Since mid-2013, we have a grid computer (called durandal) designed for the assembly of NGS data, comparative and functional genomics, phylogenomics, image analysis, environmental modelling and systems biology. It is an IBM/Lenovo Flex System (sold by NSI) composed of one big computing node (x440) and nine smaller computing nodes (x240), featuring a total of 196 physical cores, 2 TB of RAM and 58 TB of shared mass storage.
The big node has 32 physical cores (4 x Intel Xeon E5-4620 with 8 cores running at 2.2 GHz) and 512 GB of RAM, while four of the small nodes each have 16 physical cores (2 x Intel Xeon E5-2670 with 8 cores running at 2.6 GHz) and 128 GB of RAM. Two additional small nodes were installed in Summer 2015, each heaving 20 physical cores (2 x Intel Xeon E5-2670 v2 with 8 cores running at 2.5 GHz) and either 176 or 384 GB of RAM. The latter node is also equipped with a GPU accelerator (NVIDIA Tesla K40 with 2880 CUDA cores and 12 GB of RAM). Finally, three new small nodes were installed in Fall 2016, each having 20 physical cores (2 x Intel Xeon E5-2640 v4 with 10 cores running at 2.4 GHz) and 160 GB of RAM.
The ten nodes are interconnected by a fast (10 Gb) link using optical fibre. Other features of durandal include two shared mass storage subsystems composed of fast small disks (8 TB usable in RAID5) and slower large disks (50 TB usable in RAID5), respectively, as well as redundant power supplies secured by a large capacity battery (5600 W) in case of power failure. The grid is located in a dedicated room equipped with air-conditioning and secured with monitoring and alarm systems.
The operating system of durandal is CentOS 6.6. A large range of bioinformatics software packages are installed and available through a job queueing system (Open Grid Engine). When logged in the system, 392 logical cores are actually available to users, thanks to Hyper-Threading technology.
In a separate room, we also have a second machine (a Dell PowerEdge T620 called traxusIV) dedicated to data security. It has 29 TB (RAID6) of mass storage, redundant power supplies secured by a battery (1000 W) and a specialized free software (BackupPC) that backups our grid and our workstations (and laptops) every night (or day).
Together durandal and traxusIV are currently worth 160 kEUR. Both were acquired and upgraded through a series of grants awarded to Denis Baurain, Marc Hanikenne, Patrick Meyer, Pierre Cardol, Claire Périlleux, Annick Wilmotte, Sébastien Rigali and InBioS-PhytoSYSTEMS itself. Among these were three grants from the University of Liège, "Fonds spéciaux pour la recherche": "Crédit de démarrage 2012" (SFRD-12/03 and SFRD-12/04) and "Crédits classiques 2014" (C-14/73), and two grants from the Belgian FRS-F.N.R.S.: "Crédit de recherche 2014" (J.0080.15 and J.0148.15). The project was initiated by Denis Baurain and implemented by Damien Sirjacobs, who also acts as the system administrator.
The grid is managed by the Unit Eukaryotic Phylogenomics. Members of InBioS-PhytoSYSTEMS interested in high-performance computing and/or automatic backup of their workstation (or laptop) are encouraged to address their request to Denis Baurain or to Damien Sirjacobs.