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=== nodes === | === 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 'node0060'), and two so called 'fat nodes' that each have 64 cores and 1TB of RAM ('fat001' and 'fat002'). | 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 'node0060'), 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 | DEVICE INFORMATION | ||
Hostname State Memory Cores CPU Speed GPU NICs IB Category | Hostname State Memory Cores CPU Speed GPU NICs IB Category | ||
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storage02..storage06 UP 67.6 GiB 32 Intel(R) Xeon(R) CPU E5-2660 0+ 2199 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 | 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 === | fat001, fat002 UP 1.0 TiB 64 AMD Opteron(tm) Processor 6376 2299 MHz 5 1 fat | ||
=== filesystem === | |||
=== network === | === network === | ||
Revision as of 14:24, 23 November 2013
The Breed4Food (B4F) cluster is a joint High Performance Compute (HPC) infrastructure of the Animal Breeding and Genomics Centre 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 through 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 'node0060'), 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
network
Housing at Theia
include some pictures
Access Policy
etc
Cluster Management Software and Scheduler
The B4F cluster uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.