LIP Computing training basic level

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Outline

• Introduction
• LIP
• LIP/CNCA Computing infrastructure
• Computing farm structure
• Authentication mechanism
• Documentation
• How to access the infrastructure
• What is ssh & why use it
• Generate ssh keys

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• Useful information
• Linux commands
• Best practices

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LIP

LIP- Laboratório de Instrumentação e Física Experimental de Partículas

• Created in 1986
• Three nodes: Lisbon, Coimbra and Braga
• More than 202 people: staff, researchers, students, collaborations
• Four main research areas:
• Astroparticle Physics
• Particle Physics
• Detectors and Applications
• Computing

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LIP - IT infrastructure

• general IT services – Core institutional services, network services, security, and also LIP-Lisbon specific services
• Data Intensive Computing Infrastructure @CNCA (past @INCD)

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Introduction �LIP/CNCA Computing infrastructure

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CNCA - Centro Nacional de Computação Avançada

• CNCA is a digital infrastructure:
• LIP Technical coordination
• Goals:
• Provide computing and data services for the research community.
• Computing Services:
• Cloud.
• HTC and HPC (farm)

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CNCA operations centres in 2025

CNCA-A @ LNEC in Lisbon

HPC / HTC / Cloud / Federation

6000 CPU cores

5 Petabytes online raw

100 Gbps + 100 Gbps LHCONE

Includes the WLCG Tier-2

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CNCA-L @ LIP in Lisbon

Tape storage

1 Petabyte backups

10 Gbps

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CNCA-C @ UC in Coimbra

(BEING IMPROVED)

Tape storage expansion

20 Petabytes

10 Gbps

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CNCA-D @ UTAD in Vila Real

HPC / HTC / Cloud / Federation

5000 CPU cores + IB HDR200

4 Petabytes online raw

10 Gbps + 10 Gbps

CNCA-B @ REN in Riba-de-Ave

(partially moved to Lisbon)

HPC / HTC

2600 CPU cores (640 cores)

384 Terabytes raw

1 Gbps

CNCA Portuguese Distributed Computing Infrastructure

1º Encontro "Computation in Science @UAlg" - 26^th October 2018

Peerings

CNCA-D

UTAD

Vila Real

LHCONE

FCCN Géant

RCTS Internet

FCCN

CNCA-C

UC

Coimbra

CNCA-L2

FCCN

CNCA-A

LNEC

Lisboa

CNCA-L

LIP

Lisboa

Backup via RCTS

Peering CNCA L2

Default via CNCA L2

Default via RCTS

Peering LHCONE

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Tier2

CNCA Portuguese Distributed Computing Infrastructure

1º Encontro "Computation in Science @UAlg" - 26^th October 2018

Introduction �FARM Computing infrastructure

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Computing Farm:

Applications run in a compute/worker node:

• Linux:
• pauli.a.incd.pt (Centos 7 )
• curie.a.incd.pt (Alamalinux9 )
• You do not have any direct access to the compute nodes
• Access trough scheduler (slurm)
• Storage accessible in both submission node and compute nodes
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Compute nodes

Job submission�(pauli.a.incd.pt)

Job scheduling

Scheduler (slurm)

Storage

Computing Farm Advantages:

• Applications with limited execution time (minutes-weeks).
• “Almost” static environment:
• Operating System, software, compilers and libraries are deployed by the system administrator. Users request the sys admins to deployed specific software, libraries, compilers to their needs.
• Applications are scheduled into a queue for execution.
• Resources are shared with other others users
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Useful information�Linux commands �&�Best practices

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Useful Linux commands

• cd: Change directory.
• rm: Delete files.
• mkdir: Create directory.
• ls: List files.
• pwd: Print current directory name.
• cat: View files.
• Ctrl-c: press “Ctrl” and “c” keys to kill what you are running in terminal.

For more commands, check the Quick Reference guide: http://www.macs.hw.ac.uk/~hwloidl/Courses/LinuxIntro/linux-quickref.pdf

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Best practices 1/x

@LIP with Personal Laptops

• Torrents
• No licensed Software
• All software needed in the course is free or provided by your advisor.
• Windows, activate the Anti-Virus, windows defender is the best and the only needed.

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Best practices 2/x

Secrets

• PRIVATE SSH key should always be encrypted with strong password
• Don’t share the password or the private key.
• Accounts are private, there are mechanisms to share data between accounts (ask your advisor).

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Best practices 3/x

Phishing/Ransomware

• Emails (From: LIP vs From: @lip.pt)
• Attachs
• Links
• Report anything suspicious

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How to access �the infrastructure�SSH

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SSH

How to access - SSH

Allow us to connect to local or remote servers �(inside safe/isolated networks)

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HOME

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LABORATORY

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Is a secure way to establish a �connection between two machines

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Secure network

SSH (openssh free and opensource)

Linux - Is available natively in all distributions, Fedora, Ubuntu, Mint, etc

Windows - Is available via WSL in all Windows >= 10

WSL is not available to all Windows 10 users by default, but can be installed via Microsoft Store or other means.

macOS - Is available.

