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Ibex101 Sep2020 SW - Env PDF

The document provides an overview of the Ibex software environment at KAUST. It addresses how to access Ibex, including that no application is required. It describes how to log in from different operating systems like macOS, Linux, and Windows. The document outlines what users will see upon login, like messages of the day and welcome emails. It also discusses managing software on Ibex through environment modules and public installations, and categorizing the large software stack available.

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118 views28 pages

Ibex101 Sep2020 SW - Env PDF

The document provides an overview of the Ibex software environment at KAUST. It addresses how to access Ibex, including that no application is required. It describes how to log in from different operating systems like macOS, Linux, and Windows. The document outlines what users will see upon login, like messages of the day and welcome emails. It also discusses managing software on Ibex through environment modules and public installations, and categorizing the large software stack available.

Uploaded by

Gutu
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Overview on Ibex Software Environment

Passant Hafez
HPC Applications Specialist
Supercomputing Core Lab
Q: Do I need to apply to use Ibex?
The answer is NO.

Any KAUST member should be able to login and use Ibex.

First check your credentials are correct by logging into the KAUST Portal
https://portal.kaust.edu.sa

or KAUST Webmail

https://webmail.kaust.edu.sa/
If for any reason you can’t access Ibex using the verified credentials, you should contact IT, sometimes they don’t
configure Unix Attributes for new user accounts on the Active Directory.

If you experience login failures, you’ll need to wait 15 mins and try again, if it still fails then contact IT.

IT Service Desk

Phone: (in KAUST) 900 option 1

Phone: (out of KAUST) +(966) 2 808 0900 option 1

Email: ithelpdesk@kaust.edu.sa

Web: http://servicedesk.kaust.edu.sa
How to login to Ibex from different
Operating Systems?
For macOS and various Linux distributions you can use the native terminal
program.
macOS

A) Mac OS
B) Linux (Ubuntu, Debian, CentOS,
Fedora, Red Hat,..)
For MS Windows users you’ll need to use third party SSH client tool like PuTTY
or MobaXterm.

Note:
MobaXterm is an enhanced terminal for Windows which includes an X11 server, if you’re using PuTTY you’ll need to
install and run an X11 server like Xming.
MS Windows

C) Windows
MOTD (Message Of The Day)

Upon successful login to Ibex,


you’ll see a message with any
updates the team wants to
share with you.
Welcome Email

A welcome email is also sent to


you upon your first login to Ibex
providing different information
about your storage spaces
(home, scratch), modes of
support, attaching useful
documents.
Passwordless Authentication
You can login to Ibex without the need to type your password every time

(and watching out for typos..)

Contact us ibex@hpc.kaust.edu.sa and we’ll provide information based on your OS


Software on Ibex
Software on Ibex:

Two options:

1) Local Installation (user’s responsibility): customizable, Ibex team will provide


help if needed, just watch your storage quota ;)
2) Public Installation (Ibex team’s responsibility): the most common/general mode
of installation is available as shared module for multiple users.

For help with either case, as always, email ibex@hpc.kaust.edu.sa


Software on Ibex:

Environment Modules:

- Are used to manage public installations on Ibex.


- Rich AppStack of >400 modules.
Software on Ibex:

The most common subcommands you'll find useful would be:


module av/avail → With no arguments, lists all the modules available for use.
module av/avail <string> → Used to check the availability of a module that starts with string.
module load/add <module> → adding that module to your environment.
module unload/rm <module> → removing that module from your environment.
module swap/switch <module1> <module2> → switches between module1 and module2
module purge → removes ALL loaded modules
module list → lists the currently loaded modules
module show <module> → views what this module is supposed to change in your
environment.
To list ALL available modules:
To list available modules for CUDA:
To check what will the module python/3.7.0 change in your
environment:
Software on Ibex:

Note: Some tools are available on the system by default, for example
Python and GCC, so to make sure you’re using the loaded module for
example check:

which python

That’ll print the full path to the Python binary you’ll use when you type
python in your terminal.
Software on Ibex:

There are multiple ways to categorize the Software Stack by, for example:

- By Processor Type.
- By Science Domain.
- By Role.
Software on Ibex:

Software Stacks by Processor:


- Ibex is hybrid cluster of different processors, Intel (new and old) AMD and
GPUs. The software stack varies accordingly*.
- For each type there is a dedicated login node, the ones of concern are:

ilogin.ibex.kaust.edu.sa (Intel Software Stack)

glogin.ibex.kaust.edu.sa (GPU-related Software Stack, for example CUDA


Toolkit and Machine Learning modules)
*There is no fine line that separates both, sometimes it depends on the applications requests made by users to be used with
which processor type.
Software on Ibex:

Software Stacks by Science Domain:


Bioinformatics/Genomics/Biosciences: Environmental Microbiology, Analyzing 16S
Amplicon Data, Metagenomics, Differential Transcription Data, Sequencing Data Analysis,
Transcriptomics, Plants Sciences…

Chemistry, DFT: Quantum Espresso, Gaussian, Gaussrate, Polyrate, ORCA.

CFD: OpenFoam, Gerris.

Deep Learning for Computing Vision and Bioinformatics: PyTorch, TensorFlow, Python.

Electrical Engineering/Statistics: Magnetic Field Simulation, Matlab, Python, R.

Cryo Electron Microscopy: 3D reconstruction with Relion, IMOD.


Software on Ibex:

Software Stacks by Role:


Software Development (Compilers & Programming Languages): GCC, Intel, PGI, Julia,
Python, Perl, Java, R, CUDA,..

Libraries: OpenMPI, Boost, FFTW, GMP, MPFR,..

Applications: Matlab, Relion, OpenFoam, Gaussian,..

Containers: Singularity.
Software on Ibex:

To know more about using Conda for Data Science on Ibex GPU part, please
refer to the training materials

Introduction to Conda for (Data) Scientists

at: https://www.hpc.kaust.edu.sa/ibex/training
Thank You!

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