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Work plan PMP 2017/2018 #4

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eguil opened this issue Jul 27, 2017 · 30 comments
Closed

Work plan PMP 2017/2018 #4

eguil opened this issue Jul 27, 2017 · 30 comments

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@eguil
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eguil commented Jul 27, 2017

ENSO metrics notes 26/7/2017
Discussion:

  • design modular system for ENSO metrics that allows separation of concern and governance by appropriate experts
  • build on tests done at PCMDI on Bellenger et al. paper by Ji Woo and Peter

Ideas:

  • list of CLIVAR ENSO approved command lines to run enso_bellenger_compute.py (https://github.com/PCMDI/pcmdi_metrics/tree/issue_321_enso_bellenger_2017/src/python/devel/enso_bellenger)
  • develop driver_enso_metrics.py from enso_bellenger_compute.py API (Ji Woo to advise, Yann to test in ENSO metrics environment)
  • further develop enso_metrics_lib.py on github from programs by Ji Woo et al., further documenting the science - Yann and interface with ENSO CLIVAR
  • interface with CDAT/PMP libraries by Ji Woo and Peter
  • interface between CLIVAR ENSO science and metrics lib by Yann and Eric
  • provide reference json/graphics/table for past CMIPs : Ji Woo and Peter

Actions, timeline (and who):

  • telco late August to firm up work plan and timeline (Yann to organise)
  • produce first draft of work plan early Sept. (Eric to lead)
  • review by CLIVAR RF mid-Sept. (Andrew and Eric to lead)
  • implement first version by late Sept. (Yann and Ji Woo to lead)
  • present at Busan CLIVAR ENSO RF mid Oct (Yann and Eric)
  • review science contents and make final public release Nov 2017
@eguil
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eguil commented Aug 31, 2017

Meeting Jiwoo/Yann/Eric on Aug 31st:

  • see slides 8 of
    model_eval_governance_guilyardi_may17.pptx

  • Action Eric: access github x 3

  • Update enso_metrics_lib.py with more metrics from enso_bellenger_compute.py (Action: Yann and Eric)

  • Create a metrics collection (Action: Yann and Eric)

  • Modify enso_bellenger_compute.py into a driver_enso_metrics.py (Action Jiwoo)

  • Create a init_enso_metrics_obs.py (check if right data is there or download) (run by IT driver)

    • Args: MCi, local_obs_path
    • Check against a enso_ref_obs.py/json listing var/obs_file_name/var_name (defined by ENSO experts)
    • Action: produce draft enso_ref_obs.py (Yann & Eric)
    • Action: produce init_enso_metrics_obs.py (Jiwoo)

@eguil
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eguil commented Sep 14, 2017

Meeting Jiwoo/Peter/Yann/Eric on Sept. 14 st:

  • action: Jiwoo to use new initEnsoMetrics.py and metricsCollectionsLib.py in driver all the way to run
  • action: Yann to organise local set up using same driver
  • action: Yann and Eric to add other metrics/collections
  • action: review metrics calculation structure to include difference as well as model + obs calculation (Yann)
  • document GitHub management for project #6

@eguil
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eguil commented Sep 28, 2017

Meeting Jiwoo/Peter/Yann/Eric on Sept. 28th:

  • Yann presented workflow document stored on slack
  • organise exchange between PMP github and ENSO metrics gihub (PG & Jiwoo)
  • develop proposed ENSOCollectionsLib.py and ENSOMetricsLib.py (Yann)
  • init.py not needed (belongs to driver)
  • work on ENSO_metrics_driver.pyand associated my_param.py in dedicated branch (Jiwoo and PG)

@eguil
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eguil commented Oct 12, 2017

Meeting Jiwoo/Yann/Charles/Eric on Oct 12th:

