-
- Browsing
- UoL
- Faculty HPC meeting
- People:
- 9 Attendees:
- Others with views represented:
- Documentation:
- Third Progress report on a Financial Model for Sustainability
- ...
- Definition of High Performance Computing (HPC):
- Geomorphometrics
- Progress on Cairngorm runs:
- Iteration 1 Done Chunk ( 46, 58 ) Writing out results :-)
- Having to create space for this...
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Meeting with Paul :-)
- Paul confident about preparing/submitting a MoSeS Web Services abstract to the 4th type paper
- MoSeS
- What results in the Population Reconstruction for 2001 (Dynamic Model Population Initialisation) are yet to be produced? -
- This will be ongoing tomorrow...
-
- Browsing
- SoG
- BSc Open Day Coffee Time Question Session
- Terrain Data Structures: Principles and Implementations Book Proposal Review meeting with Steve Carver
- Geomorphometrics
- Progress on NextMap Cairngorm run:
- Iteration 1 Done Chunk ( 32, 2 )
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- What results in the Population Reconstruction for 2001 (Dynamic Model Population Initialisation) are yet to be produced? -
- This will be ongoing tomorrow...
-
- Browsing
- GAM
- Paul Norman arranging a practical session on GAM and wants to get Cluster working:
- Paul found it was not returning results.
- The problem was that the header needed removing from the input file.
- Here are two results I generated:
- All is well and this will form the basis of a practical now for some module Paul teaches.
- Geomorphometrics
- Progress on NextMap Cairngorm run:
- Iteration 1 Done Chunk ( 19, 5 )
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- Technical Meeting
- NGS processing check:
- NGS shutdown at 9:30 means process halted. I wonder how far it got...
- Well it nearly finished :-)
- Received and written result with 158 HSARDataRecords and 0 ISARDataRecords for 00CRFR0017 with fitness 10.04326004106267064089
- Sending input 49928 with ZoneCode 00CRFT0044 to 32
-
- SoG
- Mentoring Nanlin
- Advised her to try and get more feedack on why the paper she submitted to a conference was rejected. The referee comment only suggests to develop an application and there are already two in the paper.
- Geomorphometrics
- Progress on NextMap Cairngorms run:
- Failed due to insufficient available disc space!
- Cleared some space and set going again...
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- Preparation for the technical meeting tomorrow:
- Review notes from previous technical meetings.
- NGS processing:
- Started run for 40001 to 50000.
- Browsing
- Geomorphometrics
- Set a run going on NextMap data for Cairngorms on my PC
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Phone Chat with Chris Higgins:
- GLS Server
- Michael Koutroumpas, Niel Chue-Hong, Ally Hume
- Plan to deploy a GLS Server for use by NCeSS Portal users:
- Chris to organise pacjkaging up the OGSA-DAI version and new Activities developed by Michael.
- It is not clear yet where is best to install this:
- I should liase with Xiaobo Yang.
- weaver, NGS, something else?
- It may be that installing on the NGS is best...
- This deployment to be a trial case and so issues and information about tweeks and suggestions for improvements are to be fed back.
- This is a key part of the collaboration.
- Other dependencies include OGR.
- Need to satisfy Keith Cole and Chris that we are not going to compromise on security and allow access to the GDAS and WFS Census Data.
- I assured Chris that we would not intentionally compromise security in any way and are always thinking about this.
- We agree that this is more a matter of principal than neccessity given the data we are dealing with.
- I briefed Chris on Junaid Arshad's security work:
- He is working with Wei Jie and getting well networked.
- I will be asking Junaid to look into security for the GLS Server.
- NCeSS Showcase:
- Mark Birkin presented and mentioned our collaboration.
- I am to point Chris to my notes on this meeting.
- Misc
- Chris to send a SEE-GEO update.
- GENESIS
- DIAD(sp?)
- OGC and OGF meetings
- MoSeS
- Beowulf processing check:
- NGS processing check:
- Browsing
- CCG Web Page Updates
- Geomorphometrics
- Trying to figure out why processes are failing:
- Debugging this is not easy!
- CCG Web Page Updates
- Geomorphometrics
- Trying to figure out why processes are failing:
- Debugging this is not easy!
