From ALICE Documentation
Revision as of 11:55, 6 October 2020 by Deuler (Created page with "This wiki is the main documentation source for information about the Academic Leiden Interdisciplinary Cluster Environment (ALICE) cluster. ALICE is the research computing fac...")
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.
- 1 Full Navigation Tree
- 2 Research Acknowledgement
- 3 Why ALICE
- 4 Overview of the cluster
- 5 Future plans
- 6 How to get involved with ALICE
- 7 Costs overview
- 8 Current Status Overview
- 9 News
- 10 Maintenance
- 11 Publications
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.
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 firstname.lastname@example.org (mail request).
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.
ALICE has a second high memory. This node is not included above as it is only available to the research group which purchased the node.
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).
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 (first half 2021)
- We are in the process of getting a 250TB parellel storage system that will run BeeGFS.
- Upgrading login nodes with GPUs (Q2 2021)
- We are planning to add one NVIDIA Tesla T4 to each login node.
- Additional GPU nodes (estimated second half of 2021)
- Additional CPU nodes (estimated Q3 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
Currently, access to the ALICE cluster and related services is provided free of charge to all researchers and students at LU and LUMC.
This user guide will help you get started if you are new to ALICE and working on an HPC in general.
- More in-depth
- Security considerations
- More on login nodes
- Using Node802
- Running jobs
- Available software
- Develop your own code
- Running in parallel
- Software packages
- 29 Mar. 2021 - ALICE User Survey 2021 out: The ALICE User Survey 2021 is online. All users should have received a link and password. If you are a user and you have not received a link, please contact the ALICE Helpdesk. We hope that you take the time to fill it out and help us improve ALICE: We are looking forward to your responses.
- 29 Mar. 2021 - MATLAB 2020b available: We have updated MATLAB to version 2020b and changed the license server configuration so that ALICE can now make use of the MATLAB campus license. If you still need version 2019b, please contact the ALICE Helpdesk.
- 8 Mar. 2021 - Maintenance was successful: Login node 02 has been expanded with an NVIDIA Tesla T4. The new GPU will be tested by us in the next few weeks. So, for now please do not use the GPU. After testing has been completed, we will release the GPU for general use and provide more information.
- 25 Feb. 2021 - Next major maintenance window on 08 March 2021: Please have a look at the maintenance page for details on our planned work and how it affects you.
- 12 Feb. 2021 (Update 22 Feb. 2021) - SSH Connection Stability: If you recently started experiencing that your ssh connection is breaking up after a few minutes of being idle, please check the settings below for you ssh configuration for ALICE. If this does not solve the issue, please contact the ALICE Helpdesk.
- for Linux, MacOS, Windows using OpenSSH command line connection: Make sure you use "ServerAliveInterval 60" and "ServerAliveCountMax 3" to your ssh config settings.
- MobaXterm: Go to Settings -> SSH -> SSH settings and enable "SSH keepalive"
- PuTTY: Go to Settings -> Connection -> Set a non-0 value in "Settings between keepalives" (e.g., 60)
For older news, please have a look at the news archive: News Archive
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
The next major maintenance window will be announced here at least one week in advance.
Previous Maintenance days
Articles with acknowledgements to the use of ALICE
- Effects of stellar density on the photoevaporation of circumstellar discs, Concha-Ramirez, F. et al., MNRAS, 501, 1782 (February 2021), DOI: https://doi.org/10.1093/mnras/staa3669
- Lucky planets: how circum-binary planets survive the supernova in one of the inner-binary components, Fagginger Auer, F. & Portegies Zwart, S., eprint arXiv:2101.08033, Submitted to SciPost Astronomy (January 2021), https://ui.adsabs.harvard.edu/link_gateway/2021arXiv210108033F/arxiv:2101.08033
- Trimodal structure of Hercules stream explained by originating from bar resonances, Asano, T. et al., MNRAS, 499, 2416 (December 2020), DOI: https://doi.org/10.1093/mnras/staa2849
- Oort cloud Ecology II: Extra-solar Oort clouds and the origin of asteroidal interlopers, Portegies Zwart, S., eprint arXiv:2011.08257, accepted for publication by A&A, (November 2020), https://ui.adsabs.harvard.edu/link_gateway/2020arXiv201108257P/arxiv:2011.08257
- 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.
- Better Distractions: Transformer-based Distractor Generationand Multiple Choice Question Filtering, Offerijns, J., Verberne, V., Verhoe, T., eprint arXiv:2010.09598, (October 2020), https://arxiv.org/abs/2010.09598
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.
News articles featuring ALICE
- Hazardous Object Identifier: Supercomputer Helps to Identify Dangerous Asteroids, Oliver Peckman, HPC Wire, 04 March 2020, link
- Elf reuzestenen op ramkoers met de aarde?, Annelies Bes, 13 February 2020, Kijk Magazine, link
- Leidse sterrenkundigen ontdekken aardscheerders-in-spé, NOVA, 12 February 2020, link