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SSH (Windows WSL v2)

SSH forward keys

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1) Edit file .bashrc

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2) Add at the end of the file

eval $(ssh-agent -s)

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Generate an ssh key pair

1. Generate a new key pair in a terminal with the next command��

The key generator will ask for location and file name to which the key is saved to. The recommended is the defaults (Just pressing enter). If you have already a key named id_rsa, choose another name.

• Create a passphrase for the key when prompted

This is a password that will protect your private key from someone that is not supposed to get their hands on it.

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ssh-keygen -b 4096

More details in https://wiki.acnca.pt/books/how-to-access/page/create-a-ssh-key

Generate an ssh key pair

• See your key pair generated with the next command��

You will see the keys stored in your computer:� id_rsa → PRIVATE key.� id_rsa.pub → PUBLIC key.

• Send your public key (id_rsa.pub) to LIP administrators via email

Once the key pair was created, you must send the public key to the LIP administrators, to associate it to your account. (continue in next slide)

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ls -la ~/.ssh/

Generate an ssh key pair

(continuation) Send your public key (id_rsa.pub)

• Show the public key in a terminal

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• Copy the public key and paste it into an email�Just select the key with your mouse, right click (shift-right-click on MobaXTerm) and copy. Then paste the key into an email.���
• Send an email with the public key and your username to:

helpdesk@lip.pt

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cat ~/.ssh/id_rsa.pub

Connect to server

• Connect to remote server in a terminal with the next command��

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username → replace username with your username (Sent previously to you by email).

pauli.a.incd.pt → the name of the server you going to connect to.

When the ssh connection is establish, a passphrase will be asked to unlock the private key that is encrypted.

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ssh username@pauli.a.incd.pt

or

ssh username@paulia.a.acnca.pt

How to access - using Windows

1. Install MobaXTerm https://mobaxterm.mobatek.net

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To start a new terminal, click on “Start local terminal”

How to access - using Windows

2. Click right-click on the terminal and choose “Paste”
1. This way, to paste something into the terminal you just need to right-click.
2. To copy something from the terminal, you must shift-right-click and then click copy.

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macOS

Required for export Display:

• install: https://www.xquartz.org/

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Documentation

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Helpdesk

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Documentation

• Lip Wiki: https://wiki-lip.lip.pt/
• Eduroam access
• LIP internal groups documentation
• LIP computing FARM access and commands

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• More generic FARM: https://wiki.acnca.pt/shelves/hpc-htc-user-documentation
• Tutorials:
• https://indico.eurocc.fccn.pt/event/35/ (advanced level)
• https://indico.eurocc.fccn.pt/event/34/ (starting level)

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Slack registration

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https://join.slack.com/t/lipinternship2025/shared_invite/zt-36gln46ci-qvVcDgHb_UhI7EMD_~iDSg

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��Helpdesk ( helpdesk@lip.pt)

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Good practices:

• Slack must be the first line to support, used by all researchers and students:
• https://lipinternship2025.slack.com
• Always use the email used in the registration form
• Try to explain clearly the problem on the email
• Required information:
• login name (name provided to you by LIP IT team to access LIP services)
• Source machine (personal laptop, desktop, etc)
• Destination machine: (example: pauli.a.acnca.pt)
• Problem with job submission:
• My submission code is here: /home/userxxx/submit_to_farm.sh
• job ID: try to get the job ID of you job (Check FARM wiki)

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�Q&A

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Nice Internship for everyone!!�Um Bom Estágio para todos!!

IT infrastructure context

ISEC - Laced

Minerva Cluster

20x Dell R720

Infiniband

Miguel Couceiro

U. Coimbra

Old Datacenter

Physics Dep.

Small LIP facility

Point-of-Presence

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NCG @ LNEC

Sala-Grid Datacenter

New CNCA equipment

Old INGRID equipment

LIP specific equipment

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LIP users

LIP Tier-2

CNCA users

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U. Lisboa @ reitoria

Mail, web, VMs

Home directories

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LIP @ 3Is

Tape library

Local network+services

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BOB @ REN Riba-de-Ave

HPC cluster from FCT

Offered by TACC

20% is managed by CNCA+LIP

LIP helping in the storage

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IT network infrastructure

U. Coimbra

Old Datacenter

Physics Dep.

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NCG @ LNEC

Sala-Grid Datacenter

New L2/L3 switches

48x 10/25 GbE

18x 40/100 GbE

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LIP @ 3Is

Tape library

Local network

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BOB @ REN Riba-de-Ave

HPC cluster from FCT

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U. Lisboa @ reitoria

Mail, web, VMs

Home directories

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LIP @ U. Coimbra

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LIP @ U. Minho

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INTERNET

LNEC

Internal network

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CNCA Private Net