- Geomorphometrics
- Progress on Cairngorm run:
- On PC
-
Initialised result[52]
Done chunkRow 0
Done chunkRow 1
java.lang.OutOfMemoryError: Java heap space
- ???
- On everest:
- java.lang.NullPointerException
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadObject(
AbstractGrid2DSquareCell.java:5119)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadObject(
AbstractGrid2DSquareCell.java:5107)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadIntoCac
heChunk(AbstractGrid2DSquareCell.java:4950)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.getGrid2DSq
uareCellChunk(AbstractGrid2DSquareCell.java:425)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.getGrid2DSq
uareCellChunk(AbstractGrid2DSquareCell.java:374)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getCell(Grid2
DSquareCellDouble.java:1806)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getCell(Grid2
DSquareCellDouble.java:1754)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getCell(Grid2
DSquareCellDouble.java:1775)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getCell(Grid2
DSquareCellDouble.java:1775)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getCell(Grid2
- This looks like the same problem as per 2008-01-21. Are the files getting deleted or not created?
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- NeSS
- Submitted edits to first annual report.
- Changes to Work Package 4.1 now reflect current plan as on the NCeSS Sakai Portal : ESRC e-IP Worksite Wiki.
- University of Leeds are invoicing University of Manchester and until this happens the finance figures will not be used in the report on the say so of Mike Daw.
- Browsing
- Geomorphometrics
- Progress on Mars runs:
- java.lang.NullPointerException
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadObject(AbstractGrid2DSquareCell.java:5119)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadObject(AbstractGrid2DSquareCell.java:5107)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadIntoCacheChunk(AbstractGrid2DSquareCell.java:4950)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getGrid2DSquareCellDoubleChunk(Grid2DSquareCellDouble.java:1539)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getGrid2DSquareCellDoubleChunk(Grid2DSquareCellDouble.java:1490)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.setCell(Grid2DSquareCellDouble.java:2176)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.setCell(AbstractGrid2DSquareCell.java:2230)
at uk.ac.leeds.ccg.andyt.grids.process.Grid2DSquareCellProcessorDEM.getMetrics1(Grid2DSquareCellProcessorDEM.java:2898)
at uk.ac.leeds.ccg.andyt.grids.process.Grid2DSquareCellProcessorDEM.getMetrics1(Grid2DSquareCellProcessorDEM.java:2537)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.do_Metrics1(Test.java:441)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.run1(Test.java:251)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.run(Test.java:205)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.main(Test.java:101)
-
java.lang.NullPointerException
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.loadIntoCacheChunk(AbstractGrid2DSquareCell.java:5001)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getGrid2DSquareCellDoubleChunk(Grid2DSquareCellDouble.java:1539)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.getGrid2DSquareCellDoubleChunk(Grid2DSquareCellDouble.java:1490)
at uk.ac.leeds.ccg.andyt.grids.core.Grid2DSquareCellDouble.setCell(Grid2DSquareCellDouble.java:2176)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.setCell(AbstractGrid2DSquareCell.java:2230)
at uk.ac.leeds.ccg.andyt.grids.process.Grid2DSquareCellProcessorDEM.getMetrics1(Grid2DSquareCellProcessorDEM.java:2898)
at uk.ac.leeds.ccg.andyt.grids.process.Grid2DSquareCellProcessorDEM.getMetrics1(Grid2DSquareCellProcessorDEM.java:2537)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.do_Metrics1(Test.java:441)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.run1(Test.java:251)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.run(Test.java:205)
at uk.ac.leeds.ccg.andyt.projects.geomorphometrics.Test.main(Test.java:101)
- Caused by data from /nobackup being deleted?
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- NeSS Status Report Jan 2008:
- Colleen Palmer should be able to provide updated financial figures by tomorrow.
- I have modifying the latest document to align with changes made on the Wiki for Work Package 4.1.
- Browsing
- Geomorphometrics
- Progress on Mars runs:
- Programme terminated early and the error file reported:
- Unexpected OutOfMemoryError trying to handle OutOfMemoryError in metrics1Calcula
te_All(Grid2DSquareCellDouble,double,long,long,double,double,double,int,double[]
[],double[],double[],double[],double[],boolean,ChunkID )
- java.lang.OutOfMemoryError: GC overhead limit exceeded
- This looks to be a memory and Garbage collection issue.
