Mac OS-Getting started

From ALICE Documentation

Best Practices

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:
    1. Compile code, Developing applications,
    2. Defining and submitting your job,
    3. Post-processing and managing data,
    4. Monitoring running applications.
    5. Change your user password.
  • Avoid computationally intensive activity on the login nodes.
    1. Don't run research applications.  Use an interactive session if running a job is not appropriate.
    2. 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.
    3. That script you run to monitor job status several times a second should probably run every few minutes.
    4. 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 (mail request) and provide the following information

  • your name
  • your ULCN or LUMC account name
  • your university or institute e-mail address.
  • your supervisor name (for PostDocs, PhDs and students only).
  • 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 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

Compliance with University policy

Users of ALICE must comply with all University ICT policies, including Acceptable Use of Computers.

Resource policy

ALICE represents a unique resource for the research community. The computers have special characteristics that are not found, or are of limited availability, on other central computers. Characteristics include 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 can be used for small, short interactive jobs and for submitting batch jobs, but are not meant 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 MAC OS

Logging in with a Mac requires no extra installation on your local machine.

  • Under “File”, open a new finder window. Navigate to the “Applications” folder, then the “Utilities” folder. Open a terminal window.
  • Edit your ~/.bash_profile to incorporate:
   export LC_ALL=en_US.UTF-8
   export LANG=en_US.UTF-8 

  • Open a new tab to make sure these settings are in effect (Shell -> New Tab).
  • Edit your ~/.ssh/config file and put in:
Host hpc1 
  ProxyJump <USERNAME>
  ServerAliveInterval 60

(Replace <USERNAME> by your own ULCN account name.)

Now you can login to the ALICE login 1 node by typing on the command line:

ssh hpc1

All other settings (e.g., for password-less login) are similar to the Linux login setup