  • Charles describes new organisation on github towards creating conda packages (when the code is stabilized)
  • For now Jiwoo will work in the scripts/ directory (move parser.py back to scripts/)
  • Jiwoo presents new devs on driver
  • discussion how to define dates for observation and models (test on common/min length) - will live in ENSOCollectionsLib.py
  • discussion on re-organising the metrics collection dicts (Yann and Eric)
  • create ENSOcdmsToolsLib.py with basic routines used by ENSOMetrics.lib
  • next meeting Oct 26th

@eguil
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eguil commented Oct 27, 2017

Meeting Jiwoo/Yann/Peter/Eric on Oct 27th:

  • Busan meeting summary
    ENSO Research Foci Busan Oct 2017.pptx
  • IS-ENES3 discussions
  • Discussion on display methods of MME results (Jiwoo / Peter)
  • List of observations used for Obs4MIPs (Yann)
  • rest of actions from last time
  • next meeting Nov 2nd (Jiwoo and Yann)

@eguil
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eguil commented Nov 10, 2017

Meeting Jiwoo/Yann/Peter/Eric on Nov 10th:

  • Yann shows new organisation of ENSOCollectionLib.py and other routines
  • TODO: PMPDriver update to new organisation [Jiwoo]
  • PG informs the group of precip work who could use the same framework
  • next meeting Nov 27th

Ongoing actions:

  • Document different display methods for MME results (Jiwoo / Peter) [example for ENSO metrics]
  • List of observations used for Obs4MIPs (Yann)
  • Regridding workflow

@eguil
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eguil commented Nov 30, 2017

Meeting Jiwoo,Yann, Eric on Nov 30th:

  • Jiwoo updated driver to new organisation of metrics collection (and corrected some bugs)
  • ENSO RF telco on ENSO metrics def last week - see channel #enso_rf_discussion in slack
  • TODO (Yann): propose compute_collection() (which may include a loop oncompute_metric()):
    • compute metric as model-obs distance for each metric for one model
    • have to define this distance calculation for each metric
    • the idea is to leave as little as possible to driver (only loop on models, path to files)
    • propose normalisation options to plot all metrics on same figure in a later stage

Ongoing actions:

  • Document different display methods for MME results (Jiwoo / Peter) [example for ENSO metrics]
  • List of observations used for Obs4MIPs (Yann)
  • Regridding workflow

@eguil
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eguil commented Dec 14, 2017

Meeting Jiwoo, Yann, Eric on Dec 14th:

  • Yann demonstrates the new compute_collection() and associated procedures
  • the term metric is now reserved for the distance between model and observation
  • Driver will use info from my_Param.py to create dicts loop for compute_collection()
  • new metrics to be implemented for next telco (TODO Yann)
  • Jiwoo update use of database interface
  • TODO: Jiwoo to adapt new version (commited now, comments needed)

Ongoing actions:

  • Document different display methods for MME results (Jiwoo / Peter) [example for ENSO metrics]
  • List of observations used for Obs4MIPs (Yann)
  • Regridding workflow

@eguil
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eguil commented Dec 21, 2017

Meeting Jiwoo, Yann, Eric on Dec 21st:

  • Jiwoo's work last week:
    • confirmed the revised code by Yann which works well with the PMP driver
    • Build consistent XML files so I can easily apply all CMIP5 models to current version of code and parameter file
    • Revisited the portrait plot to clean up code and prepare documenting
  • Yann's work:
    • created a branch for new version (called yann for now but we should find a new name)
    • further development of compute_collection() and associated tools (regrid, filter,...)
    • new MC2
  • TODO [Jiwoo]: use compute_collection() from driver to remove loop on metrics - just keep loop on models
  • TODO [Eric]: start a shared document describing requirements for interface from this first experience

Ongoing actions:

  • Document different display methods for MME results (Jiwoo / Peter) [example for ENSO metrics]
  • List of observations used for Obs4MIPs (Yann)
  • Regridding workflow

@eguil
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eguil commented Jan 10, 2018

Meeting Jiwoo, Yann, Peter, Eric on Jan 10th:

