- Events:
- Those I am planning to attend/attended:
- Other relevant events:
- Events on the horizon:
- Mark Baker: eSI Public Lecture: "How Web 2.0 Technologies and Innovations are Changing e-Research Activities"
- First Open Source GIS UK Conference at Centre for Geospatial Science
- ComputationWorld 2009
- Funding Opportunities
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- Browsing
- e-Science
- Prepared the following NGS Renewal Application for MoSeS/GENESIS work:
- Renewal Case
- This allocation is for MoSeS (http://www.geog.leeds.ac.uk/people/a.turner/projects/MoSeS/) and GENESIS (http://www.geog.leeds.ac.uk/people/a.turner/projects/GENESIS/) work.
- All the details of this research are available via these links and progress was presented at the last UK e-Science All Hands Meeting.
- MoSeS involved the development of a demographic model of the UK and the creation of individual and household level population datasets for the UK for 2001.
- These data have approximately 60 million records and are constructed as an integration of various UK 2001 Census data outputs.
- These are currently under going a process of submission to the Economic and Social Data Service at the UK Data Archive.
- Unfortunately progress on the development of the demographic model for MoSeS hit a number of technical problems in the last year.
- This mean't that only a fraction of the resources asked for were used.
- I believe that most of these issues are now resolved and that we are almost ready to use the substantial resources allocated for the demographic modelling.
- I did have the same belief last year, but now we have completed some tests and are confident this work can be pushed through in the next two months.
- GENESIS builds on MoSeS and progresses from a demographic model of the UK to develop city and regional models incorporating detailed socio-economics.
- Over the next 3 years we hope to develop these models and exploit NGS resources to produce outputs to put online and present at International conferences.
- Case Summary
- This allocation is for MoSeS (http://www.geog.leeds.ac.uk/people/a.turner/projects/MoSeS/) and GENESIS (http://www.geog.leeds.ac.uk/people/a.turner/projects/GENESIS/) work.
- 100000 CPU Hours
- 10GB Disc Storage
- 10GB SRB Storage
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- Browsing
- Miscellanea
- PC Crash
- Chat with Paul about what operating system to use
- I think it is way past time for a move back to *NIX...
- Perhaps debian stable is a good choice
- Perhaps OpenSolaris is a good choice
- e-Science
- ...
- NeSS
- Planned to meet Paul Townend and Junaid Arshad to organise delivery of Work Package 4.1
- Unfortunately Junaid notified me earlier in the week that he would be unable to make it.
- I should email to suggest a new date 2009-06-11.
- Meeting with Paul Townend
- Taking a step to get the MoSeS portlets onto the NCeSS Sakai Portal:
- Paul zipped up all the MoSeS Portlets and uploaded them to the NCeSS Sakai Portal : MoSeS Worksite : Resources
- Paul plans to install Sakai locally next week and have a go at installing the portlets and see where it breaks
- There is going to be an issue because the portlets rely on data and are currently configured to pick these up locally.
- Andy is to email June Finch, Steve Swinsberg and copy in Paul to report progress.
- Issues
- The work done for a user using the installed portlets will be a demand on the server hosting the NCeSS Sakai Portal
- It may be that the NCeSS Sakai Portal administrator (Steve Swinsburg) will want to do something to safeguard the server such as limit the resources made available for users running the portlets and for this server function generally.
- I had envisaged that any heavy processing work would be done on NGS rather than run on the local server via tomcat, but that isn't going to be the case for these MoSeS portlets.
- Data security and not leaving unnecessary copies of the data hanging around
- It would perhaps be best to have input data copied from SRB and stored temporarily locally.
- Perhaps we can configure to use Resources of the NCeSS Sakai Portal : MoSeS Worksite for this...
- Maybe Steve knows about this...
- GENESIS
- Meeting with Paul
- Paul showed me the Client he has been developing for GENESIS
- I got a local copy of the Netbeans project on my PC and could run it from Netbeans
- Paul said this was calling the web services on geo-s12, so we had a look and had a look at the code
- Very soon all Paul will be doing with portlets is calling web services...
- MoSeS, EUAsiaGrid
- Continuing development form yesterday...
- Code now seemingly exits cleanly from PBS...
- Code now seemingly exits cleanly from Globus...
- The globus command I tested that worked:
- globus-job-submit ngs.leeds.ac.uk/jobmanager-pbs -np 4 -x '(jobtype=single)' ./globus-job
- I contacted Gabor Szmetanko who plans to have a look at getting the legacy application working in P-GRADE tomorrow...
- I should thank Gabor as I think the way I fixed my code was based on his suggestions :-)
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- Browsing
- e-Science
- Meeting with Jason Lander to chat about how I am using NGS
- Thinking about NGS3, Jason is exploring what users (that are not computer scientists) want...
