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The LOFAR Cluster
This page describes the LOFAR cluster for (potential) users. The cluster is used to store the data from the BlueGene and to run the pipelines that will do the “standard” reduction and calibration of this data. After this pipeline processing, the results are stored in the Lofar Export (staging) Archive.
We welcome authorized users on the cluster. For the time being the users are bound to only a part of the cluster. This part is called a subcluster. Various users groups have been appointed to use a specific subcluster.
User Access
Access through portal to Cluster frontend
You can access the Lofar cluster through the portal. On your own system, try:
> ssh -X portal.lofar.eu
to connect. We maintain a ssh whitelist, so only registered institutes are able to login.
Please send an email to grit at astron.nl or h.paas at rug.nl to add your institute or personal IP number to this white list.
When you are logged in for the first time, you'll have an empty home directory. You'll have to login at one of the two frontend nodes lfe001
oflfe002
using ssh -X
(as above). When you don't know which one, please use lfe001
by default.
For more sophisticated useage of ssh
read this page.
LOGIN environment
See The Lofar Login Environment page for information on your default login environment. Only the default environment is supported, so if you defer from this, you're on your own..!
Do and Don'ts
DON'T:
- Store data in your
$HOME
onportal.lofar.eu
; this system has a ridiculously small disk and filling it will prevent other users to access properly - Pump around large amounts of data between nodes.
- Leave unused data on the systems. Clean it up, so others can make use of the available disk space.
DO:
- Help improve the system by sending suggestions for improvements or new packages to the administrators
Short LOFAR Cluster layout
The Lofar cluster is devided into 8 subclusters. Each subcluster is a processing cluster for a specific commsissioning group. There are 72 compute nodes (named lcexxx
) and 24 storage nodes (named lsexxx
) in total. Each subcluster has 9 compute nodes and 3 storage nodes of 24TB raw capacity. The storage nodes have 4 RAID5 partitions of 5.1TB each. Each partition holds a single XFS filesystem. Each filesystem is NFS mounted on all 9 compute nodes in the subcluster (but NOT in other subclusters). So 1 compute node has 12 NFS data volumes of approx. 5.1 Tbyte mounted.
Frontend
A frontend has 2 Intel Xeon L5420 quad core processors, 16GB internal meomory, 2 GbE interfaces and 2TB disks in RAID5 configuration.
There are actually two identical frontends: lfe001
and lfe002
. Both of them serve a specific group of subclusters. The frontends are used to build the software and regulate the workload on the subclusters.
Processing units
The compute elements have 2 Intel Xeon L5420 quad core processors, 16GB internal meomory, 2 GbE interfaces and 1TB disks in RAID0 configuration. They can be accessed by secure shell and they are grouped.
Storage Units
The storage nodes are HP DL180G5 boxes, having 2 Intel Xeon L5420 quad core processors, 16GB internal memory, 6 GbE network interfaces and a total of 24TB disk space.
The nodes have been named lsexxx
with xxx
a number from 000
to 024
.
The disk space is divided into 4 partitions of 6 disks each, set up in RAID5 configuration. The partitions are called “/data1” - “/data4”. The installed filesystem is the XFS filesystem.
Available Subclusters
The current subcluster assignment is:
lfe001:~> showsub
This script shows the subcluster definitions
sub lce-nodes lse-nodes cexec-lce cexec-lse In use for: ==== ========= ========= ========= ========= =========== sub1 lce001-lce009 lse001-lse003 lce:0-8 lse:0-2 production group sub2 lce010-lce018 lse004-lse006 lce:9-17 lse:3-5 no power sub3 lce019-lce027 lse007-lse009 lce:18-26 lse:6-8 imaging group sub4 lce028-lce036 lse010-lse012 lce:27-35 lse:9-11 no power sub5 lce037-lce045 lse013-lse015 lce:36-44 lse:12-14 pulsar group sub6 lce046-lce054 lse016-lse018 lce:45-53 lse:15-17 no power sub7 lce055-lce063 lse019-lse021 lce:54-62 lse:18-20 developers group sub8 lce064-lce072 lse022-lse024 lce:63-71 lse:21-23 no power
The lce-nodes ar ethe compute/processing nodes, the lse-nodes are the associated storage nodes. Only use the storage nodes that are associated with your processing node!