  • PG describes how an obs database is being developed in addition to obs4MIPs, using the same format (second bullet of ongoing actions)
  • PG suggest to use several regridding to assess impact (ESMF, regrid2,...)
  • EG suggest to not develop the interface in too much detail before we start interacting with ESMValTool.
  • Jiwoo completed pre-processor to ease use of driver
  • TODO [Jiwoo]: use compute_collection() from driver to remove loop on metrics - just keep loop on models
  • TODO [Eric]: start a shared document describing requirements for interface from this first experience
  • Yann developing MC2
  • Need to check all observations required are present

Ongoing actions:

  • Document different display methods for MME results (Jiwoo / Peter) [example for ENSO metrics]
  • List of observations used to be put in new ref obs database
  • Regridding workflow

@eguil
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eguil commented Jan 26, 2018

Meeting Jiwoo, Yann, Peter, Eric on Jan 26th:

  • Yann and Peter: 2 normalization techniques illustrated in slack (vs. median or vs. ratio to obs)
    • may want to separate different statistics in multi window plots with different color scales
  • PG: started to prepare observational database to follow obs4MIPs structure
  • Jiwoo: driver now calls compute_collection() - see metrics_collection slack channel and MC2 branch on github - required changes in obs database and internal organisation of driver
  • Yann: developed MC2 collection (from first proposal by CLIVAR group) and tested them
  • TODO [Yann]: explore how to override the collection default period per metric
  • TODO [Jiwoo]: consolidate driver code, try different regrid
  • TODO [Yann]: think about regrid specification (metric level, driver level, ?)
  • first meeting with ESMValTool next week (Feb 1st)

Ongoing actions:

  • TODO [Eric]: start a shared document describing requirements for interface from this first experience

@eguil
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eguil commented Feb 2, 2018

Meeting Jiwoo, Yann, Peter, Eric on Feb 2nd:

  • summary of meeting with Veronika and Axel
  • idea to move pre-preprocessing to driver using specific encoding in ENSOCollectionsLibs.py
  • TODO [Yann+Jiwoo]: prepares a branch to test extracting pre-processing to driver
  • TODO [Jiwoo]: explore how to put portrait plot and provenance (per metrics) on a web/wiki
  • TODO [Jiwoo]: run MC2 to produce a portrait plot

Ongoing actions:

  • Eric: start a shared document describing requirements for interface from this first experience (in wiki to start with)
  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization

@eguil
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eguil commented Feb 15, 2018

Meeting Jiwoo, Yann, Peter, Eric on Feb 15th:

  • Yann shows the pre-process branch with just one metric
  • TODO [Jiwoo]: try again the MC2 branch to identify bug
  • Once this is working, then move to pre-process branch and update the rest of MC1 and MC2
  • Put pre-process branch back to master and work from there (create issues, related branches and pull back to master once issue is solved)

Ongoing actions:

  • Eric: start a shared document describing requirements for interface from this first experience (in wiki to start with)
  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization

@eguil
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eguil commented Feb 22, 2018

Meeting Jiwoo, Yann, Eric on Feb 22th

  • 2 bugs identified (time checking, jason file issue wrt use of "mv2.multiply" vs. "*")
  • jason file made for the IPSL model / MC1
  • still an issue with one model
  • Once this is working, then move to pre-process branch and update the rest of MC1 and MC2, put pre-process branch back to master and work from there (create issues, related branches and pull back to master once issue is solved)
  • Jiwoo introduces Vega visualisation for jason files
  • Meeting with ESMValTool group see ESMValTool integration #14

Ongoing actions:

  • Eric: start a shared document describing requirements for interface from this first experience (in wiki to start with)
  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization

@eguil eguil changed the title Work plan summer/fall 2017 Work plan PMP 2017/2018 Feb 22, 2018
@yyplanton
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Meeting (a quick hello from Eric) Jiwoo, Peter, Yann, on Mar 8th

  • uvcdat's cdutil.averager cannot handle irregular grids => we use areacello to average oceanic variables
  • for now Jiwoo added areacello to the xml file of oceanic variables but it should be in separate files
  • if we still have issues with averaging oceanic variables => use atmospheric ts (instead of tos) and tauu (instead of tauuo)

