Login

Currently, when logging into the new platform using a proxy you will be prompted for authentication twice.

MobaXterm

The session login process of MobaXterm is not compatible with Tuakiri 2-factor authentication.

ssh through a terminal will still be possible with MobaXterm, but it is recommended to use OnDemand for file browsing, file transfer (for files under 9.8 GB) and terminal access if you would normally have used MobaXterm. Watch a demo of how to use MobaXterm on the new platform.

Login nodes

The initial login nodes are smaller than the Mahuika ones, have slower disk I/O, and may not yet have per-user CPU, memory, and /tmp disk limits.

OnDemand (including Jupyter)

The resources dedicated to interactive work via a web browser are smaller, and so computations requiring large amounts of memory or many CPU cores are not yet supported.

Slurm jobs can be submitted, but only from the Clusters > NeSI HPC SHell Access dropdown menu which opens a standard terminal window in the browser. Watch a demo here.

Globus

There are currently no endpoints configured, workflows that make use of Globus will not work.

Filesystem snapshots

Snapshots are happening (eg: ls /home/.snapshots/) but we don't yet have the convenience of symlinks to them from inside a $HOME/.snapshots directory.

Compute nodes

So far there are all the new Genoa nodes but only two of the Milan nodes present, the rest of those being still in Mahuika, or in transit. So please only use the limited Milan resource for small benchmarking tests.

None of the 3 Mahuika hugemem nodes are present yet, but the largest of the new Genoa nodes do have 1.5 TB of memory.

GPUs

No A100 GPUs have been moved yet, so only the new H100 and L4 GPUs are available. To specify the GPU type, use #SBATCH --gpus-per-node=H100:1 (or L4:1)

Software

MATLAB, ANSYS, ABAQUS, and COMSOL make use of external license servers, so won't work until institutional IT department firewall rules have been updated to match out new IP address range.

Cylc has not been installed. You can use these instructions to install it.

QChem and any other software using node locked licences won't work on nodes which are not yet registered with that license.

Delft3D_FM wasn't working in Mahuika's Milan partition so probably needs rebuilding.

As was already the case on the Milan nodes in Mahuika (where they had a Rocky 8 OS), some of our environment modules cause system software to stop working, e.g: load module load Perl and svn stops working. This is usually the case if they load LegacySystem/7 as a dependency. The solutions are to ask us to re-build the problem environment module, or just don't have it loaded while doing other things.

MPI software using 2020 or earlier toolchains eg intel-2020a, may not work correctly across nodes. Trying with more recent toolchains is recommended eg intel-2022a. Please let us know if you find any problems.

email

Slurm options --mail-type is not yet effective.

Internet

As at 7th May Internet connectivity from compute nodes is available but may change and should not be relied upon. Downloads can be done from login nodes as normal.

ssh into Slurm jobs

You cannot yet ssh into compute nodes, even if you are running jobs there. That will break any software which depends on ssh to reach remote compute nodes.

Slurm native profiling

The Slurm option --profile will generate profile data, but that data is as yet only visible to NeSI staff.

WEKA Filesystems

The Filesystems on the new platform are not yet as fast as they will be.