Science Studio CANARIE Review July 7, 2009. Team: People and Orgs Dionisio Medrano Dylan Maxwell...
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Transcript of Science Studio CANARIE Review July 7, 2009. Team: People and Orgs Dionisio Medrano Dylan Maxwell...
cience Studio
Science Studio CANARIE Review
July 7, 2009
Team: People and Orgs
Dionisio Medrano
Dylan Maxwell
*Elder Matias
*Lavina Carter
Dong Liu
Chris Armstrong
John Haley
Mike Bauer
Stewart McIntyre
*Todd Simpson
Marina Suominen Fuller
Jinhui Qin
Nathaniel Sherry
*Yuhong Yan
Ludeng (Eric) Zhao
*Dan Ni
*Owen Jian
*Zahid Anwar
*Glenn Wright
*Ru Iragashi
*Daron Chabot
*Gillian Black
Today’s agenda
8.30: Welcome and Introduction to CLS (Elder Matias) 8.35: Scientific Goals for Science Studio and review of its components (Stewart
McIntyre) 8.45: Review of Architecture of Science Studio (Chris Armstrong) 9.00: Demonstration of VESPERS XRF remote operation (Dylan Maxwell) 9.30: Demonstration of User Services software (Diony Medrano) 9.45: Review of Task Schedule and update on immediate plans (Stewart
McIntyre)10.00: Coffee and further discussion10.20: VESPERS remote software: accomplishments future additions (Stewart
McIntyre, Chris Armstrong and Elder Matias)10.40: Development of XRD analysis software for Science Studio (Michael Bauer)11.00: Development of XRF analysis software for Science Studio (Stewart
McIntyre)11.15: Planning for Nanofab lab software development (Stewart McIntyre)11.30: Development of User Office Software (Elder Matias)11.40: Potential use of UCLP (Michael Bauer) 11.50: Comparisons with ANISE, discussion on IP issues (Chris Armstrong)12.00: Lessons Learned (Group)12.30: Lunch (provided in room or nearby) 1.00: Wrap up questions from CANARIE visitors 1.30: Tour of CLS for CANARIE visitors 2.30: Depart for airport
Welcome to Canadian Light Source
Objectives of CLS
170.88 m circumference 2.9 GeV DBA lattice with 12-fold periodNominal Tune:
x = 10.22 y = 3.26
Eloss per turn: > 0.876 MeVBend magnet radiation:
c = 1.6 Å Ec = 7.6 keV
x = 18.1 nm•radDamping times:
x = 2.4 ms, y = 3.8 ms, E = 2.7 ms~10 mm bunch length
MAX-II
TLS-I
BESSY-IIALS
ELETTRA
PLS
SLS(240m)
ANKA
ESRFAPS
Spring-8
CLS (171m)SPEAR3 (240m)
Super-SORLSB
BOOMERANGTLS-II
SOLEIL(2006,354m)
NSLS-II
DIAMOND(2007,562m)
ESRFAPS Spring-8ELETTRA
1
10
100
0 1 2 3 4 5 6 7 8 9Energy(GeV)
Em
ittan
ce(n
m·r
ad)
KSRS (124m)
Machine Layout
Current Plans at CLS
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 7 additional
beamlines and building expansion.
Current Controls software: EPICS
Future: EPICS and Science Studio
Goals 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)
8
Science Studio Goals
Allow collaborators to watch and comment on the experiments being undertaken and (in some cases) to take control.
Provide a bank of data analysis services that are compatible with the data produced.
Provide an enhanced single platform user access to the most useful beamline functions and keep keeps intricate records of the scientific steps taken and provides the user with easily downloadable results whether he/she is in Saskatoon or Samarkand. Science Studio@VESPERS: provide access for XRD and
XRF Science Studio@Nanofab: provide access for high
resolution microscopic measurements Provide some common user services.
User Services Intended to provide a “one stop, one site” service
to remote and traditional users of VESPERS (and other lines)
Provides training/testing, “End of Run” report, user scheduling, sample handling and peer review.