- I explained that most of my modelling code is Java based.
- We are continuing to use MPJ Express
- Jason knows I was using MPJ Express and recalled writing the PBS launcher script so that it would work on NGS Leeds.
- Jason made me aware of some limitations and concerns about the existing launcher
- The port configuration is not great currently and there could be port conflicts especially if other users are setting off MPJ Express jobs.
- We discussed the development of a more robust and capable MPJ Express job launcher for use on NGS
- This could more robustly allocate ports by running a job to reserve ports and the opening them up for reuse within the 2minute period Jason says are allowed for such things.
- It might also use HARC to run across multiple sites...
- NGS probably do not have much developer resource for this, but MPJ Express might offer some?
- We had a look at some of the existing launcher code
- Jason was surprised that the '(jobtype=mpi)' in the globus launcher would work
- I remembered Gabor puzzling about this in a meeting in Westminster.
- The issue with jobtype=mpi is that this should mean that the job script is launched via 'mpiexec' but the script itself used 'mpiexec', so it is mpiexecing twice...
- For job submission I showed Jason my use of the Westminster P-GRADE Portal...
- Jason noted that the Westminster P-GRADE portal is being used widely by NGS users but remarked that the NGS had another portal that might be used for this...
- Jason was interested in what data we were using and if NGS could help in getting access to these
- I pointed out the various census data we were using and the various providers and talked a bit about the work going on to provide access to data...
- Jason suggested http://www.gridsite.org/ as a way forward.
- I wonder what Junaid Arshad knows about this...
- e-ISS
- Set up Profile on NCeSS Sakai Portal
- MoSeS, EUAsiaGrid
- Picking up the development threads for running MoSeS Population Initialisation on NGS through the P-GRADE portal
- Tested uk.ac.leeds.ccg.andyt.projects.moses.process.IndividualCensus_ISARHP_ISARCEP_PC on PC
- All seemed to work fine except I noticed there was some unnecessary initialisation which resulted in extra directories and files being created for output...
- Modified code to remove unnecessary initialisation and simplify.
- Tested uk.ac.leeds.ccg.andyt.projects.moses.process.IndividualCensus_ISARHP_ISARCEP_NGS on NGS
- Program fails to exit after all results are written...
- In an attempt to remedy the exit failure code was modified so that each slave should return once it is has completed its final job
- This happens by the slave being sent a non job and relies on a ClassCastException being thrown and caught.
- It may have been that the code worked like this before and for some reason I removed this part...
- Another test queued, but the queue is reasonably big and that might be it until tomorrow...
- If a walltime is specified less than 48hours then my jobs should have a better chance of getting through the queue faster
- With PBS for a ten minute run I can specify:
- With globus Jason Lander informs me to specify the walltime in minutes using something like:
- globus-job-run ... -x '(walltime=1)' ...
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- Browsing
- e-Science
- EUAsiaGrid
- Meeting with Alex Voss, David Fergussen and Nick Mallesson to prepare for Workshop/tutorial on Social Simulation at The 5th International Conference on e-Social Science
- Alex going to test running repast under GILDA
- Need to test which version of Java is being used?
- What is prefered compute element to submit jobs to?
- How to get it installed?
- Stage everything in with the job using g-eclipse
- Ideal is 1 node per student
- We should try to limit the size of runs the students run...
- Tutorial overview
- Welcome
- Set up and run a simple model
- Have a short presentation on modelling and social simulation
- Set up and run a more complex spatial model
- Introduce parameter studies
- Consider group work in say groups of 3
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- Visualisation
- Should we try to have this as a batch at the end.
- Repast can write csv files as output
- Want some way to take this csv output back into eclipse to make videos.
- Video is very big, so we don't really want to be storing or moving large amounts of it...
- What is happening with the machines in the room?
- Will we have access before the tutorial starts.
- Get them installed with eclipse and the plugins: repast, (subclipse,) g-eclipse
- GILDA
- Base what we do on something real
- For EUAsiaGrid Alex very keen to do something on the spread of disease like influenza.
- So called Spanish flu killed about 50% of the population...
- How would this effect things depending on who was killed?
- Economic
- We could have a concept of resources and show how resource stores are effected by having too many dependents in a population...
- Andy actions
- Try to get running on own Windows PC that does not have the managed environment set up like his work PC and Laptop...
- Andy to get signed up to the GILDA VO and apply for a tutor account...
