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From ALICE Documentation
This wiki is the main documentation source for information about the Academic Leiden Interdisciplinary Cluster Environment (ALICE) cluster. ALICE is the research computing facility of the partnership Leiden University and Leiden University Medical Center. It is available to any researcher from both partners. In this wiki, we will introduce the ALICE cluster in detail.
Below you find a collapsible tree structure of our documentation set which gives you a quick overview of the full navigation tree. The root tree items are also directory accessible from the top navigation bar.
Contents
ALICE (Academic Leiden Interdisciplinary Cluster Environment) is the high-performance computing (HPC) facility of the partnership between Leiden University and Leiden University Medical Center (LUMC). It is available to any researcher from both partners. Leiden University and LUMC aim to help deliver cutting edge research using innovative technology within the broad area of data-centric HPC. Both partners are responsible for the hosting, system support, scientific support and service delivery of several large super-computing and research data storage resources for the Leiden research community.
This wiki is the main source of documentation about the ALICE cluster.
Research Acknowledgement
We request that you acknowledge the use of the ALICE compute facilities in all publications and presentations which use any results generated through your use of ALICE. The following acknowledgement can be used:
"This work was performed using the compute resources from the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University."
or in shorter version:
"This work was performed using the ALICE compute resources provided by Leiden University."
We request also that you send copies of your publications that acknowledge the use of ALICE resources (or provide the links) to helpdesk@alice.leidenuniv.nl (mail request).
Why ALICE
High-Performance Computing (HPC) previously the domain of theoretical scientists and computer and software developers is becoming ever more important as a research tool in many research areas. An HPC facility, providing serious computational capabilities, combined with easy and flexible local access, is a strong advantage for these research areas. ALICE is the HPC facility that answers those needs for Leiden University (LU) and Leiden University Medical Center (LUMC). It is available to all researchers and students from both LU and LUMC.
The ALICE facility currently implemented is a first phase edition of what will be a larger Hybrid HPC facility for research, exceeding the capabilities of what individual institutes can build and will provide a stepping stone to the larger national facilities. Although the current implementation is located at two data centres (LU and LUMC) it is one.
The facility aims to be an easily accessible, easily usable system with extensive local support at all levels of expertise. Given the expected diverse use, diversity is implemented in all aspects of computing, namely: the number of CPU's, GPU's and the ratio of these two numbers; the size of the core memory to the CPU's; the data storage size and location; and the speed of the network.
ALICE provides not only a sophisticated production machine but is also a tool for educating all aspects of HPC and a learning machine for young researchers to prepare themselves for national and international HPC.
Overview of the cluster
The ALICE cluster is a hybrid cluster consisting of
- 2 login nodes (4 TFlops)
- 20 CPU nodes (40 TFlops)
- 10 GPU nodes (40 GPU, 20 TFlops CPU + 536 TFlops GPU)
- 1 High Memory CPU node (4 TFlops)
- Storage Device (31 * 15 + 70 = 535 TB)
In summary: 604 TFlops, 816 cores (1632 threads), 14.4 TB RAM.
Below you will find a more comprehensive description of the individual components. Also see a photo gallery of the hardware.
ALICE is a pre-configuration system for the university to gain experience with managing, supporting and operating a university-wide HPC system. Once the system and governance have proven to be a functional research asset, it will be extended and continued for the coming years.
The descriptions are for the configuration which is housed partly in the data centre at LMUY and the data centre at Leiden University Medical Center (LUMC).
Future plans
ALICE will be expanded over the coming years. Apart from our own expansion plans, we are always open to collaborate with other groups/institutes on expanding and improving ALICE.
The expansion that are currently being discussed include:
- Expansion of temporary storage (late 2020)
- Additional login node(s) with GPUs (late 2020)
- Additional GPU nodes (estimated early 2021)
- Additional CPU nodes (estimated Q2 2022)
...
How to get involved with ALICE
There are several levels at which you can get involved. They are fully detailed in Getting involved, in-depth. For now, you probably want to start getting to know the system and take your first (baby) steps toward High Performance Computing. This wiki has several pages explaining details of the steps toward using ALICE. These steps are:
- User Guides Getting an account and Connecting to ALICE
- Understanding how to work on an HPC cluster see HPC Basic concepts
- Prepare for your first job
- Learning more advanced stuff
Costs overview
Currently, access to the ALICE cluster and related services is provided free of charge to all researchers and students at LU and LUMC.
Current Status Overview
This user guide will help you get started if you are new to ALICE and working on an HPC in general.
- General documentation
- System description
- HPC Software
- Policies
- More in-depth
- Security considerations
- More on login nodes
- Running jobs
- Other
- Software
- Available software
- Develop your own code
- Running in parallel
- Software packages
News
Latest News
- 08 Jan. 2021 - SURF HPC Workshops: SURF is offering HPC-related workshops on various topics. You can find a list of upcoming workshops (and more) on the SURF website (Link). Workshops of interest to HPC users are:
- Webinar Introduction Supercomputing
- Webinar Introduction HPC Cloud
- Using the Amsterdam Modeling Suite in HPC systems
- SURF Research Week
- 04 Jan. 2021 - Happy New Year: We wish all users a Happy New Year and all the best for 2021. We are looking forward to the exciting research and education that will be done with ALICE in 2021. Happy computing.
Older News
For older news, please have a look at the news archive: News Archive
Maintenance
This section is used to announce upcoming maintenance and provide information before, during and after it. For general information about our maintenance policy, please have a look here: To maintenance policy
Next Maintenance
The next major maintenance window will be announced here at least one week in advance.
Previous Maintenance days
Publications
Articles with acknowledgements to the use of ALICE
The ecological impact of high-performance computing in astrophysics. Portegies Zwart, S. Nature Astronomy 4, 819–822 (September 2020). DOI: https://doi.org/10.1038/s41550-020-1208-y.
Leiden researchers and their use of HPC
Identifying Earth-impacting asteroids using an artificial neural network. John D. Hefele, Francesco Bortolussi and Simon Portegies Zwart. Astronomy & Astrophysics, February 2020.