Will be accessed through Science Studio site for VESPERS users.
10
11
Next Steps Heavy emphasis on development of SS/XRD image analysis
and transfer until September, because of its sucessful inauguration on VESPERS
VESPERS SS/XRF VESPERS is being tested by user groups.
Development of user service software at CLS and Concordia is mid-way in its pathway
Nanofab lab SS developments to be accelerated by September
Limited VESPERS SS/ XRF-XRD service to be available to internet users worldwide by November 2009
Planning for SS interaction with the ANISE project is underway.
Distributed Architecture
CLSI
UWO
Concordia U.
Data Storage as A Service
Data Processing as a Service
OptionsScience Studio Version 1.1
CLS
UWONanofab Lab
Science Studio Version 1
Chalk River
UBC
CLS
UWONanofab Lab
Chalk River
UBC
Object Exchange
Object Exchange(e.g. proposal)
Object Exchange
CLS-proposal-vespers
UWONanofab Lab
-proposal-electron mic.
Chalk River-proposal
-beamlineX
UBC-proposal
-beamlineY
Project Repository
- project-samples
-data
Common Service
(Processing)
Common Services
(Processing, Data Storage, Exchange Mediation)
Architecture Overview
Browser
RDBMS
Business ModelLayer
PersistenceLayer
DeviceProxies
Client ServicesLayer
Browser Browser
IOCs
LabatoryControl Module
IOCs
LaboratoryControl Module
ProcessingService
ServiceProxies
DataService
Science Studio
Beamline
Beamline
Product Mapping
Browser
RDBMS
Business ModelLayer
PersistenceLayer
DeviceProxies
Client ServicesLayer
Browser Browser
Beamline
IOCs
LabatoryControl Module
Beamline
IOCs
LaboratoryControl Module
ProcessingService
ServiceProxies
DataService
Science Studio
ExtJSFirefox | Chrome
XML / AJAXHTML
SPRING MVC
J2EE / TOMCAT SERVLETS
TBD
TBD
TBD
DERBY | SQL Server | MySQL
JDBC
JMS
SPRING IOC
IBATIS
jsecurity
Infrastructure Services
User Interface Services
Common Services
Data Forms
Experiment Control
Message Broker, Transformation & other SOA
Middleware
Business Application Services
External Services i.e. Existing Applications and
Information Assets
Common Event Infrastructure (error
handling)
Experiment Management
Services
User Services
User Training Proposal
ProcessProject & Task Mgt
Lab Scheduling
Sample Mgt
Information Services
File Transfer
Search Engine
Config Mgt
EPICS
LDAP
SHARCNET
File System
VESPERS Beamline
Analysis s/w
Information Model
Audit & Logging
Application Framework
Services MgtManage and secure services, applications and resources
Access MgtFacilitate interactions with exiting assets
DAO
Data Processing
Module
EPICS JCA
Web Services Engine
Common Directory Services
Security
Business Process Management
Workflow Engine
Scheduling
Lab Control Module
Lab Mgt
Data Mgt
Legend
Science Studio Component
Science Studio Common Infrastructure
& Frameworks
External Component
Browser Framework
UI Framework
Navigation Tree
Data Processing Module
Device Simulation
NanoFab
Parallel Processing Services
Spring MVC
Ext JS, JQuery, Custom
Custom
Ext JS & JQuery
Custom
YAWL Custom
ActiveMQ
Custom CVS, MKS
Custom
Active Directory@CLS,
Spring LDAP
iBATIS
Custom
Custom
SpringApache KiTomcat, Apache
Custom
Custom, Spring
Custom
Custom
Distributed Architecture
CLSI
UWO
Concordia U.
Data Storage as A Service
Data Processing as a Service
OptionsScience Studio Version 1.1
CLS
UWONanofab Lab
Science Studio Version 1
Chalk River
UBC
CLS
UWONanofab Lab
Chalk River
UBC
Object Exchange
Object Exchange(e.g. proposal)
Object Exchange
CLS-proposal-vespers
UWONanofab Lab
-proposal-electron mic.