Old Obsoleted Stuff (only here for completeness)
The lioffen processing cluster
Hardware setup
The 10-node post processing cluster has lioffen
as frontend node. The cluster nodes are called lioff021
- lioff030
.
Each node has 2-Gbyte of physical RAM, and another 2-Gbyte swap space. Each node contains two AMD Opteron 2-GHz CPUs with 1 Mbyte cache. They are currently running Ubuntu 7.10 (Gutsy).
Usage
The offline nodes are used for processing the CS1 data products that are stored on the lifs-nodes. To this purpose, all disks of all lifs-nodes are NFS mounted on all offline nodes.
Environment
There is a login environment with some startup-scripts that make it easier to use several available tools. Please see this description with more information.
Disks and NFS mounts
The big disks on the off-line storage nodes (lifs001
- lifs012
) are NFS auto-mounted when access is required. See this section below.
On each node is a 360 Gbyte /data
partition to store and process local data.
Finally, there is the NFS mounted /home
partition, where the user's home directories are, and the /app
-mount on lioffen
, where the centrally stored applications reside.
Applications
Most applications can be found in directory /app
.
- See the login environment for how to start using any of the software packages installed.
listfen 32-bit cluster
The old 32 bit offline cluster has been removed. Only frontend “listfen” and the 10 lifs storagenodes are still available.
LIFS storage nodes
There are 12 old 1TB storage nodes, lifs001 till lifs012. They are still in use for development and testing. Lifs001 till lifs008 are used by the Observatory to store recent observations. Lifs009 til lifs012 hold datasets that are a result of some kind of processing. We are already observing with the new cluster hardware. The lifs nodes will be removed the end of November.
Offline processing clusters
The disks of the offline storage nodes are NFS mounted on all these offline nodes. These systems are in use for offline processing (i.e. when data has been transfered from the central storage facility).
Offline storage cluster
This cluster acts as a temporary data buffer. Data is copied from the online storage systems to these systems, so that the online systems can be used to store new data. These systems are accessable from the offline processing clusters, allowing post-processing of the data. More information can be found on this page.
Bootleg mechanism
The new cluster is subject to the “bootleg” deployment regime. This service and installation facility was developed by Harm Paas of the CIT department of the RUG University in Groningen. He already had many years of experience with this system at the Computer Science Faculty. One server in the CEP domain is capable of installing many cluster nodes at once in less than 10 minutes. The administration of all nodes is done on this single Bootleg server.
Central administration
The way the CEP cluster has been set up is as follows: We are using Ubuntu Linux LTS-8.04 as Operating System within the whole cluster. Bootleg takes care of all of the server management in the cluster by creating new images, administering servers, keeping track of updates and correct start up of servers by sending them new images when it finds outdated versions at boot time.
Profiles
Bootleg also administers machine profiles: Depending on the function of the server in the cluster it needs other settings and profiles. This management strategy implies that we have to keep track of all programs installed in the Linux system itself, so we will be able to add them to the image. We plan to build fresh images every month (at the maintenance days).
Instantanious changes
We are also able to respond quickly on extra-program demands for system programs. Within bootleg there is a mechanism to roll-out extra programs through the cluster from a central administration point (CAP). From the CAP we order to deploy a program or a settings-change and after 1 minute the whole cluster will be updated with the change. So if you need extra system programs, simply ask, and you get it almost instantly on every server in the cluster!
Application programs
For an application program change or addition there is another method. Of course you develop your programs in your own user space and/or svn repositories. So you have completely control over all of this. Program releases for the cluster itself reside on a central disk. Normally we (as system administrators) are not involved in the application program deployment. Only if a completely new package is added under a new directory name we need to make this available in the cluster by connecting it in the O.S. via a link to the newly created package name. So there is a clear interface between system programs and applications: The connection between them is at a well defined point, the /opt directory is intended for this. The same goes for database content (mysql, postgresql, …). Although it might involve OS program installation and services, the database content itself will never be on the Linux system image but stored on a separate data server.
Again: Simply ask, we can connect your program and make it available cluster-wide.