Ongoing actions:

  • Yann: merge MC2 branch to master
  • Yann: finalize preprocess branch
  • Jiwoo: run preprocess branch and take ownership of pre-processing functions (Yann will help to understand and develop them)
  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization

@eguil
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eguil commented Mar 20, 2018

Meeting Jiwoo, Peter, Yann, Eric on Mar 20th

  • MC1 and MC2 json file now working
  • portrait plot in the making - issue of structure (nested dict + model AND obs)
    • leave models out that don't have the right data for now
  • work on identifying ESMValTool pre-processing
  • bring MC2 branch into master [DONE]
  • use preprocess branch to investigate interface for ESMValTool
  • keep separate until ESMValTool interface works and then merge in Master

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization 3) verification suite using correlations

@eguil
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eguil commented Apr 5, 2018

Meeting Jiwoo, Peter, Yann, Eric on April 5th:

  • MC2 merged in to master
  • Portrait plots provided by Jiwoo
  • relative errors shown wrt to mean error - ok to identify outliers
  • TODO [Jiwoo] explore absolute error view:
    • parallel coordinates plot
    • use of scale factor needed to show absolute error
    • add metric numbers in boxes to combine relative and absolute

Book keeping:

  • use preprocess branch to investigate interface for ESMValTool
  • keep separate until ESMValTool interface works and then merge in Master

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) portrait plot normalization 3) verification suite using correlations

@eguil
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eguil commented May 3, 2018

Meeting Jiwoo, Peter, Yann, Eric on May 3rd:

  • new portrait plots with actual metrics value as number on slack
  • add unit [Jiwoo]
  • create legend (online or doc) [Yann]
  • rename MC2 into "ENSO perf"
  • to start interacting with Andrew and al:
    • make version with atmos fields in new branch:atmos_regrid [Yann]
    • try other regridding options - add option in current code to allow overwrite by driver [Yann]
    • [add GFDL-CM2.1 (using atmos field is necessary) [Jiwoo]]
    • change relative into absolute metric calculation [Yann]
  • think about adding other obs references (triangle)

Book keeping:

  • use preprocess branch to investigate interface for ESMValTool
  • keep separate until ESMValTool interface works and then merge in Master

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations

@eguil eguil closed this as completed May 3, 2018
@eguil eguil reopened this May 3, 2018
@eguil
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eguil commented May 17, 2018

Meeting Jiwoo, Peter, Yann, Eric on May 17th:

  • work on regrid done by Yann ( to be commited soon)
  • move from matplotlib to VCS for graphics (better for interactive plots) done by Jiwoo
  • add units [Jiwoo]
  • create legend (online or doc) [Yann]
  • rename MC2 into "ENSO perf"
  • work on regrid (e.g. ts vs. tos): add option to have it per variable
  • look into Yann being able to rerun the portrait plot by himself

Book keeping:

  • use preprocess branch to investigate interface for ESMValTool
  • keep separate until ESMValTool interface works and then merge in Master

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations
  • think about adding other obs references (triangle)

@eguil
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eguil commented May 29, 2018

Meeting Jiwoo, Peter, Yann, Eric on May 29th:

  • regrid work by Yann in branch regrid:
    • added option user_regridding=<option> in Compute_Collection call in driver
    • documented in README_regridding in scripts
    • works per collection or per metrics
    • tested in a few cases
    • next step: Jiwoo to test this
  • set up call with Andrew weeks 3 and 4 of June
    • units
    • redo a few portrait plots (different combinations of color/numbers)
    • documentation
  • Next major milestone: portrait plots of ENSO perf with validated science and cleaned up codes

Book keeping:

  • use preprocess branch to investigate interface for ESMValTool
  • keep separate until ESMValTool interface works and then merge in Master
  • look into Yann being able to rerun the portrait plot by himself: wait for clean up of code for now

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations
  • think about adding other obs references (triangle)
  • further organise provenance (both technical and scientific)