Chalk River-proposal
-beamlineX
UBC-proposal
-beamlineY
Project Repository
- project-samples
-data
Common Service
(Processing)
Common Services
(Processing, Data Storage, Exchange Mediation)
Architecture Overview
Browser
RDBMS
Business ModelLayer
PersistenceLayer
DeviceProxies
Client ServicesLayer
Browser Browser
IOCs
LabatoryControl Module
IOCs
LaboratoryControl Module
ProcessingService
ServiceProxies
DataService
Science Studio
Beamline
Beamline
Product Mapping
Browser
RDBMS
Business ModelLayer
PersistenceLayer
DeviceProxies
Client ServicesLayer
Browser Browser
Beamline
IOCs
LabatoryControl Module
Beamline
IOCs
LaboratoryControl Module
ProcessingService
ServiceProxies
DataService
Science Studio
ExtJSFirefox | Chrome
XML / AJAXHTML
SPRING MVC
J2EE / TOMCAT SERVLETS
TBD
TBD
TBD
DERBY | SQL Server | MySQL
JDBC
JMS
SPRING IOC
IBATIS
jsecurity
Infrastructure Services
User Interface Services
Common Services
Data Forms
Experiment Control
Message Broker, Transformation & other SOA
Middleware
Business Application Services
External Services i.e. Existing Applications and
Information Assets
Common Event Infrastructure (error
handling)
Experiment Management
Services
User Services
User Training Proposal
ProcessProject & Task Mgt
Lab Scheduling
Sample Mgt
Information Services
File Transfer
Search Engine
Config Mgt
EPICS
LDAP
SHARCNET
File System
VESPERS Beamline
Analysis s/w
Information Model
Audit & Logging
Application Framework
Services MgtManage and secure services, applications and resources
Access MgtFacilitate interactions with exiting assets
DAO
Data Processing
Module
EPICS JCA
Web Services Engine
Common Directory Services
Security
Business Process Management
Workflow Engine
Scheduling
Lab Control Module
Lab Mgt
Data Mgt
Legend
Science Studio Component
Science Studio Common Infrastructure
& Frameworks
External Component
Browser Framework
UI Framework
Navigation Tree
Data Processing Module
Device Simulation
NanoFab
Parallel Processing Services
Spring MVC
Ext JS, JQuery, Custom
Custom
Ext JS & JQuery
Custom
YAWL Custom
ActiveMQ
Custom CVS, MKS
Custom
Active Directory@CLS,
Spring LDAP
iBATIS
Custom
Custom
SpringApache KiTomcat, Apache
Custom
Custom, Spring
Custom
Custom
VESPERS Techniques
1. Phase composition, orientation and distortion using Laue Diffraction (‘pink’ beam).
2. Elemental composition using X-Ray Fluorescence.
3. Chemical information using XAS (’sharp’ beam)
…all in a volume of 2 microns diameter
and 10-50 microns deep!
VESPERS Beamline
VESPERS — Very Sensitive Elemental and Structural Probe Employing Radiation from a Synchrotron
A new bending magnet beamline at the Canadian Light Source.
Techniques: X-Ray Fluorescence (XRF) & X-Ray Diffraction (XRD)
XRF has widespread use; XRD has great potential and enormous computing needs.
