Download - Canadian Light Source
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cience Studio
Canadian Light Source
Elder Matias (CLS)EPICS April 09 Collaboration Meeting
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Index
Where is the CLS? CLS – Current projects ScienceStudio ANISE – Data streaming expansion to
ScienceStudio
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Where is Saskatoon?
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• 1964 Saskatchewan Accelerator Lab (SAL) was established for chemistry and nuclear physics research.
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1964 Saskatchewan Accelerator Lab (SAL) was established for chemistry and nuclear physics research.
1999 SAL operations were discontinued, and the accelerator was refurbished as an injector for a new storage ring.
SR1 Machine Parameters 2.9 GeV DBA lattice with 12-fold period170.88 m
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Phase 1 (operation): Total of 7 scientific
and 2 diagnostics beamlines.
Phase 2 (commissioning): Total of 7 additional
beamlines and building expansion for
medical imaging. Phase 3 (pre-design):
Total of 8 additional beamlines and
building expansion.
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Major Projects
Common Control Server virtualization
Accelerator Linac upgrade - Replace/upgrade Linac Modulators, RF
Sections, Power Supplies Transverse feedback and bunch cleaning Upgrade to existing power supplies Injection with shutters open
Beamlines Phase 2 Beamlines – Final commissioning Phase 3 Beamline Projects including a building expansion ScienceStudio
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vmWare ESX Virtualization
Network
Redundant Network Connection
VM Physical Node VM Physical Node
SAN
EMC Storage Array
ISCSI ISCSI
VM Virtual CentreEnvironmet
Redhat
ScientificLinux
Windows
VM Virtual CentreEnvironmet
ScientificLinux
Windows
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cience Studio
ScienceStudio
Elder Matias (CLS)EPICS April 09 Collaboration Meeting
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What Is Web 2.0?
In plain English …. Automating tedious tasks using web technology Tools to help people and software collaborate
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Scientific American May 2008Science 2.0 – The Risk and Reward of Web-Based Research
---------------------------------
“Our real mission isn’t to publish journals but to facilitate scientific communication” Timo Hannay – Head of Web Publishing at Nature Publishing Group
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Traditional Beamline Controls
EPICS Tools Configuration Tool User GUI & ROOT
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User Access to Synchrotrons
What middleware was needed to resolve the limitations? Workflow management Engine for the User Office Web Portal for remote data access (during and post
experiment) Enterprise Service Bus and SOA to integrate internal and
external data analysis services How do your plans meet the needs
Users will have frequent remote access to the VESPERS beamline at the Canadian Light Source under conditions where many collaborators can participate in the experiment.
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Science Studio serves three purposes:
Management of all aspects of a scientific experiment including data storage, collaboration with others, processing of data;
Control of, or interaction with, remote experiments on the CLSI VESPERS Beamline and UWO Nanofabrication Laboratory and
User Services (sample management, scheduling, peer review, user training)
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Team: People and Orgs
Remote Control
User Services
System Deployment
Integration
System Architecture
System Requirements
Testing
Data Analysis/Grid Computing
User Office Software
Scientific Workflow Engines
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Team: People and Orgs
Dionisio Medrano
Dylan Maxwell
Daron Chabot
Elder Matias
Chris Armstrong
John Haley
Mike Bauer
Stewart McIntyre
Marina Suominen Fuller
Jinhui Qin
Nathaniel Sherry
Yuhong Yan
Zahid Anwar
Ludeng (Eric) Zhao
Dan Ni
Yaofeng Xu
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System Architecture
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
1. VESPERS Beamline2. EPICS control system3. Beamline Control Module (BCM)4. Web Application5. Database6. File Storage7. Web Interface
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VESPERS Beamline
VESPERS — Very Sensitive Elemental and Structural Probe Employing Radiation from a Synchrotron
A bending magnet beamline on sector 6 at the Canadian Light Source synchrotron in Saskatoon, Saskatchewan.
A hard x-ray microprobe with an energy range of 6 to 30keV.
Techniques: X-Ray Fluorescence (XRF) & X-Ray Diffraction (XRD)
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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VESPERS Endstation
CCD Detector (XRD)
Microscope
MCA Detector (XRF)Sample
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EPICS Low-level Control System
EPICS — Experimental Physics and Industrial Control System
The standard control system at the CLS.
EPICS consists of a network of Input-Output Controls (IOCs) which are connected to directly to devices.
An IOC provides many Process Variables (PVs) which relate to either an input or output from a device and have a unique name.
Channel Access (CA) is used to read or write to any PV without knowing which IOC provides the PV.
