Page tree
Skip to end of metadata
Go to start of metadata

Introduction

Snellius under construction at the Amsterdam Science Park

After a very successful 8 years of service, Cartesius will be replaced this year by a new Dutch National Supercomputer called Snellius. 

Snellius will be built by Lenovo and will contain predominantly AMD technology, plus NVIDIA GPUs. A high-level news item on the new system can be read here.

This page will be the main source of information where we will keep you as user updated on the progress of the installation of Snellius and the corresponding transition from Cartesius to Snellius. The purpose of this page is to help you adapt your research schedule to take into account the upcoming transition.

The details of the system configuration and the transition schedule are currently still being decided. 

This page will be continuously updated while Snellius is being prepared to go into production. Please check here regularly for new or updated information on the migration.

What is the timeline for this transition?

The hardware of Snellius will be delivered and installed in tranches. The first hardware has already been delivered to the data center at Amsterdam Science Park and is currently being installed next to Cartesius.

The projected start of production of Snellius will be September 1st. We expect this date will also be the end date of service for Cartesius.

Of course, these dates are only valid when everything goes according to plan and no major delays are encountered in the delivery, installation, setup and acceptance of the system.

What does the Snellius system look like?

Like Cartesius, Snellius will also be a heterogeneous system, with thin nodes, fat nodes, high-memory nodes and a number of nodes with GPU accelerators. Snellius will be delivered in several phases, so the growth of Snellius will follow the anticipated growth in usage of Snellius. The growth phases are as follows.

Phase 1 (Q3 2021)

The hardware installed in this phase provides a peak compute performance of 3.2 PFLOP/s (CPU) + 2.8 PFLOP/s (GPU).

TypeAmountTechnical DetailsMemory/core (GiB)Total #cores

Total #GPU
cards

thin nodes504

AMD Rome 7H12@2.6GHz processor, dual socket,
64 cores/socket

264,512
fat nodes72AMD Rome 7H12@2.6GHz processor, dual socket,
64 cores/socket
89,216
high-memory nodes2AMD Rome 7H12@2.6GHz processor, dual socket,
64 cores/socket,
32256
high-memory nodes2AMD Rome 7H12@2.6GHz processor, dual socket,
64 cores/socket
64256
GPU nodes36

Intel Ice Lake 8360Y@2.4GHz processor, dual socket,
36 cores/socket

4x NVIDIA A100 Tensor Core GPU

7.1


40

2,592


144

total616

76,832144

Phase 2 (Q3 2022)

An extension will be added with more CPU-only thin nodes (future generation AMD EPYC processors, 2 GB per core), with a peak performance of 5.1 PFLOP/s.

Phase 3 (Q3 2023)

There are three options for this extension:

  1. CPU thin nodes (same future generation AMD EPYC processors, aggregate: 2.4 PFLOP/s), or
  2. GPU nodes (future generation NVIDIA GPUs, aggregate: 10.3 PFLOP/s), or
  3. Storage (the amount still needs to be determined)

The choice will be made 1.5 years after the start of production of Phase 1 and will be based on actual usage and demand of the system.

When Phase 3 is complete Snellius will have a total performance (CPU+GPU) in the range 13.6 - 21.5 PFLOP/s. This corresponds to roughly 7 - 11.5 times the total peak compute performance of Cartesius.

I still have an active account on Cartesius, what will happen with this account and the budget?

Active accounts will be migrated to Snellius, with a cutoff date for being active to be published soon. The remains of the budget which you had on Cartesius will be transferred to Snellius. A conversion factor from Cartesius budget to Snellius budget has yet to be determined.

Newly granted projects, that have a start date after 1 August 2021 will receive new accounts only on Snellius. We will not create a Cartesius account for granted projects which start after 1 August 2021. If the new grant is a continuation of a previous project, the new budget will be accessible on Cartesius along with an already existing account.

How do I get all my data from Cartesius to Snellius?

SURF will migrate relevant user data, the exact data migration schedule and included set of data will be published here soon.

In general, the data migration includes the following:

  • /home/<user> from accounts that were active on, or after, the cutoff date mentioned above

  • Project spaces that have a (co-)owner that has a valid login, again dependent on being active on a cutoff date as defined above
  • Tape archive does not need to be migrated and will still be accessible from Snellius

All data that is not included in the above will not be migrated to Snellius and will become unavailable as soon as Cartesius is taken offline.

Scratch

Files that reside on scratch filesystems of Cartesius will not be migrated to Snellius

When is the data migrated? What is the Freeze Date?

Somewhere in the second half of August (the exact date is yet to be published), the project spaces on Cartesius will be frozen and migrated to Snellius. For the time being we will refer to this date as the Freeze Date. We will not do any incremental migration of files on project spaces that were generated after this Freeze Date.

Data cleanup and preparation by users

To keep the data migration from Cartesius to Snellius to manageable proportions, we kindly ask the cooperation of all users. 

Minimize the content of your /home  directories and of your project space(s) as much as possible:

  • Clean up your /home  directory and project space as much as possible.
    • Remove obsolete files and directories.
    • Move files from project space, that you would have transferred to local storage anyway, as soon as possible to this local storage.
    • If you have access to the tape archive, please compress and move all data to the tape archive that you will not immediately need after migration. You can restore them at a later time on Snellius from the tape archive.
  • Make sure that you don't have links in your /home  folder that reference storage outside the /home  folder, as these links will be broken after the migration to Snellius.
  • Make sure that you move all legacy files from Huygens that you want to keep outside of the ~/HUYGENS  location, i.e. copy the contents of ~/HUYGENS  to a different location in your home directory.
  • If you intend to upload large input datasets to project space, consider postponing this operation until the transition to Snellius is complete.

How can I get access to Snellius?

