Site structure
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.
This user guide will help you get started if you are new to ALICE and working on an HPC in general.
- General documentation
- About ALICE
- System description
- HPC Software
- Policies
- More in-depth
- Security and privacy
- More on login nodes
- Using Node802
- Running jobs
- Other
- Software
- Available software
- Develop your own code
- Running in parallel
- Software packages
News
Latest News
- 17 Aug 2022 - REMINDER - ALICE system maintenance on 22 Aug 2022: We will perform system maintenance on ALICE on 22 Aug 2022 between 09:00 and 18:00 CEST. Our primary focus will be the high-availability set up of ALICE in addition to other maintenance tasks. This will require us to take all compute and login nodes of the cluster offline. It will not be possible to run any jobs and access data on ALICE. The login nodes will be rebooted and all active terminal or X2Go sessions will be terminated. Until maintenance starts, you can continue to use ALICE as usual and submit jobs. Slurm will also continue to run your job if the requested running time will allow it to finish before the maintenance starts. If you have any questions, please contact the ALICE Helpdesk.
- 01 Aug 2022 - ALICE system maintenance on 22 Aug 2022 - First announcement: We will perform system maintenance on ALICE on 22 Aug 2022 between 09:00 and 18:00 CEST. Our primary focus will be the high-availability set up of ALICE in addition to other maintenance tasks. This will require us to take all compute and login nodes of the cluster offline. It will not be possible to run any jobs and access data on ALICE. Until maintenance starts, you can continue to use ALICE as usual and submit jobs. Slurm will also continue to run your job if the requested running time will allow it to finish before the maintenance starts. If you have any questions, please contact the ALICE Helpdesk.
- 01 Jun 2022 - Disabled access to old scratch storage: As previously announced, we have disabled access to the old scratch storage. We will keep the data available until 30 June 2022. Afterwards, we will start to delete data so that we can repurpose the storage within ALICE. You can request temporary access by contacting the ALICE Helpdesk. See also the wiki page: Data Storage.
Older News
For older news, please have a look at the news archive: News Archive
Events
Here you can find information about upcoming events related to ALICE.
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
System Maintenance on ALICE will take place on 22 Aug 2022 between 09:00 and 18:00 CEST (See the Maintenance Announcement)
We will perform system maintenance on the ALICE HPC cluster on Monday 22 August 2022 between 09:00 and 18:00.
On this day, it will not be possible to run any jobs and access data on ALICE. Until maintenance starts, you can continue to use ALICE as usual and submit jobs. Slurm will also continue to run your job if the requested running time will allow it to finish before the maintenance starts.
Our primary focus will be the high-availability set up of ALICE in addition to other maintenance tasks.
We understand that this represents an inconvenience for you. If you have any questions, please contact the ALICE Helpdesk.
Previous Maintenance days
ALICE node status
Gateway: UP Head node: UP Login nodes: UP GPU nodes: UP CPU nodes: Up High memory nodes: UP Storage: UP Network: UP
Current Issues
- Copying data to the shared scratch via sftp:
- There is currently an issue on the sftp gateway which does prevents users from copying data to their shared scratch directory, i.e.,
/home/<username>/data
- A current work-around is to use scp or sftp via the ssh gateway and the login nodes.
- Status: Work in Progress
- Last Updated: 30 Nov 2021, 14:56 CET
- There is currently an issue on the sftp gateway which does prevents users from copying data to their shared scratch directory, i.e.,
See here for other recently solved issues: Solved Issues
Publications
Articles with acknowledgements to the use of ALICE
Astronomy and Astrophysics
- High-level ab initio quartic force fields and spectroscopic characterization of C2N−, Rocha, C. M. R. and Linnartz, H, Phys. Chem. Chem. Phys, November 2021, DOI: https://doi.org/10.1039/D1CP03505C
- 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.
Computer Sciences
- 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
Ecology
- Improving estimations of life history parameters of small animals in mesocosm experiments: A case study on mosquitoes, Dellar, M., Sam, B.P., Holmes, D., Methods in Ecology and Evolution, (February 2022), https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13814
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