More than 50,000 PVs in the CLS control system.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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EPICS at the CLS
ProfibusTCP/IP
Siemens S7/300 PLC
ModbusTCP/IP
GPIB
RS-232
Channel Access Protocol
IOC
IOC
IOC
IOC
State MachineEngine
CA
CA
CA
CA
CA
CA
Operator WorkstationUser Applications
TouchPanels
CA
CA
Telemecanique Momentum PLC
VME
IOC
CA
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Beamline Control Module (BCM)
The BCM provides a high-level interface to the low-level control system (EPICS).
Logical and physical separation of business logic and control logic.
Virtual device abstraction that provides independence from low-level control system.
Virtual devices can be logically organized into a device hierarchy.
Basic devices can be combined to build more functional devices.
Communication with external applications using two message queues (ActiveMQ).
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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Web Application
A J2EE Servlet application that provides a web-based interface Science Studio.
Tools: Spring (MVC), iBATIS (ORM), JSecurity (Apache Ki), Apache Tomcat
Divided into two parts: the Core application and the VESPERS beamline application.
Core application is responsible for providing access to the business objects.
VESPERS application is responsible for remote control of the VESPERS beamline.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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Database
Metadata associated with the operation of a remote controlled beamline and the organization of experimental data collected on that beamline.
A project is the top level organizational unit and is associated with a project team.
A session defines a period of time allocated to a project team to conduct experiments.
An experiment relates a sample and the technique being applied to that sample.
A scan records the location of the acquired experimental data.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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Database Schema
person
project_person
project_role
project
session
laboratory
sample experiment scan
techniqueinstrument
Instrument_technque
facility
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Experimental Data Storage
Experimental data is stored at the CLS.
Common directory structure shared with other beamlines. A large data storage facility is now operational at the
University of Saskatchewan as part of WestGrid.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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VESPERS Web Interface
Rich web interface to Science Studio and the VESPERS beamline.
Designed to be used over commodity broadband internet.
Developed for the Firefox web browser without any additional plugins or extensions.
Known to work with other browsers, but requires the Canvas HTML tag.
AJAX is used for the VESPERS interface to provide device values in pseudo real time.
ExtJS, a JavaScript framework, provides many advanced GUI elements.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
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Beamline Setup
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Experiment Setup
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XRF (X-Ray Fluorescence)
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Beamline Hutch Cameras
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Experimental Data Viewer
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User Office Workflow
Goal: Many tasks in proposal & sample management at CLS To develop a workflow management system that
manages ordering of tasks e.g. (training before shipping) Tracks manual as well as SS task progression
Mar6-month cycle
CLS call for proposals
Proposal submissionTo CLS
CLS gathers proposals
CLS reviews proposals
CLS grants scientistBeamline time
cientist packs sample
I wonder if CLS
received my sample
yet?
Scientist must complete Online SS training
CLS health & safetyinspection
Many other tasks•Perform Experiment•Return Sample•Take Survey•…
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User office Workflow StatusWorkflow Management Engine
Beamline User
User Office
Task :Training
Completed
Notify
ApprovedNotify
PersistentStore
Record Progress
Features Open source Petri-nets based Direct support for workflow
control flow patterns Ability to interact with web
services declared in WSDL Relies on XML standards e.g.
XPath and XQuery for data & doesn’t use proprietary languages
Architecture System Core: YAWL engine. Engine instantiates specifications
designed using YAWL designer. managed by the YAWL repository
Environment composed of YAWL services inspired by “web services”
paradigm, end-users, applications, and
organizations are all services in YAWL.
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Screenshot: User Training Test Creation
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Screenshot: User Survey Taking Page
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Screenshot: User Survey Edit Page
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Screenshot: Workflow Sample Management
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Screenshot: Workflow Call for Proposals
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User Office Workflow Example
Prototype Implementation1. CLS issues a call for proposals and gives deadline2. Beamline users submit proposals3. User Office administrator ends registration or extends deadline4. User Office administrator assigns proposals to user office reviewers5. Reviewers look at proposals and rank them6. User Office looks at ranking and chooses the proposals to accept7. Accepted proposals contact persons are notified8. Beamline User completes training (web service)9. After training is completed (simulated by a delay) the CLS is notified
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Scheduling Module
Goal: To automate the review process and the method by which beam time is allocated and scheduled to users depending on the access mechanism chosen by the user and the stage of operation (construction, commissioning or
operation) of the beamline. Side effects:
Facilitate the management of cycles, runs and modes of operation
Use automatic scheduling to handle more scheduling conditions and constraints than human beings are able to handle manually and identify optimal solutions.