The procedure for obtaining access to Snellius will be similar to the one for Cartesius. For large applications, you have to submit a proposal through isaac.nwo.nl and for small, pilot, applications you can apply via the SURF access portal (more information on the latter can be found here). Of course, the definitions of what is considered big and small will be adapted to reflect the increased capacity of Snellius.

How does the Snellius software environment compare to the Cartesius environment?

Snellius will use the same type of modules environment for providing software packages as used on Cartesius. We will do our best to port the software from the 2020 modules environment on Cartesius to the new 2021 modules environment on Snellius. This implies that Snellius will host newer versions of the software that is currently available on Cartesius.

If you are missing essential software from the current 2020 environment on Cartesius, please let us know via the ServiceDesk as soon as possible. You can also install the missing modules by yourself in your home folder, see https://userinfo.surfsara.nl/documentation/new-software-environment-based-easybuild.

We have already started building a new 2021 modules environment on Cartesius. This environment currently contains the most important core libraries and development tools. We will continue to enhance the 2021 modules-environment on Cartesius by frequently adding more packages. Please note, the 2021 modules environment on Cartesius is subject to changes. This environment is opened to users for testing only. Thus, users can already try to rebuild their software on Cartesius, test new versions of libraries, and adapt their current workflow to the upcoming new system. This can reduce the effort of setting up your environment on Snellius after the migration.

On Snellius we will use a GNU-based toolchain (foss) as the main one. However, for advanced users, we will provide a complete intel toolchain as a module in the new 2021 modules-environment.

It is unlikely that we will support software installed with the intel toolchain in the 2021 modules-environment on Snellius.

2019 and pre2019 module environments

We will not migrate the 2019 and pre2019 modules environments to Snellius.

If you still use modules from the pre2019 or 2019 modules environment, replace them as much as possible with the equivalent from the 2020 modules environment on Cartesius. Or wait for the transition to Snellius to test and choose a replacement module from the 2021 modules environment on Snellius.

Custom built software and locally-installed modules

Users that use in-house developed software, or more generally that build software themselves on Cartesius, will have to rebuild that software on Snellius. The same applies for locally installed modules, where you will have to rebuild these modules on Snellius.

To facilitate the transition from Cartesius to Snellius for users who have locally installed modules, we intend to install the intel/2020a and foss/2020a toolchains on Snellius. Please note, we will provide these toolchains only for compatibility with the previous modules-environment on Cartesius. We will not install any software system-wide on Snellius using these toolchains.

Similarities and Differences between Cartesius and Snellius

Hardware characteristics

FeatureCartesiusSnellius

CPU architecture 

Intel Sandy Bridge, Ivy Bridge, Haswell, Broadwell, Knights LandingAMD 7H12 (Rome), 64 cores/socket, 2.6GHz
GPU architectureNVIDIA Kepler - K40NVIDIA Ampere - A100
Node typesthin nodes, fat nodes, GPU nodesthin nodes, fat nodes, high-memory nodes, GPU nodes
Number of nodes (total cores/GPUs)

Thin nodes: 1620 (38,880 cores)

Broadwell nodes: 177 (5,664 cores)

Fat nodes: 32 (1,024 cores)

GPU nodes: 66 (132 GPUs, 1,056 cores)

Thin nodes: 504 (64,512 cores)

Fat nodes: 72 (9,216 cores)

High-memory nodes: 4 (512 cores)

GPU nodes: 36 (144 GPUs, 2,592 cores)

Cores per node

Thin nodes: 24 (2S x 12 cores/socket)

Broadwell nodes: 32 (2S x 16 cores/socket)

Fat nodes: 32 (4S x 8 cores/socket)

GPU nodes: 2 GPUs/node + 16 CPU cores (2S x 8 cores/socket)

Thin nodes: 128 (2S x 64 cores/socket)

Fat nodes: 128 (2S x 64 cores/socket)

High-memory nodes: 128 (2S x 64 cores/socket)

GPU nodes: 4 GPUs/node + 72 CPU cores (2S x 36 cores/socket

Memory per node

Thin nodes: 64 GB (2.66 GB/core)

Broadwell nodes: 64 GB (2GB/core)

Fat nodes: 256 GB (8 GB/core)

GPU nodes: 96GB (6GB/node, 48 GB/GPU)

Thin nodes: 256GB (2 GB/core)

Fat nodes: 1TB (8GB/core)

High-memory nodes: 4/8 TB (32-64GB/core)

GPU nodes: 512GB (7.11 GB/core, 128 GB/GPU)

InterconnectInfiniband FDR (56Gbps), prunedInfiniband HDR100 (100Gbps), fat tree
Storage filesystems

Home filesystem: 180TB

Parallel filesystem: Lustre, 7.7PB

Home filesystem: 720 TB

Parallel filesystem: Spectrum Scale (GPFS), 12.4PB

NVMe parallel filesystem: Spectrum Scale (GPFS), 200TB

Fat nodes include 6.4 TB of NVMe local storage

Software and usage characteristics

FeatureCartesiusSnellius
SchedulerSLURMSLURM
Node usageExclusive (jobs take full nodes)Shared (jobs can share nodes) and exclusive 
Operating systemCentOS7CentOS8/Rocky Linux/RHEL8
Supported compiler suitesIntel, GNU, PGI (NVIDIA)Intel, GNU, PGI (NVIDIA), AMD
Accounting1 SBU/core-hour1 SBU/core-hour
Pilot application limits500,000 SBUs1,000,000 SBUs (tentatively)
Modules environmentpre2019, 2019, 2020, (part of) 20212021
Supported toolchainsfoss and intel; versions 2018b and 2020a

foss and intel; versions 2020a and 2021a

Toolchains used for the software installationfoss, intelfoss





  • No labels