From ALICE Documentation
Revision as of 12:11, 14 June 2020 by Dijkbvan
Know when you are on a login node. You can use your Linux prompt or the command
hostname. This will tell you the name of the login node that you are currently on. Note that the ssh gateway host itself is a secure portal from the outside and serves no compute function.
- Appropriate activities on the login nodes:
- Compile code, Developing applications,
- Defining and submitting your job,
- Post-processing and managing data,
- Monitoring running applications.
- Change your user password.
- Avoid computationally intensive activity on the login nodes.
- Don't run research applications. Use an interactive session if running a job is not appropriate.
- Don't launch too many simultaneous processes. While it is fine to compile on a login node, avoid using all of the resources. For example "make -j 14" will use half of the cores.
- That script you run to monitor job status several times a second should probably run every few minutes.
- I/O activity can slow the login node for everyone, like multiple copies or "ls -l" on directories with 000's of files.
- Hyperthreading is turned off. Running multiple threads per core is generally not productive. MKL is an exception to that if it is relevant to you.
Getting a User account for ALICE
To get a user account on ALICE, mail a request to email@example.com (mail request) and provide the following information
- your name
- your ULCN or LUMC account name
- your university or institute e-mail address.
- What do you plan to do on ALICE (1 or 2 sentences are sufficient)?
- Do you plan to process sensitive data (related to persons) or other data that must be treated confidentially?
At ALICE, we will create local ALICE accounts with the same account name.
If you are a student, we need confirmation from your supervisor that you require access to ALICE.
Once we have created your account, you will receive an e-mail from firstname.lastname@example.org providing you with an initial password to log in
IMPORTANT: Make sure to change the password in our e-mail when you log in to ALICE for the first time. You can use the command
passwd for this.
IMPORTANT: Please read the section on Acceptable Use before requesting an account.
Acceptable use policy
Complience with University policy
High Performance Computing (HPC) facility users are responsible for complying with all University policies, including Acceptable Use of Computers.
The supercomputers represent a unique resource for the campus community. These computers have special characteristics that are not found, or are of limited availability, on other central computers, including parallel processing, large memory, and a Linux operating system. The allocation of High Performance Computing (HPC) resources requires close supervision by those charged with management of these resources.
The login nodes are designated for small, short interactive jobs, and submitting batch jobs and not for running compute jobs.
Data Storage Policy
ALICE does not provide support for any type of controlled data. No controlled data (GDPR, HIPAA, EAR, FERPA, PII, CUI, ITAR, etc.) can be analysed or stored on any HPC storage. Users must not transfer sensitive data (data related to people) to ALICE. Data must be anonymized before it can be transferred to ALICE. In case you are unsure about the contents/classification of the data, please contact the helpdesk.
ALICE is not a datamanagement system where research data can be stored for longer periods of time. All data that is transferred to ALICE must be copies of data. Users must make sure that data that is transferred to ALICE remains available somewhere else. All data with value that is generated on ALICE must be moved off ALICE as soon as this is possible after the job completed.
Data in the user’s home directory is backed up (see Backup & Restore). The home directory is intended to store scripts, software, executables etc, but is not meant to store large or temporary data sets.
Login to ALICE from Windows
There are multiple ways to connect to ALICE from Windows. Below a list in order of complexity using:
Fine-tuning Job Specifications
Compiling and testing your software on the HPC
Job script examples
Graphical applications with VNC
Graphical applications with X2Go
ALICE GPU cluster
Software-specific Best Practices
MATLAB OpenFOAM Mympirun Singularity SCOOP Easybuild Hanythingondemand (HOD)