WebApplication
BeamlineControlModule
DBSANSAN
JMS CA
VESPERS
HTTP
(a) X ray Fluorescence spectra and mapping
(b) Laue X ray Diffraction and mapping Orientation Strain
VESPERS Demo
User Services Demo
Tasks and Schedule
Duration Start_Date Finish_Date Completion as Today Deliverables Start_Date % Completion Finish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.54%
Phase 1 87 days 05/01/2008 08/31/2008 100.00% 87%Requirements and initial design 18 days 05/01/2008 05/26/2008 100.00% 6/1/2008 100% 8/31/2008Requirements workshop 0 days 05/26/2008 05/26/2008 100.00% 10/28/2008 100% 10/28/2008Initial product selection and prototyping 18 days 05/27/2008 06/19/2008 100.00% 6/1/2008 100% 6/28/2008Setup software infrastructure 17 days 06/20/2008 07/14/2008 100.00% 6/10/2008 100% 6/28/2008User services - proposal management 17 days 07/15/2008 08/06/2008 100.00% 9/15/2008 10% 11/28/2009Refine frameworks and start core development 17 days 08/07/2008 08/31/2008 100.00% 7/5/2008 100% 8/30/2008
Phase 2 88 days 09/01/2008 12/31/2008 100.00% 76%User Services - additional services 13 days 09/01/2008 09/17/2008 100.00% 9-Jan 50% 11/28/2009Release ScienceStudio on VESPERS 0 days 09/17/2008 09/17/2008 100.00% 5/12/2008 100% 5/12/2008Demo to CANARE and interested parties 0 days 09/17/2008 09/17/2008 100.00% 10/29/2008 100% 10/29/2008Simulated beamline 13 days 09/18/2008 10/06/2008 100.00% 9/10/2008 100% 10/27/2008Refine frameworks 13 days 10/07/2008 10/23/2008 100.00% 9/22/2008 100% 11/28/2008Define Strategy for Stream Computing Integration with ScienceStudio13 days 10/24/2008 11/11/2008 100.00% 9/10/2008 100% 26-NovImplement scheduling service 12 days 11/12/2008 11/27/2008 100.00% 5/1/2009 20% 11/1/2009Performance tuning 12 days 11/28/2008 12/15/2008 100.00% 11/15/2008 100% 12//15/2008User profile services 12 days 12/16/2008 12/31/2008 100.00% 12/4/2008 30% 11/1/2009
Task_NamePlanned Actual or Expected
Tasks and Schedules
Duration Start_Date Finish_DateCompletion as TodayDeliverables Start_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%
Phase 3 86 days 01/01/2009 04/30/2009 100.00% 71%Harden user services 12 days 01/01/2009 01/16/2009 100.00% 1/6/2009 90% 9/1/2009Refine frameworks and core development 12 days 01/19/2009 02/03/2009 100.00% /6/2009 100% 1/26/2009Performance tuning 12 days 02/04/2009 02/19/2009 100.00% 11-Jan 100% 4/30/2009VESPERS Remote Access – Integrate Processing of Data and Sample Management 12 days 02/20/2009 03/09/2009 100.00% 1/15/2009i/ 100% 3/15/2009VESPERS/XRF – Working with Selected Users 12 days 03/10/2009 03/25/2009 100.00% 1/20/2009 100% 3/200/2009Redeploy ScienceStudio in User Office 12 days 03/26/2009 04/10/2009 100.00% 3/26/2009 75% 9/1/2009Deploy and Configure ScienceStudio for NanoFab Facility (Servers installs at UWO) 12 days 04/15/2009 04/30/2009 100.00% 6/1/2009 10% 12/22/2009
Phase 4 87 days 05/01/2009 08/31/2009 54.81% 96%Performance Tuning Existing System 22 days 05/01/2009 06/01/2009 100.00% 5/1/2009 100% 6/15/2009VESPERS Remote Access – Integrate Processing of Data and Sample Management 22 days 06/02/2009 07/01/2009 100.00% 5/1/2009 100% 6/15/2009Release ScienceStudio 0 days 07/01/2009 07/01/2009 0.00% 1/5/1900 100% 6/15/2009Demo to CANARIE and Interested Parties 0 days 07/01/2009 07/01/2009 0.00% 7/7/2009 0% 7/7/2009Project and experiment management service 22 days 07/02/2009 07/31/2009 17.26% 11/1/2008 100% 1/5/2009Job management service 21 days 08/03/2009 08/31/2009 0.00% 11/1/2008 90% 8/30/2009
Task_NamePlanned Actual or Expected
Tasks and Schedules
Duration Start_Date Finish_DateCompletion as TodayDeliverables Start_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%
