Example production server set-ups

CellNanOs (Center of Cellular Nanoanalytics), University of Osnabrück

The OMERO server at CellNanOS serves a community of 75-100 users and 17 microscope stations (13 different systems), producing 180-1360 GB of data per day. It is hosted on RedHat 7.3 with data stored on an IBM GPFS file system.

Hardware

  • Dell R630 running RedHat 7.3, 32 cores, 128 GB RAM
  • IBM GPFS storage, 6 TB SSDs, 178 TB SATA

Network infrastructure

1-10 GBit connection between microscope workstations and OMERO

Backup/archive

  • IBM TSM 1.4 PB
  • daily migration of new data to tape, archive on tape

Micron, Oxford

The OMERO server at Micron, Oxford houses two OMERO instances, the databases for both these instances, and a single OMERO.web instance which serves them both. The second OMERO instance (Raff OMERO) originated from another group’s private OMERO server, which is now managed by Micron, but there was no way to merge this data into the main server. The main OMERO instance is configured to interface to a departmental LDAP server to authenticate users and get initial authorization details.

server set-up diagram

OMERO Data1 in the diagram is a large filestore server which hosts all the image data. This is made available to the OMERO server itself via a Samba mount. This server has 36 TiB of space of which OMERO is using 16 TiB and Raff OMERO is using 600 GiB. This is backed up to a tape robot.

OMERO Processor1 consists of a 32 core, 128GiB RAM processing machine for doing image analysis. This is connected on a completely private network to the OMERO server (to avoid issues with configuring OMERO.grid to be secure) and runs scripts using OMERO.grid.

Stats

  • 90 users
  • 40 groups
  • 36 TiB of data storage space, of which 16.6 TiB is currently in use
  • Performance statistics to come

Biozentrum, University of Basel

The OMERO server at Biozentrum has around 270 users and currently uses 52 TB of data storage space, with an average monthly increase of 1 TB. It is run on CentOS 7.1 with data hosted on an native-mounted GPFS file system (General Parallel File System, IBM).

Hardware

Remote storage consists of:

  • native-mounted GPFS volume

Local storage consists of:

  • 2 x 240 GB SATA SSD, RAID 1, OS and OMERO software
  • 2 x 400 GB SATA SSD, RAID 1, Postgres DB

Computational resources:

  • Lenovo System x3650 M5, dual-CPU Intel Xeon Processor E5-2643 v3 6C 3.4GHz 20MB Cache 2133MHz
  • 256 GB of memory

Network infrastructure

  • 10 Gbit/s Infiniband connection to GPFS storage, 10 Gbit/s Ethernet connection to the client network, local, VPN support, dedicated

GReD Research Center, Clermont-Ferrand, France

The Genetics, Reproduction and Development Research Center has 65 users and currently uses 3 TB of storage, with an average monthly increase of 90 GB. It is run on Debian Squeeze.

Hardware

  • 11 TB of storage spread over 8 local hard drives (2 TB), RAID 5

Computational resources:

  • 1 Intel Xeon E5506 (4 physical cores)
  • 8 GB of memory

Network infrastructure

The server is hosted inside the faculty of medicine where the network works at 100 Mbit/s. There are are 4 Gbit/s ports on the server but only one is currently in use.