- I had been using the following VM options:
- The qsub execution command was:
- I have changed these as follows:
- VM options:
- -Xmx31000m -Xms31000m -XX:-UseGCOverheadLimit
- qsub execution command:
- qsub -l h_vmem=31G run.sh
- Not only have I increased the memory demands for the VM, but I have made a memory grab rather than setting memory limits.
- -XX:-UseGCOverheadLimit is to overcome the "java.lang.OutOfMemoryError: GC overhead limit exceeded" issue (see below).
- The memory demanded is as close to the upper limit that I think everest can currently handle:
- The larges nodes have 32G of RAM.
- It seems that others have experienced a similar problem (java.lang.OutOfMemoryError: GC overhead limit exceeded):
- Browsing
- PC Crash :-(
- Time 18:43
- What a pain, this sort of thing is thankfully rare and I think what I'll do is not bother investigating and just get on...
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Browsing
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Considered getting SimCity Societies
- Some of the feedback is far from complimentary:
- Based on this feedback, I’m not going to bother!
- NCeSS Show Case 2008 Meeting in Manchester
- Andy Turner's NCeSS Show Case 2008 Web Page
- http://redress.lancs.ac.uk/Workshops/Presentations.html#showcase08
- NCeSS Sakai Portal : MoSeS Worksite : Wiki : NCeSS Showcase 2008-01-16
- http://weaver.dl.ac.uk/portal/tool/c7e9465d-283d-41a9-803b-2e5cec5b25ef?pageName=%2Fsite%2Fmoses%2Fncess+showcase+2008-01-16&action=view&panel=Main&realm=%2Fsite%2Fmoses
- Wiki Code
-
h2 NCeSS Showcase 2008-01-16
A page about this event.
h3 People
* {link:Marzieh Asgari-Targhi|http://www.ncess.ac.uk/about_us/people/?centre=&person=10}
* {link:Kenny Baird|http://www.ncess.ac.uk/about_us/people/?centre=&person=12}
* [Mark Birkin]
* {link:Iain Buchan|http://www.medicine.manchester.ac.uk/staff/iainbuchan}
* {link:Andy Crabtree|http://web.mac.com/andy.crabtree/iWeb/.Mac/Home.html}
* {link:Rob Crouchley|http://www.cas.lancs.ac.uk/people/robcrouchley.html}
* {link:Mike Daw|http://www.ncess.ac.uk/about_us/people/?centre=&person=5}
* {link:Pete Edwards|http://www.csd.abdn.ac.uk/~pedwards/}
* {link:John Farrington|http://abdn.ac.uk/itrr/Members%20Pages/jfarrington.html}
* {link:Dan Grose|http://www.lums.lancs.ac.uk/profiles/dan-grose/}
* Sally Halper
* {link:Andy Hudson-Smith|http://www.casa.ucl.ac.uk/people/person.asp?ID=7}
* {link:Paul Lambert|http://www.dass.stir.ac.uk/staff/showstaff.php?id=37}
* {link:YuWei Lin|http://www.ncess.ac.uk/about_us/people/?centre=&person=6}
* {link:Eric Meyer|http://people.oii.ox.ac.uk/meyer/}
* {link:Meik Poschen|http://www.ncess.ac.uk/about_us/people/?centre=&person=11}
* {link:Muneeb Shaukat|http://www.cs.bris.ac.uk/~muneeb/}
* Paul Tennet
* [Andy Turner]
* {link:Dylan Tutt|http://www.kcl.ac.uk/schools/sspp/mgmt/staff/researchstaff.html}
* {link:Lucy Yardley|http://www.psychology.soton.ac.uk/people/ShowProfile.php?username=ly3&source=health}
h3 Notes
* Arrival
** {link:Andy Hudson-Smith|http://www.casa.ucl.ac.uk/people/person.asp?ID=7} showed me MapTube
** I showed and our GeoServer Demo
*** {link:GeoServer on GEO-S12|http://geo-s12.leeds.ac.uk:8080/geoserver}
** We are both looking forward to working together on {link:GENESIS|http://www.genesis.ucl.ac.uk/} and neither of us know much about Agent Based Modelling in Geography
*** We could do with looking at some software:
**** RepastS
**** Mason
**** {link:GIS & ABM CASA Blog|http://gisagents.blogspot.com/}
* Digital Record (DReSS)
