Research computing at ILRI

50 %
50 %
Information about Research computing at ILRI
Technology

Published on March 6, 2014

Author: ILRI

Source: slideshare.net

Description

Presented by Alan Orth at the CGIAR ICT Managers Meeting, ILRI, Kenya, 5 March 2014

Research Computing at ILRI Alan Orth ICT Managers Meeting, ILRI, Kenya, 5 March 2014

Where we came from (2003) - 32 dual-core compute nodes - 32 * 2 != 64 - Writing MPI code is hard! - Data storage over NFS to “master” node - “Rocks” cluster distro - Revolutionary at the time!

Where we came from (2010) - Most of the original cluster removed - Replaced with single Dell PowerEdge R910 - 64 cores, 8TB storage, 128 GB - Threading is easier* than MPI! - Data is local - Easier to manage!

To infinity and beyond (2013) - A little bit back to the “old” model - Mixture of “thin” and “thick” nodes - Networked storage - Pure CentOS - Supermicro boxen - Pretty exciting! --->

Primary characteristics Computational capacity Data storage

Platform - 152 compute cores - 32* TB storage - 700 GB RAM - 10 GbE interconnects - LTO-4 tape backups (LOL?)

Homogeneous computing environment User IDs, applications, and data are available everywhere.

Scaling out storage with GlusterFS - Developed by Red Hat - Abstracts backend storage (file systems, technology, etc) - Can do replicate, distribute, replicate+distribute, geo-replication (off site!), etc - Scales “out”, not “up”

How we use GlusterFS [aorth@hpc: ~]$ df -h Filesystem Size ... wingu1:/homes 31T wingu0:/apps 31T wingu1:/data 31T Used Avail Use% Mounted on 9.5T 9.5T 9.5T 21T 21T 21T 32% /home 32% /export/apps 32% /export/data - Persistent paths for homes, data, and applications across the cluster. - These volumes are replicated, so essentially application-layer RAID1

GlusterFS <3 10GbE

- Project from Lawrence Livermore National Labs (LLNL) - Manages resources - Users request CPU, memory, and node allocations - Queues / prioritizes jobs, logs usage, etc - More like an accountant than a bouncer

Topology

How we use SLURM - Can submit “batch” jobs (long-running jobs, invoke program many times with different variables, etc) - Can run “interactively” (something that needs keyboard interaction) Make it easy for users to do the “right thing”: [aorth@hpc: ~]$ interactive -c 10 salloc: Granted job allocation 1080 [aorth@compute0: ~]$

Managing applications - Environment modules - http://modules. sourceforge.net - Dynamically load support for packages in a user’s environment - Makes it easy to support multiple versions, complicated packages with $PERL5LIB, package dependencies, etc

Managing applications Install once, use everywhere... [aorth@hpc: ~]$ module avail blast blast/2.2.25+ blast/2.2.26 blast/2.2.26+ blast/2. 2.28+ [aorth@hpc: ~]$ module load blast/2.2.28+ [aorth@hpc: ~]$ which blastn /export/apps/blast/2.2.28+/bin/blastn Works anywhere on the cluster!

Users and Groups - Consistent UID/GIDs across systems - LDAP + SSSD (also from Red Hat) is a great match - 389 LDAP works great with CentOS - SSSD is simpler than pam_ldap and does caching

More information and contact a.orth@cgiar.org http://hpc.ilri.cgiar.org/

Add a comment

Related presentations

Related pages

start [ILRI Research Computing]

This is the ILRI Research Computing wiki. Here you'll find information about the research computing infrastructure, including information about software ...
Read more

about [ILRI Research Computing]

Agricultural research at ILRI and its partners are aimed at producing healthier crops and livestock to alleviate poverty and hunger in the developing world ...
Read more

International Livestock Research Institute (ILRI) is ...

The International Livestock Research Institute (ILRI) seeks to recruit a Computing Systems Analyst to analyse, develop and implement systems to ensure ILRI ...
Read more

International Livestock Research Institute | Better Lives ...

ILRI Research Methods Group outputs. ILRI research repository - Mahider. ILRI research repository - Mahider. Website. ... ILRI research computing wiki.
Read more

Research methods group | International Livestock ... - ILRI

The ILRI Research Methods Group provides Consortium Research Program and project level support covering all aspects of research methods (design of surveys ...
Read more

Jobs | International Livestock Research Institute (ILRI)

Computing Systems Analyst. Nairobi, Kenya. Internal Audit. Internal Audit Clerk. ... International Livestock Research Institute (ILRI) Jobs. Company Website;
Read more

International Livestock Research Institute · GitHub

GitHub is where people build software. ... Ansible playbooks for ILRI research-computing infrastructure Updated Sep 7, 2016. Java 4 553 DSpace ...
Read more

Research Computing | LinkedIn

View 4226 Research Computing posts, presentations, experts, and more. Get the professional knowledge you need on LinkedIn.
Read more

LiveGene

Research Computing Cluster; Azizi Biorepository; LiveGene. Delivering improved genetics to the world’s small-scale livestock keepers
Read more