LSG specifications

This page describes the specifications for the Life Science Grid (LSG) clusters. For a list of the clusters, see Life Science Grid clusters.

Warning

The Life Science Grid infrastructure is scheduled to be decommissioned mid 2018. After the decommissioning the smaller LSG clusters within the UMC’s and other universities will cease to exist; the large central Grid clusters at NIKHEF and SURFsara will remain. More details about the decommissioning can be found here: https://userinfo.surfsara.nl/documentation/decommissioning-life-science-grid

Quick summary

Last update: December 2016

At the time of writing two different hardware setups coexists in the LSG. The “classic” hardware setup is being progressively replaced by an updated one. The present document will differentiate between this two setups.

“Classic” hardware setup

LSG cluster Capacity
Operating system Linux CentOS 6.x 64bit
Total number of cores 128 CPU cores at 2.3 GHz
Total amount of memory 512 GB
Total scratch space 10TB
Disk storage 40TB of staging area
Network backbone 10Gbit/s local switch, 1Gbit/s external connectivity
Clusters still using the “classic” hardware setup:
  • AMS
  • BCBR
  • EMC
  • RUG
  • TUD

Updated hardware setup

LSG cluster Capacity
Operating system Linux CentOS 6.x 64bit
Total number of cores 184 CPU cores at 2.2 GHz (Intel Xeon E5-2650)
Total amount of memory 656 GB
Total scratch space 20TB
Disk storage 40TB of staging area
Network backbone 10Gbit/s local switch, 1Gbit/s external connectivity
Clusters using the updated hardware setup:
  • AMC
  • KUN
  • LUMC
  • UM
  • VU
  • WUR

Worker Nodes

The jobs will be actually executed on this kind of nodes; this is the hardware specification:

Classic hardware setup

  • Dell PowerEdge R815 4xAMD Opteron(tm) Processor 6376
  • Type: Bulldozer
  • Cores: 64
  • RAM: 256GB
  • Number of nodes: 2

Updated hardware setup

  • Fujitsu Primergy RX2530 M2, Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
  • Type: Broadwell
  • Cores: 23 (46 threads with HT enabled)
  • RAM: 164 GB
  • Number of nodes: 4

Storage Node

This node stores all the data related to the user jobs:

  • PowerEdge R515 2xAMD Opteron(tm) Processor 4280
  • Type: Bulldozer
  • Cores: 16
  • RAM: 128 GB
  • Number of nodes: 1
  • Storage space: 40TB

Computing Element

The Computing Element (CE) is a virtual machine hosted by the corresponding LSG cluster; the CE gets the jobs from the users and sends them to the appropriate WNs:

Classic hardware setup:
  • Cores: 2
  • RAM: 4 GB
  • Number of nodes: 1
Updated hardware setup:
  • Cores: 2
  • RAM: 8 GB
  • Number of nodes: 1

User Interface

Each LSG cluster hosts a User Interface (UI) a virtual machine from where the users can prepare and submit their jobs. Please be aware that this server’s purpose is NOT to execute directly your programs. Use instead Torque commands such us ‘qsub’ to submit your jobs to the Worker Nodes which have more CPU/Memory capacity. The VM specifications of the UI are: This is a virtual machine running on one of the Service Nodes; please be aware that this server’s purpose is NOT to execute directly your programs. For local datasets every user has a default quota of 50GB, unless more is required for a specific purpose. Temporary datasets may be placed under the /scratch directory, which will be cleaned up periodically. Use instead Torque commands such us ‘qsub’ to submit your jobs to the Worker Nodes which have more CPU/Memory capacity. Thank you for your understanding. The VM specifications of the UI are:

Classic hardware setup:

  • Cores: 8
  • RAM: 16 GB
  • Number of nodes: 1
Updated hardware setup:
  • Cores: 8
  • RAM: 8 GB
  • Number of nodes: 1

Queues

Each LSG cluster offers a set of job queues:

Queue Max. Walltime (hh:mm:ss)
express 00:30:00
infra 00:30:00
medium 36:00:00
long 72:00:00

The infra queue is reserved for system checking and maintenance, final users are not allowed to submit jobs to this queue.

The above queues can be used by both grid jobs and PBS jobs.