** Paul Tennet, {link:Andy Crabtree|http://web.mac.com/andy.crabtree/iWeb/.Mac/Home.html}
** {link:Digital Record Digital Replay System (DRS) Software|http://www.ncess.ac.uk/research/digital_records/drs}
** Andy specialises in ripping location information from devices.
** Using Google Earth to display results.
* Policy Grid
** {link:Pete Edwards|http://www.csd.abdn.ac.uk/~pedwards/}, {link:John Farrington|http://abdn.ac.uk/itrr/Members%20Pages/jfarrington.html}
** Evidence trails in government decision making and policy formation.
** APAT Policy Assessment Tool
*** Workflow
** {link:ourSpaces|www.ourspaces.net/} protoype
*** What's the difference with {link:myExperiment|http://www.myexperiment.org/}?
** Discussion
*** What can be ontologised?
**** Some social science communities question whether their subject area can be ontologised!
***** I don't follow this arguement.
*** British Library and Library of Congress have been working on subject specific ontologies for over 5 years.
*** Sally Halper(?) from the {link:British Library|http://www.bl.uk} is here and keen to collaborate on metadata and ontology work.
* {link:OeSS|http://www.oii.ox.ac.uk/microsites/oess}
** {link:Eric Meyer|http://people.oii.ox.ac.uk/meyer/}
** {link:Questionaire|http://www.oii.ox.ac.uk/}
* {link:MiMeG|http://www.ncess.ac.uk/research/video/mimeg/}
** {link:Dylan Tutt|http://www.kcl.ac.uk/schools/sspp/mgmt/staff/researchstaff.html}
** {link:Muneeb Shaukat|http://www.cs.bris.ac.uk/~muneeb/}
** Some similar work to Digital Record.
** Software being open sourced and hosted on sourceforge.
* MoSeS
** [Mark Birkin]
** http://www.mercatorgeosystems.com
*** {link:User Guide|http://www.mercatorgeosystems.com/docs/userguide.pdf}
** Questions
*** What about environmental inputs into the model, things like pollution, waste, crime?
**** {link:Paul Upham|http://tyndall.web.man.ac.uk/people/pu.php}
* GeoVue
** {link:Andy Hudson-Smith|http://www.casa.ucl.ac.uk/people/person.asp?ID=7}
** Quick in quick out software.
** {link:MapTube|http://maptube.casa.ucl.ac.uk/search.aspx}
* Tea
** Chat with {link:Marzieh Asgari-Targhi|http://www.ncess.ac.uk/about_us/people/?centre=&person=10} and {link:Meik Poschen|http://www.ncess.ac.uk/about_us/people/?centre=&person=11}
*** Did we save the First NCeSS Wiki?
**** Maybe not! I want to talk to Kenny Baird about this.
* CQeSS
** {link:Dan Grose|http://www.lums.lancs.ac.uk/profiles/dan-grose/}, {link:Rob Crouchley|http://www.cas.lancs.ac.uk/people/robcrouchley.html}
** MultiR
** SabreR
* LifeGuide
** {link:Lucy Yardley|http://www.psychology.soton.ac.uk/people/ShowProfile.php?username=ly3&source=health}
** A Second Phase Node just starting...
** Formally known as Behavioural Intervention Gridor BIGrid.
** About behavioural change information and advice.
** Diagnostics questions and personal preferences leads to tailored/personal advice.
** Assessment required.
** Many advantages in automating this via web interfaceand capturing data.
** {link:lifeguideonline.org|https://www.lifeguideonline.org/}
*** Currently not working
* Obesity e-Lab
** {link:Iain Buchan|http://www.medicine.manchester.ac.uk/staff/iainbuchan}
** Body Mass Index measures and classification suggests we have an epidemic.
* Data Management in e-Social Science (DAMES)