Phase 5 88 days 09/01/2009 12/31/2009 0.00% 25% Data processing packages services installed for VESPERS 13 days 09/01/2009 09/17/2009 0.00% 9/15/2008 90% 8/30/2009VESPERS/Laue X-Ray diffraction working 13 days 09/18/2009 10/06/2009 0.00% 6/1/2009 20% 8/30/2009Harden Scheduling Service 13 days 10/07/2009 10/23/2009 0.00% 5/1/2009 20% 11/11/2009Update Job management service 13 days 10/26/2009 11/11/2009 0.00%Implement security services 12 days 11/12/2009 11/27/2009 0.00%Harden Sample Management Services 12 days 11/30/2009 12/15/2009 0.00%Implement integration collaboration tools 12 days 12/16/2009 12/31/2009 0.00%
Phase 6 86 days 01/01/2010 04/30/2010 0.00%Harden collaboration integration 22 days 01/01/2010 02/01/2010 0.00%NanoFab facility data analysis integration 22 days 02/02/2010 03/03/2010 0.00%Opportunistic Access for VESPERS 21 days 03/04/2010 04/01/2010 0.00%Refine core services including security services 21 days 04/02/2010 04/30/2010 0.00%Demo to CANARIE and Interested Parties 0 days 04/30/2010 04/30/2010 0.00%
Task_NamePlanned Actual or Expected
Tasks and Schedule
Duration Start_Date Finish_DateCompletion as TodayDeliverablesStart_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%
Phase 7 87 days 05/01/2010 08/31/2010 0.00%NanoFab Facility Data Integration 22 days 05/01/2010 06/01/2010 0.00%Experiment Automation on VESPERS 22 days 06/02/2010 07/01/2010 0.00%Integrate with SHARCNET Data Storage 22 days 07/02/2010 08/02/2010 0.00%Integrate eLog-Book Capability 21 days 08/03/2010 08/31/2010 0.00%
Phase 8 88 days 09/01/2010 12/31/2010 0.00%VESPERS Running 30% Time in Automation Mode 0 days 09/01/2010 09/01/2010 0.00%Harden System Management and Administration Services 44 days 09/01/2010 11/01/2010 0.00%Update ScienceStudio based on operational feedback 44 days 11/02/2010 12/31/2010 0.00%
Phase 9 64 days 01/01/2011 03/31/2011 0.00%Conference Presentation 32 days 01/01/2011 02/15/2011 0.00%Demo to CANARIE and Interested Parties 0 days 02/15/2011 02/15/2011 0.00%Update ScienceStudio documentation and code cleanup 32 days 02/16/2011 03/31/2011 0.00%
Task_NamePlanned Actual or Expected
31
Milestones for Science studio@VESPERS
Nov/Dec 2008-migration of RBA to SS; incorporation of GlenRu scanning engine; live test without scanning.
Jan/Feb 2009- Scanning and downloading demonstrated Mar/April 2009-Definition of capabilities for SS1.0 June 2009-First stress test-multi scans and multi
users(nsm) July 2009- Second stress test (mf and tk)
32
Positive features
Reliable sample movement
Download feature functions well
System readily recovered after a dump
Scanning service appears robust
Latency is acceptable
Negative Features Messaging issues (under control) 2D scan issues Ambiguous accumulation instructions Lack of communication on testing issues Readouts of all ion chamber currents seem spotty Spotty dead time readout? Stage movements are confusing (2 sets of
controls)
33
New Slate of Objectives for Science [email protected] Stage coordinates displayed (leftover from 1.0?) Operation of CCD (with corrected Synaps) Operation of CCD and XRF simultaneously Machine and beamline status information Peer to peer data sharing Macro camera enabled (discuss camera calibration) Control of sample illumination Filter change Active version of Peakaboo for XRF data collection Better user instructions Creation of Experiment Accounts at CLS Display additional beamline status informationBUT... No movement of any other motors is contemplated
34
Traditional EPICS Controls: are they history?Not likely, I think that motor scanning is still too specific to each application and idiosyncratic
Better to concentrate on applications involving detectorsand fixed irradiation conditions.
