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.
Dell R630 running RedHat 7.3, 32 cores, 128 GB RAM
IBM GPFS storage, 6 TB SSDs, 178 TB SATA
1-10 GBit connection between microscope workstations and OMERO
IBM TSM 1.4 PB
daily migration of new data to tape, archive on tape
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.
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.
36 TiB of data storage space, of which 16.6 TiB is currently in use
Performance statistics to come
IMCF, Biozentrum, University of Basel¶
The OMERO server at the IMCF / Biozentrum has around 650 users and uses more than 200 TB of data storage space, with an average monthly increase of 10 TB (as of mid-2021). It is run on CentOS 7 with data hosted on a native-mounted GPFS file system.
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
Lenovo System x3650 M5
12 Cores (2 x Intel Xeon E5-2643v3 3.4GHz)
256 GB RAM
40 Gbit/s Infiniband connection to GPFS storage
10 Gbit/s Ethernet connection to the client network
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.
11 TB of storage spread over 8 local hard drives (2 TB), RAID 5
1 Intel Xeon E5506 (4 physical cores)
8 GB of memory
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.
Image Data Resource¶
The Image Data Resource is an OMERO repository maintained by OME and deployed on the EMBL-EBI Embassy Cloud which publishes reference imaging datasets. See the IDR deployment page for more information about the architecture and the IDR studies page for the most up-to-date metrics.