** {link:Paul Lambert|http://www.dass.stir.ac.uk/staff/showstaff.php?id=37}
** Based on a previous NCeSS project.
** Interesting work on Health and Social Care relevant to MoSeS.
** {link:Grid Enabled Occupational Data Environment (GEODE)|http://www.geode.stir.ac.uk/}
* Developing an e-Infrastructure for the Social Sciences
** {link:Mike Daw|http://www.ncess.ac.uk/about_us/people/?centre=&person=5}
* Further Discussions
** In a personal conversation {link:YuWei Lin|http://www.ncess.ac.uk/about_us/people/?centre=&person=6} asked [Andy Turner] what work he was involved in concerning workflows. She has seen that I started a {link:myExperiment|http://www.myexperiment.org/} group for the NCeSS e-Infrastructure for the Social Sciences Project Work Package 4.1?
*** Andy has little experience with workflow technologies like Taverna or ActiveBPEL
*** I suggested that she might like to find out what Gobe Hobona is doing if she is interested in some GeoSpatial Workflows.
* Things [Andy Turner] didn't get around to:
** Talk to {link:Kenny Baird|http://www.ncess.ac.uk/about_us/people/?centre=&person=12} about the First NCeSS Wiki and my NCeSS Home Page: I want it to link to my School of Geography home page.)
h3 References
* {link:NCeSS Showcase Page|http://www.ncess.ac.uk/events/showcase/}
* {link:GeoServer on GEO-S12|http://geo-s12.leeds.ac.uk:8080/geoserver}
* {link:Digital Record Digital Replay System (DRS) Software|http://www.ncess.ac.uk/research/digital_records/drs}
* {link:GENESIS|http://www.genesis.ucl.ac.uk/}
* {link:GIS & ABM CASA Blog|http://gisagents.blogspot.com/}
* {link:MapTube|http://maptube.casa.ucl.ac.uk/search.aspx}
* {link:myExperiment|http://www.myexperiment.org/}
- Browsing
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Meeting with Paul
- GeoServer now on GEO-S12 :-)
- We can serve out maps using this now :-)
- We could do with Junaid looking into security regarding this...
- With the KML we can load into Google Earth and it looks very pretty.
- Well it will do when we know a bit more about constructing an appropriate SLD.
- First Aid Course
- Browsing
- Geomorphometrics
- Progress on Mars runs:
- Runs over the weekend failed on writing out images :-(
- Added a bit more OutOfMemoryErrorHandling and set running again...
- Configuring to use WRG/everest:
- First Aid Course
UoL
- Library Request
- How to get a copy of a book into the University of Leeds Library?
- It was simple :-), I just filled out the following form once I had checked that the book was not in the catalogue:
Geomorphometrics
- Progress on Mars runs:
- Iteration 2 complete!
- Iteration 3 Initialised result[26] then hit the following error:
-
java.lang.StackOverflowError
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.writeToFileGrid2DSquareCellChunk(AbstractGrid2DSquareCell.java:3431)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.writeToFileGrid2DSquareCellChunk(AbstractGrid2DSquareCell.java:3324)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.swapToFileGrid2DSquareCellChunk(AbstractGrid2DSquareCell.java:4056)
at uk.ac.leeds.ccg.andyt.grids.core.AbstractGrid2DSquareCell.swapToFileGrid2DSquareCellChunk(AbstractGrid2DSquareCell.java:4012)
at uk.ac.leeds.ccg.andyt.grids.core.OutOfMemoryErrorHandler._SwapToFileGrid2DSquareCellChunk(OutOfMemoryErrorHandler.java:582)
at uk.ac.leeds.ccg.andyt.grids.core.OutOfMemoryErrorHandler.init_MemoryReserve(OutOfMemoryErrorHandler.java:212)
at uk.ac.leeds.ccg.andyt.grids.core.OutOfMemoryErrorHandler.init_MemoryReserve(OutOfMemoryErrorHandler.java:213)
at uk.ac.leeds.ccg.andyt.grids.core.OutOfMemoryErrorHandler.init_MemoryReserve(OutOfMemoryErrorHandler.java:213) ...
- Unsure what to do about this now, so set a new run going...
OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- WRG
- Emailed Alan Real about planned use of WRG:
- I want to use WRG to process DEM data for the UK and Mars, starting with the Mars data.