@eguil
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eguil commented Jul 16, 2018

Meeting Jiwoo, Peter, Yann, Eric on July 16th:

  • json output reviewed to fit wider framework - update dict{} structure to fit this requirement (work around currently exists)
  • technical need to create a tag (e.g. v0.1) to create conda version to start integration in PMP
  • discuss science needs from telco with Andrew:
    • more portrait plot with absolute/relative metrics
      • interesting plot on slack (june 28th) mixing metric and relative MME color
      • TODO: [Jiwoo] have 2 portraits plots (RMSE & non RMSE)
    • // coord plots
    • dive down plots
    • science prioritisation (correlations between metrics)
  • new version of code pushed by Yann Friday
    • some dive down diags included (values used to compute the metric)
    • [Jiwoo] to start producing a plot for dive down
  • MC news:
    • [Yann] start work on ENSO teleconnections

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations
  • think about adding other obs references (triangle)
  • further organise provenance (both technical and scientific)

@yyplanton
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yyplanton commented Jul 26, 2018

Meeting Jiwoo, Yann on July 26th:

  • technical need to create a tag (e.g. v0.1): done. Jiwoo explained to Yann how to do it
  • // coord plots created by Jiwoo (with or without lines): very nice to see the spread among models
    • it would be nice to be able to select several models for the plot and not always all of them (interactive plots)
    • is there a way to have the full markers for the first un last metrics of the plot? (and not half of it as it is now)
  • discuss science needs from telco with Andrew:
    • more portrait plot with absolute/relative metrics
      • interesting plot on slack (june 28th) mixing metric and relative MME color
      • TODO: [Jiwoo] have 2 portraits plots (RMSE & non RMSE)
    • interesting // coord plots on slack (july 24th)
    • TODO: [Jiwoo] to start producing a plot for dive down (using the last version of the atmos_regrid branch)
    • science prioritisation (correlations between metrics)
  • MC teleconnections:
    • [Yann] first two metrics will be available quickly (still some science to discuss with Scott Power)
    • [Yann] these metrics will be used to test the json output reviewed to fit wider framework - update dict{} structure to fit this requirement

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations
  • think about adding other obs references (triangle)
  • further organise provenance (both technical and scientific)

@eguil
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eguil commented Aug 16, 2018

Meeting Jiwoo, Peter, Yann, Eric on Aug. 16th:

  • discussion on parallel plots:

    • very nice complement to portrait plot
    • issues with taux (2 models) and sst (?)
  • version testing ready - will be included in PMP release for testing (hidden)

  • Yann: MC3 on ENSO teleconnection: branch Test_MC3

    • science discussion with Scott P on going
  • format of the dict for the json format

    • same depth level currently has mix of metrics (values) and meta-data (strings)
    • fix structure to have only one type: how ?
      • work on package side or work on server side ?
      • Yann & Jiwoo to test: have 2 dict (current and data only) embedded into one
    • Jiwoo and Peter to create an issue to document that, Yann uses the branch
  • discuss science needs from telco with Andrew:

    • more portrait plot with absolute/relative metrics
      • TODO: [Jiwoo] have 2 portraits plots (RMSE & non RMSE)
    • interesting // coord plots on slack (july 24th)
    • TODO: [Jiwoo] to start producing a plot for dive down (using the last version of the atmos_regrid branch)
    • science prioritisation (correlations between metrics)
  • MC teleconnections:

    • [Yann] first two metrics will be available quickly (still some science to discuss with Scott Power)
    • [Yann] these metrics will be used to test the json output reviewed to fit wider framework - update dict{} structure to fit this requirement

Ongoing actions:

  • PG and JL to explore and document 1) regriding impact on results and 2) verification suite using correlations
  • think about adding other obs references (triangle)
  • further organise provenance (both technical and scientific)

@eguil
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eguil commented Sep 13, 2018

Meeting Jiwoo, Yann, Eric on Sept. 13th:

  • ENSO RF discussion two days ago

    • summary of progress presented - people are getting excited by the results
    • MC3 / ENSO teleconnections discussed
  • json format and dive down diags

