Data Centre Deployment

This page describes the installation of SCAPE platform in a High Performance Computation centre. The hardware platform is described here.

Overview

Deployment of SCAPE platform in large data centres or in Cloud Computing environments raises specific challenges, such as dynamic allocation of components to compute nodes, monitoring the platform, quality of service etc. Automated cluster provisioning and platform deployment is achieved by integrating and/or extending a set of specific tools, such as: a Node Deployment system (Cobbler)

• a node deployment system, such as Cobbler, helps administrators to dynamically allocate the nodes: systems can be added and removed from the management of the node deployment and configuration management systems on the fly, both on bare-bones computing hardware and on virtualized computing resources
• On the fly software deployment using the customized Configuration Management System (Puppet): it allows the evolution of SCAPE software packages by providing “high-level” recipes describing the tools and relations between them. It enables dynamic allocation of SCAPE components to computing resources with minimal human intervention, providing, in this way, a more deterministic software deployment process. It ensures that software is deployed as expected by the developers, meeting all required expectations.
• Monitoring/Quality measures: the integrated Puppet Configuration Management system natively provides capabilities for integration with and deployment of the Nagios monitoring solution. This allows operators/administrators to provide a better QoS.
  

Cloud Deployment Toolkit for SCAPE Platform

The toolkit aims to provide the software components and corresponding puppet modules for deploying critical SCAPE Components in Cloud Environments. The PoC (Proof of Concept) aims at demonstrating the operation of selected SCAPE Platform Components in Cloud Environments, focusing on Eucalyptus and Amazon EC2 and fostering their scalability for providing on demand computing capacity. The toolkit is composed of:

• Developing a GUI (web based portal) for the management of an SCAPE Platform deployment on Eucalyptus based clouds, and in the next stages on Amazon Web Services EC2
• Integrating Puppet and PuppetDB Rest API’s
• Abstracting EC2 and Eucalyptus API for providing an uniform programming environment, ensuring this way the portability

More details, plus user guide on SCAPE Cloud Toolkit, one can find on Bitbucket. In order to orchestrate the deployment of different components we are using Puppet Configuration Management System customized to SCAPE needs. More details on modules used within the SCAPE project are given in this Bitbucket project. Below are Puppet recipes for most common components and tools of the SCAPE platform:

• Taverna server
• Tomcat server
• SCAPE packages: For now, following tools are integrated: jpylyzer pagelyzer and xcorrsound. Please check project home on Bitbucket for regular updates.

Another tool aims to provide integration between the Hadoop Filesystem (HDFS) and more ‘classical’ products like FTP. It is an Apache Mina based FTP server for exposing HDFS filesystem to local/remote clients that lack HDFS capabilities. One of the main use cases of this tool is to facilitate data staging between legacies HPC systems and Hadoop based computing clusters. See Bitbucket project for source code and installation instructions.

PSNC Data Center services

Based on the scenarios identified by WCPT it was agreed to implement and deploy several services at PSNC for integrating WCPT working environment. The following services are needed to execute specific scenarios at WCPT:

• DICOM Download server - this service is responsible for providing access to all anonymized DICOM files stored at PSNC. This service is necessary to execute scenario named large-scale access at hospital because the working environment at WCPT needs stored DICOM files in order to present them for all interested WCPT users. It will be also used in the educational portal (related to large scale access for educational purposes scenario) as a background service for accessing DICOM files. Project repository: https://git.man.poznan.pl/stash/projects/SCAP/repos/dds/browse
• DICOM HDFS-enabled server - this service provides the possibility to upload anonymized DICOM files to the PSNC's HDFS cluster. It is necessary to execute scenario named large-scale ingest of medical data as the working environment at WCPT needs to transfer anonymized DICOM files to PSNC Data Center. This service is also important building block for the scenario named large scale access for educational purposes because the educational portal will provide on-line viewer of the stored DICOM files. Project repository: https://git.man.poznan.pl/stash/projects/SCAP/repos/dicom/browse
• HL7 HDFS-enabled gateway - this service provides the possibility to upload HL7 metadata files about patient's visits. It is necessary to execute scenarios named large-scale ingest of medical data as the working environment at WCPT needs to transfer HL7 files to PSNC Data Center. This service is also important in the context of scenarios named large scale access for educational purposes and large scale analysis because in the former scenario HL7 needs to be presented on-line, while in the latter scenario HL7 files will be analyzed with dedicated Hadoop jobs. Project repository: https://git.man.poznan.pl/stash/projects/SCAP/repos/hl7/browse 

All of the services are currently deployed on the PSNC Development cluster and are the subject of tests at the WCPT working environment. After the testing period and additional improvements that will be necessary to implement, it is envisioned to start production mode environment. The final deployment of all the tools at the Data Center is envisioned to happen in M40.