Where are we going with Nanafab?
Device: Zeiss 1540XB FIB/SEM
Technique: Scanning Electron Microscopy (SEM) combined with Energy Dispersive X-ray (EDX) Analysis
A highly focussed electron (primary) beam is scanned across a sample surface at an energy between 0.5-30 keV. Low energy secondary electrons are generated as a result. An image of the sample surface is constructed by measuring secondary electron intensity as a function of the primary electron beam position on the sample.
Back scattered electrons and x-rays are also emitted from the bombardment of the sample surface by primary electrons. The intensity of the backscattered electrons is related to the atomic number of the element present and provides element contrast.
X-rays emitted are characteristic of elements present in the sample. Quantitative elemental information can be obtained. Elemental maps can be generated.
◊ The Scanning Electron Microscope is controlled by a computer system. ◊ The system is also fitted with an Oxford Instruments x-ray system allowing for elemental mapping and analysis of the sample.
◊ The x-ray system is controlled by a separate computer. This system is connected to the microscope and detector, and takes control of the microscope and detector in order to collect the emitted x-rays during elemental mapping and analysis of the sample.
Incorporation into Science Studio
◊ The Oxford Instruments x-ray system is proprietary. Incorporating the microscope/x-ray system into Science Studio would be done by means of ‘wrapping’, i.e., creating an interface between Science Studio and the system.
A basic screen capture interface (terminal window) can be included in ScienceStudio to enable a user to operate the Oxford Instruments software. The terminalwindow can be provided within the main SS window.
Sample Analysis Data
► Scanning electron micrographs (secondary electron images)► Backscattered electron images► EDX spectra and elemental maps
Resulting data from sample analyses are incorporated into a Word document report. Data can also be exported in other formats.
Data will be accessible for download from Science Studio.
Data is organized under the context of project, similar to our scheme in Science Studio
Software is user friendly.
System has its own analysis software with automatic identification of element peaks during acquisition.
User Services
44
User Services Status Overview
User Services Draft Reqs Solid Reqs Design Code Test Production
User Training
User Survey and Feedback
Scheduling
Proposal, Task and Sample management Workflow
Reporting Search Security
User management
User Training Module Features
User Management• Registration• User and Admin Views
Intuitive Materials Categorization• Modules• Exams• Sections• Questions• Presentation
Reports• Search results• Validate training• Export to Excel• Trace generated tests• Statistics and charts
Test Taking• Timed Examination• Support for disconnections• Time stamps• Multiple attempts e.g. successful, firstUnsuccessful, lastUnsuccessful, alternative
Test Creation• Flexible question format• Randomized questions• Test Expiry• Automatic Validation
e.g. empty choice selected as correct
User Survey and Feedback Module
Goal: To automate the user feedback and survey process at CLS to facilitate scientists
Enables User Office experiment monitoring service and accurate metrics on whether: Check in procedures are efficient and user-friendly End station equipment is ready & in good working order Shifts are being utilized Beam is being delivered without interruption Identify unforseen problems
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.
Calendar view
ULCP
Science Studio and ANISE
Science Studio and ANISE
ProcessingService
DataServiceData
ServiceProcessing
Service
ANISE
Business ModelLayer
PersistenceLayer
DeviceProxies
Client ServicesLayer
BrowserBrowser
LaboratoryControl Module
ServiceProxies
Science Studio
LabatoryControl Module
IOCs
Beamline
IOCs
Beamline
General, commonComponent
XRD Processing
XRF Processing
Science Studio specificComponent
Lessons Learning, etc.
Lessons Learned Questions CLS Tour