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- Browsing
- http://www.spatialanalysisonline.com/output/html/Simulationmodellingsmsystemsforagent-basedmodelling.html
- http://www.spatialanalysisonline.com/output/
- http://www.gisagents.blogspot.com/
- http://crowdsimulation.blogspot.com/
- http://www.geocomputation.org/what.html
- http://en.wikipedia.org/wiki/Cities_XL
- http://en.wikipedia.org/wiki/SimCity_Creator
- http://en.wikipedia.org/wiki/SimCity
- http://en.wikipedia.org/wiki/OpenCity
- http://en.wikipedia.org/wiki/Micropolis_(video_game)
- http://www.sbs.ox.ac.uk/news/archives/research/EPSRC+grant+awarded+for+complexity+science+project.htm
- Murgante, B., Borruso, G., Lapucci, A., (Eds.), 2009, Geocomputation and Urban Planning
- Guan, Q., Zhang, T., Clarke, K.C., (2006) GeoComputation in the Grid Computing Age
- Xue, Y., Sheng, X., Jayaram, N., (2003) Geocomputation
- McMaster, R.B., Usery, E.L., (2004) A Research Agenda for Geographic Information Science
- e-Science
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- Browsing
- e-Science
- Signed up to the OpenABM email list and sent an introductory message...
- WRi Meeting
- EUAsiaGrid
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- Browsing
- e-Science
- Preparing for trip to Reading 2009-05-20
- Andy Turner's : NCeSS Sakai Portal : My Workspace Worksite : Wiki : Seminar in the School Of Systems Engineering, University Of Reading 2009-05-20 Page
- Seminar in the School of Systems Engineering, University of Reading (Centre for Advanced Computing and Emerging Technologies (ACET), Parallel Emergent and Distributed Architecture Laboratory (PEDAL)).
- People
- Information sent to Garry Smith who is organising the seminar:
- Proposed title:
- Developing e-Infrastructure and Geographical Models
- Proposed abstract:
- An introduction to: geographical modelling and computational geography; MoSeS, GENESIS and NeISS.
- Geographical modelling is a window into modelling everything that focuses on here and now at human scales.
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MoSeS has been concerned with modelling, simulation and social science.
As a first phase research node of the UK National Centre for e-Social Science (NCeSS), it focussed on the development and use of a demographic model of the UK from 2001 to 2031.
Part of the model used MPJ Express and some of the outputs were generated by running this on the UK National Grid service.
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GENESIS is a second phase research node of NCeSS which began in October with a focus is on generative geographical simulation.
As part of GENESIS I am developing "agent based models" of two types: those based on publicly available data that can be freely distributed, and; those that take account of more resticted data, but which might be more realistic/detailed.
I am developing models that operate with a daily time step and run for years and models that operate on a second time step and run for a day.
The computational requirements for these models are considerable and I am investigating ways to scale and partition the task.
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NeISS is about developing a National e-Infrastructure for Social Simulation in the UK.
Part of this is to orchestrate the data and computation, and part of it is about developing modelling and analysis tools.
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Let us think collectively about what we do and how we might collaborate.
- Brief bio:
- Andy Turner has a background in mathematics, geography and information systems and has been a researcher based at the University of Leeds, Centre for Computational Geography since 1997.
- Some ideas for collaboration
- Assessing the performance of MPI jobs when run in a VM either locally or in the cloud.
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- Browsing
- Miscellanea
- Xiaolin called about relocating equipment on to the roof of the Geography Main Building
- This follows a conversation at the OS-CGS Think Tank 2009-03-17
- School of Geography Inter-cluster Event
- e-Science
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- Browsing
- Miscellanea
- I added a comment on the Twine "Universities will be 'irrelevant' by 2020"
- http://www.twine.com/item/1284d8mn1-17l/universities-will-be-irrelevant-by-2020?cmpid=e_05132009
- My Comment
- I think important skills/abilities for the future are adaptive and collaborative. While computer interfaces will no doubt change, an ability to use them to get and put information will be generally useful. I don't think we are going to install directly into our nervous systems, so it is going to interface with our senses for the time being. So, being able to work together and with computers and other people and their organisation is still going to be core to research.
- The world of information and information processing is changing fast, but schools and universities and society in general seems to be changing more slowly. This seems at odds and it is hard to know if things will suddenly flip or not. The near future seems uncertain on so many levels. May peace be with you!
- e-Science
- Gave Mark Birkin a lesson on using the NCeSS Sakai Portal to set up a Worksite :-)
- ...
- NeSS
- NCeSS e-Infrastructure for the Social Sciences Meeting 2009-05-14
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- e-Science
- JISC Repositories and Preservation Conference
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- e-Science
- JISC Repositories and Preservation Conference
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- Browsing
- Miscellanea
- e-Science
- Preparation for 5th International Conference on e-Social Science
- Preparation for JISC Repositories and Preservation Conference
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