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Big Data Cluster in “Shared Nothing” Architecture in Leipzig - Overview on Galaxy Operations Concept

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Overview on Galaxy Operations Concept

Diversity of Scientists Needs

There is a high diversity in software and requirements of big data scientists, similar to the broad field of big data research and software frameworks used in the field. In our experience just an Apache Hadoop cluster does not fit all.

Only a small part of the researchers computing demand can be queued as an Apache Hadoop batch job. Often scientists need quite specific software, at times with specific software versions or configurations that conflict the ones required by other scientists. Sometimes they want to get performance benchmarks on a dedicated specific cluster environment.

Cluster Partitioning as Solution

Our approach to tackle this problem of diversity is to divide the cluster as needed into cluster partitions. Each partition can be equipped with different software and configuration. Each partition can be seen as smaller (sub) cluster with a subset of designated worker nodes. Worker nodes can get reassigned to new or other clusters when the requirements or reservations shift. Some of the cluster software seen so far is even capable of accepting or decommissioning nodes during operation. Examples for this are the decommissioning feature of Apache Hadoop or the node removal in Slurm.

Of course cluster partitioning has it’s downsides as well. Probably the main one is suboptimal cluster utilization because shifting partitions not fast or fine granular enough. But currently we see no alternative. As far as we know there is no cluster scheduler capable of hosting most of the big data software without configurational or performance drawbacks.

The cluster of 90 worker nodes is split in this example into 4 node subsets = cluster partitions, here with 30 nodes, 32 nodes, 18 nodes and 20 nodes.
The cluster of 90 worker nodes is split in this example into 4 node subsets = cluster partitions, here with 30 nodes, 32 nodes, 18 nodes and 20 nodes.

Practical Cluster Partitioning

For practical cluster partitioning the usage of Foreman + Puppet as management software helps us again. We can utilize the management software to reconfigure cluster nodes or even get fresh installed nodes when needed. But only a whole node is the finest cluster granularity so far. And reconfiguration and data transfer for the addition and removal of nodes take quite some time. Therefore, we try to limit the amount of partition shifting by recommending cluster reservation time to be something between a couple of days and a couple of weeks, depending on the scientist’s requirements, the partition’s size and cluster utilization.

Cluster Partition Types

At Galaxy we support the following partition and usage types:

  • Apache Hadoop Batch Job: Submission of batch jobs in a cluster shared with other users. Apache Flink or Apache Spark Jobs can be run on this partition as well as both frameworks support running on Hadoops scheduler YARN.
  • Apache Hadoop Exclusive Partition: Reserved Partition with Apache Hadoop dedicated for one user or user group.
  • Exclusive Flexible Partition: Reserved partition individually configured and dedicated for one user or user group. Realized either via Puppet, manual configuration or with Docker containers.
  • Slurm Batch Jobs (coming soon): With the Slurm scheduler some big data tasks not compatible with Apache Hadoop can get scheduled without the need for a dedicated flexible partition.

For the future we consider supporting e.g. Apache Mesos batch jobs or OpenStack as well.

Cluster Manager

The cluster manager helps us with organizing the cluster partitions and the scientists’ usage of them. This part of the cluster is still under development. As a first step a calendar with web GUI is realized where we can track reservations for partition usage and transform them to users’ access rights. In future versions the cluster manager could automate the cluster partition resizing, creation and removal.

Screenshot from a development version of the Cluster Manager with a calendar view on cluster partition reservations.
Screenshot from a development version of the Cluster Manager with a calendar view on cluster partition reservations.