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Scheduling Module Features
Users Submit proposals
Integer Programming and
Heuristic Algorithm
Schedule
INPUT:
SEARCH ANDCONSTRAINTSATISFIABILITY:
OUTPUT:
Beamlines 2
Experiments 3
Release Times [1,1,2]
Deadlines [8,15,5]
Weights [4,5,1]
Processing Times [10,4,3]
Eligibility [[0,1,0],[1,0,1]]
CONSTRAINTS1. One beamline per experiment2. Start time after release time3. Only eligible beamlines can be selected..7. No overlap of experiment per beamline
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X-Ray Fluorescence (XRF): Reveals Elemental CompositionCharacteristic Element Lines Selected and Mapped Over a 2D Scan Area
S: Kα Cr: Kα & Cr: Kβ Fe: Kα & Fe: Kβ Ni: Kα & Ni: Kβ
2D Maps Generated for Selected Elemental Lines
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X-Ray Diffraction (XRD): Reveals Structural InformationPeak Fitting and Indexing of Image Set to Create a Grain Orientation Map
Peak Search
Old IDL Programme – Matched Peak
Old IDL Programme – Matched Peak
New C Programme – Matched Peak
New C Programme – Expected Peak
The XRD Indexing programme examines the locations of peaks in an image in order to determine the kind of lattice structure the samples constituent atoms are arranged in. Shown here are the results of an older indexing programme written in IDL, and the new indexing programme, written in C. The new indexing programme is proving to be more versatile, and more reliable than the old programme, often indexing sets of data that the old programme failed with.
Grain Orientations
Indexing Process
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How do I get access to a HPC Machine?
Compute Canada Responsible for High Performance Computing in Canada Each regional grid is a member of Compute Canada
ACEnet – Atlantic Canada CLUMEQ - Quebec SCINET - UofT HPCVL – Queens, Royal Military Collage
St. Lawrence, Carlson, Ottawa, … RQCHP - Quebec SHARCNET - Ontario WESTGRID – Western Canada
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Grid Data Storage?
UofS is the host for the new WestGrid data storagefacility
Cost: $3.2 M Includes on-line and
archival storage Two sites on campus
Photo: tape backup unitholding 6,000 tape(each @1TB)
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IBM Cell Processor (3.2 GHz)
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cience Studio
ANISE
Elder MatiasCLS – 09-04-28
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ANISE: Active Network for Information from Synchrotron Experiments
“Active” means near-instantaneous stream processing of complex data during transfer to the user or to storage.
Cell processing using Infosphere Streams software from IBM and lightpath provided by CANARIE network.
Distributed processing on facilities provided by SHARCNET and WESTGRID.
Objective: Develop such a network to provide processed results from experiments such as Laue diffraction at APS (34-ID) and VESPERS at CLS
The network would assist the integration of diffraction data from multiple and large area detectors.
The network would facilitate faster resolution of research problems and free up time for more users.
The network would encouage common data formats and protocols leding to closer collaboration.
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ANISE: Active Network for Information from Synchrotron Experiments
Some project outcomes:
1 Accessibility of Laue diffraction methods to a greater number and variety of users could be achieved by reducing the time required to accumulate meaningful data.
2 The results of complex diffraction measurements involving a wider segment of angles could be assessed rapidly.
3. Data and experiment management processes of Science Studio could enable very brief follow-up experiments to answer crucial questions sometime later.
4. Distant collaborators could participate in, and learn from experiments on samples of critical importance to a project.
5. User support software could result in more rapid publications.
6. Expansion to include APS and NSLS beamlines.
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X-Ray Fluorescence (XRF): Reveals Elemental CompositionCharacteristic Element Lines Selected and Mapped Over a 2D Scan Area
S: Kα Cr: Kα & Cr: Kβ Fe: Kα & Fe: Kβ Ni: Kα & Ni: Kβ
X-Ray Diffraction (XRD): Reveals Structural InformationPeak Fitting and Indexing of Image Set to Create a Grain Orientation Map
The XRD Indexing programme examines the locations of peaks in an image in order to determine the kind of lattice structure the samples constituent atoms are arranged in. Shown here are the results of an older indexing programme written in IDL, and the new indexing programme, written in C. The new indexing programme is proving to be more versatile, and more reliable than the old programme, often indexing sets of data that the old programme failed with.
Peak Search Indexing Process
Grain Orientations
Apply to Entire Data Set
2D Maps Generated for Selected Elemental Lines
VESPERS Beamline Experimental Setup
Sample
Beam
XRD Area Detector
XRF OutputXRD Output