- Mars Data:
- Each Input data is 433 MB (454,175,838 bytes).
- Workspace (used during processing for swapping and cacheing data) requires about 70 times this.
- Output data is about 1000 times this.
- Mars Data Processing:
- In all there are 16 inputs to process and each run will probably take several days, but this depends on the amount of memory that can be allocated to the JVM (The more memory that can be allocated, the faster this will run).
- What do I need?
- A later version of Java (1.5 or 1.6). Currently 1.4 is available.
- To know how much (?) memory I can ask for in the java -Xmx?m:
- I have only run on 32 bit systems before and had to manage with about 1200.
- To know if there is a resource where I can put the large temporary files (input, workspace, results) before I copy the results back to my PC.
- To develop a run test.
- To know if it is OK to submit my jobs, when and how.
- Subsequently Alan got back to me with some great advice and I started submitting jobs in the hope of generating some useful results...
- MoSeS
- Progress check for UK Population initialisation:
- 60001-65000:
- 4998 processed Zones
2 Zones still to process!
RecordID, ZoneCode
60002, 00DBFS0007
60003, 00DBFS0008
- Browsing
- Geomorphometrics
- Meeting with Steve Taylor who is working with Steve Carver on the Cairngorms:
- Steve gave me a copy of the 10 metre resolution digimap DEM for the cairngorms national park plus a 250 metre buffer for testing with my Grids software :-)
- Steve will give me a copy of the nextmap data at a 5 metre resolution when it arrives and I'll generate some geomorphometrics with it.
- We chatted about the Mars work I'm doing:
- Progress on Mars runs:
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Browsing
- Geomorphometrics
- Meeting with Steve Carver
- Possible "Ruggedness" metrics:
- Roughness in Grids.
- Standard Deviation of sslope profile, plan curvature, gradient.
- Fractal dimension.
- Some derivative of slope and aspect.
- Looked at some Grids results from Drumlin field.
- Steve getting a 5 metre resolution NextMap DEM for Cairngorms soon:
- I'll get a copy to process to test out my Grids software :-)
- Progress on Mars runs:
- Grid2DSquareCellAbstract( Grid2DSquareCellDouble( _NoDataValue( -Infinity ), chunkNcols( 512 ), chunkNrows( 512 ), dimensionsScale( 0 ), _NChunkCols( 23 ), _NChunkRows( 11 ), ncols( 11520 ), nrows( 5632 ), directory( D:\Work\Projects\Geomorphometrics\Workspace\data\Mars\Workspace\_Metrics1\sumd_hxhx_ai_hhhl ), name( sumd_hxhx_ai_hhhl_2.0 ), dimensions( 1, -0.5000, -0.5000, 11519.5000, 5631.5000 ), memoryReserve.length( 2000000 ), grid2DSquareCellChunks.size( 64 ), unsignedLongPowersOf2( null ), ), Statistics( uk.ac.leeds.ccg.andyt.grids.core.GridStatistics1( nonNoDataValueCountBigInteger( 0 ), maxBigDecimal( -4294967296 ), minBigDecimal( 4294967294 ), maxCountBigInteger( 0 ), minCountBigInteger( 0 ), sumBigDecimal( 0 ) ) ), grid2DSquareCells.size( 66 ) ) ), File( D:\Work\Projects\Geomorphometrics\Workspace\data\Mars\Output\_Metrics1\sumd_hxhx_ai_hhhl_2.0.asc ) )
- Stuck?
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- NeSS Finance Meeting
- We agreed that salary wise for 2007, 2 months (2007-01-01 to 2007-02-28) of Paul Townend, and 2 months (2007-10-01 to 2007-12-31) of Junaid Arshad (53%) would be charged to this.
- I should have a meeting with Mark about finance and the tranisition from MoSeS to GENESIS.
- I am to check with Mark what the end date for MoSeS is and report back to Colleen.
- MoSeS
- Beowulf processing check:
- Completed 60001-65000.
- Check what else needs doing for this UK run and possibly set more runs off...
