Anunna

The Breed4Food (B4F) cluster is a joint High Performance Compute (HPC) infrastructure of the Animal Breeding and Genomics Centre (WU-Animal Breeding and Genomics and Wageningen Livestock Research) and four major breeding companies: Cobb Vantress, CRV, Hendrix Genetics, and TOPIGS.

Rationale and Requirements for a new cluster

The B4F Cluster is, in a way, the 7th pillar of the Breed4Food programme. While the other six pillar revolve around specific research theme, the Cluster represents a joint infrastructure. The rationale behind the cluster is to enable the increasing computational needs in the field of genetics and genomics research, by creating a joint facility that will generate benefits of scale, thereby reducing cost. In addition, the joint infrastructure is intended generate cross-organisational knowledge transfer. In that capacity, the B4F Cluster acts as a joint (virtual) laboratory where researchers across the isle (academic and applied) can benefit from each other's know how. Lastly, the joint cluster, housed at Wageningen University campus, allows retaining vital and often confidential data sources in a controlled environment, something that cloud services such as Amazon Cloud or others usually can not guarantee.

Process of Acquisition and financing

The B4F cluster was financed by CAT-AGRO <insert further details>

Architecture of the cluster

overview of nodes, fs, etc.

nodes

The cluster consists of a bunch of separate machines that each has its own operating system. The default operating system throughout the cluster is RHEL6. The cluster has two master nodes in a redundant configuration, which means that if one crashes, the other will take over seamlessly. Various other nodes exist to support the two main file systems (the Lustre parallel file system and the NFS file system). The actual computations are done on the worker nodes. The cluster is configured in a heterogeneous fashion: it consists of 60 so called 'slim nodes', that each have 16 cores and 64GB of RAM (called 'node001' through 'node060'), and two so called 'fat nodes' that each have 64 cores and 1TB of RAM ('fat001' and 'fat002').

Information from the Cluster Management Portal, as it appeared on November 23, 2013:

 DEVICE INFORMATION
 Hostname	State	Memory	Cores	CPU	Speed	GPU	NICs	IB	Category
 master1, master2	UP	67.6 GiB	16	Intel(R) Xeon(R) CPU E5-2660 0+	2199 MHz		5	1	
 node001..node042, node049..node054	UP	67.6 GiB	16	Intel(R) Xeon(R) CPU E5-2660 0+	1200 MHz		3	1	default
 node043..node048, node055..node060	DOWN	N/A	N/A	N/A	N/A	N/A	N/A	N/A	default
 mds01, mds02	UP	16.8 GiB	8	Intel(R) Xeon(R) CPU E5-2609 0+	2400 MHz		5	1	mds
 storage01	UP	67.6 GiB	32	Intel(R) Xeon(R) CPU E5-2660 0+	2200 MHz		5	1	oss
 storage02..storage06	UP	67.6 GiB	32	Intel(R) Xeon(R) CPU E5-2660 0+	2199 MHz		5	1	oss
 nfs01	UP	67.6 GiB	8	Intel(R) Xeon(R) CPU E5-2609 0+	2400 MHz		7	1	login
 fat001, fat002	UP	1.0 TiB	64	AMD Opteron(tm) Processor 6376	2299 MHz		5	1	fat

filesystem

Parallel File System: Lustre

At the base of the cluster is an ultrafast file system, a so called Parallel File System (PFS). The PFS implemented in the B4F Cluster is called Lustre. Lustre has become very popular in recent years due to the fact that it is very feature rich, deemed very stable, and is Open Source. Lustre nowadays is the default option for PFS in Dell clusters as well as clusters sold by other vendors. The PFS is mounted on all head nodes and worker nodes of the cluster, providing a seamless integration between compute and data infrastructure. The strength of a PFS is speed - the total I/O should exceed .... by design. With a very large number of compute nodes - and with very high volumes of data - these high read-write speeds that the PSF can provide are necessary. The Lustre filesystem is divided in several partitions, each differing in persistence and backup features. The Lustre PSF is meant to store (shared) data that is likely to be used for analysis in the near future. Personal analysis scripts, software, or additional small data files can be stored in the $HOME directory of each of the users.

Network File System (NFS): $HOME dirs

Each user will have his/her own home directory. The path of the home directory will be:

 /home/[name partner]/[username]

/home lives on a so called Network File System, or NFS. The NFS is separate from the PFS and is far more limited in I/O (read/write speeds, latency, etc) than the PFS. This means that it is not meant to store large datavolumes that require high data transfer or small latency. The /home partition will be backed up daily.

Housing at Theia

include some pictures

Access Policy

Access policy is still a work in progress. In principle, all staff and students of the five main partners will have access to the cluster. Access needs to be granted actively (by creation of an account on the cluster by FB-ICT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated.

Contact Persons

A request to access the cluster needs to be directed to one of the following (please refer to appropriate partner):

Cobb Vantress

• Wes Barris
• Jun Chen

ABGC

Animal Breeding and Genetics

• Alex Hulzebosch
• Hendrik-Jan Megens

Wageningen Livestock Research

• Mario Calus
• Ina Hulsegge

CRV

• Frido Hamoen
• Chris Schrooten

Hendrix Genetics

• Ton Dings
• Abe Huisman
• Addie Vereijken

Topigs

• Henk van Dongen
• Egiel Hanenbarg
• Naomi Duijvensteijn

Cluster Management Software and Scheduler

The B4F cluster uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.

• Logging into cluster using ssh
• Monitor cluster status with BCM
• Submit jobs with Slurm