- Browsing
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Browsing
- Correspondence with Marcelo de C. C. Stabile
- His PhD working title is :
- "Determining Land Use Dynamics and Potential Land Suitability under Climatic Uncertainty"
- I agree, it is a good and challenging subject :-)
- Geomorphometrics
- Progress on Mars runs:
- Stuck again. Masking is OK, but problem in Outputting:
- Probably recursively hitting OutOfMemoryError initialising image array:
- This is annoying! The input could be output in this way, so there is about enough memory for this operation:
- A difference at execution time is the existence of more references to grids (which does take up some memory):
- Hopefully this is it rather than a memory leak caused by something like one of the grids not being referenced properly (this is unlikely as it should cause a more obvious failure!)
- Set run going again outputting only ESRIAsciiGrid format and not Images (such output is more streamed).
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- NeSS
- Preparation for meeting tomorrow
- Meeting with Paul and Junaid
- Developed Wiki page for the meeting:
- Wiki code:
-
h3 NeSS Workflow, Portals, Security and Grid Computing Meeting 2008-01-08
This page is for information about this meeting on 2008-01-08 in Manchester.
h4 Meeting Particulars
* Location
** Room G.030/031, ground floor of the Arthur Lewis Building. A campus map can be found at:
*** http://www.manchester.ac.uk/medialibrary/maps/campusmap.pdf (The Arthur Lewis Building is #36.)
* Meeting date
** Organised by meetomatic:
*** http://www.meetomatic.com/respond.php?id=D3N3H9
** 10am start!
h4 People
* Alphabetical List by Surname, Firstname:
** [Rob Allan]
** [Junaid Arshad]
** [Pascal Ekin]
** [Wei Jie]
** Larry Tan (Stirling University invited because of work on the [GEODE] project)
** [Paul Townend]
** [Andy Turner]
h4 Documentation
* ???
h4 Meeting focus
* How [MoSeS] may fit into the e-Infrastructure in terms of the Sakai portal, workflows, access to Grid-enabled data and security.
* Defining work for [Work Package 4.1] and [Work Package 3.4].
* Impact and inform [Wei Jie]'s work on security for the e-Infrastructure and [Pascal Ekin]'s work on Grid-enabled datasets.
* If there is time, work can be done on loading some portlets...
h4 Agenda
* Junaid presentation on MoSeS security
* Wei presentation on security requirements and proposed solution
* What to do with the portal
* Collaboration between White Rose Grid and North West Grid
h4 Notes
* Mike Daw who could not make this meeting to facilitate has requested that notes are made available.
- Documentation
- Received and read Decemeber 2007 Monthly Activity report from Junaid Arshad
- MoSeS
- Beowulf processing check:
- Received and written result with 130 HSARDataRecords and 0 ISARDataRecords for 00EYNA0017 with fitness 18.46909500372937830083
- Sending input 63887 with ZoneCode 00EYNB0019 to 20
- Browsing
- Web Page Updates:
- Geomorphometrics
- Progress on Mars runs:
- Iteration 1 Done Chunk ( 10, 22 )
- Probably still getting stuck with the masking or outputting of results, added some print output to try and work out where its getting stuck and changed some memory handling to swap out all chunks. Running again over the weekend...
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- Beowulf processing check:
- Browsing
- Geomorphometrics
- Correspondence with Marcelo de C. C. Stabile :-)
- Let him know that I was processing some Mars data.
- He is working on a feature recognition paper for his PhD
- Progress on Mars runs:
- Iteration 1 Done Chunk ( 10, 22 )
- Something is going slow or getting stuck with the masking or outputting of results:
- Improved masking, but it could still do with some work, but I'll set it going again overnight to see if this works...
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- Updating documentation
- Distilling blog into web pages...
- Browsing
- Geomorphometrics
- Mars:
- Run Failure :-(
- Fixed fault and set running again.
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- MoSeS
- Beowulf processing check:
![[Validate RDF]](http://www.geog.leeds.ac.uk/people/a.turner/images/rdf_w3c_button.gif "W3C RDF Validation")
![[Validate CSS]](http://www.geog.leeds.ac.uk/people/a.turner/images/vcss.gif "W3C CSS Validation")
![[An image of Andy Turner]](http://www.geog.leeds.ac.uk/people/a.turner/a.turner.png)