    • branch to test ideas
    • pb with dive down diags (too long a file)
    • Start with option for dive down -> creates a new json file
    • but netCDF will eventually be required
    • Yann will commit a version with new json structure (test by Jiwoo and bring back to trunk)
  • display topics

    • TODO: [Jiwoo] have 2 portraits plots (RMSE & non RMSE)
    • TODO: [jiwoo] // plot: issues with taux (2 models) and sst (clustering ?)
    • Jiwoo demonstrates an interactive // plot - link on slack
    • have science ready plots for ENSO meeting (Ecuador Oct 12-15th)

See above for other on-going actions

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eguil commented Sep 28, 2018

Meeting Jiwoo, Yann, Eric on Sept. 28th:

  • review tickets/issues
  • review branches
    • atmos_regrid can go
    • merge needed for json_structure - review pull request
  • correcting data
    • taux: reversed - correct data rather than the code (driver issue)
    • sst: using ocean-only points - ENSO metrics package calculation to integrate this
    • currently debugging on test_MC3 branch (use one/two models for now)
  • Guayaquil material
    • 2 portrait plots
    • // coord. plot fixed
    • // coord. interactive

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eguil commented Oct 8, 2018

Meeting Jiwoo, Yann, Eric on Oct. 8th:

  • material for Guayaquil todo before end of week:
    • // plot fixed
    • portrait non-RMSE (MC1)
    • still an issue with some incoherent data/LS mask (driver issue ? e.g ACCESS)
    • taux issue:
      • fixed in data but not yet in portrait - either remove or fix
  • Yann still investigating how issue was fixed (maybe interpolation and masking?)
  • branches reviews
    • Yann still investigating so merge will wait

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eguil commented Nov 15, 2018

Meeting Jiwoo, Yann, Peter, Eric on Nov. 15th:

  • Meetings
    • ENSO Guayaquil - clear support
    • ENSO CLIVAR work
      • work on MC1 (5 new metrics) and MC2 (more changes coming up) [TODO: Yann]
      • suggestions to add options in // plot - keep track of wish list in new issue [TODO:Yann]
      • [TODO:Yann]: redo correlation in a more readable way and put on wiki
    • CMIP6 Barcelona abstract < 15 Dec
      • ENSO metrics
    • DOE meeting
      • overview of PMP and ENSO metrics - lot's of interest (other metrics such as MJO)
      • provide current work to demonstration site
  • Dive down diags
    • stored in other json file - ok for 1D, more complex for 2D (use netCDF with option)
    • naming of file: file of root sent by driver and metric name appended
  • MC ENSO perform two portrait plots RMSE, non-RMSE - add as property in output or rather add description in metric collection file

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eguil commented Nov 28, 2018

Meeting Jiwoo, Yann, Peter, Eric on Nov. 28th:

  • option to save netCDF ready in computeMetrics file
  • ENSO CLIVAR work
    • work on MC1 (5 new metrics) and MC2 (more changes coming up) [TODO: Yann]
    • suggestions to add options in // plot - keep track of wish list in new issue [TODO:Yann]
    • [TODO:Yann]: redo inter-metrics correlation in a more readable way and put on wiki
    • add references to wiki metrics info
    • DONE: MC ENSO perform two portrait plots RMSE, non-RMSE - add description in metric collection file
  • CMIP6 Barcelona abstract < 15 Dec
    • ENSO metrics

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yyplanton commented Dec 19, 2018

Meeting Jiwoo, Yann on Dec. 19th:

  • [TODO: Yann] option to save more information in netCDF
  • ENSO CLIVAR work
    • [TODO: Yann] work on ENSO_perf (one new metric has still to be coded: spectrum) and ENSO_tel (more changes coming up)
    • suggestions to add options in // plot - keep track of wish list in new issue [TODO:Yann]
    • [TODO:Yann]: redo inter-metrics correlation in a more readable way and put on wiki
    • add references to wiki metrics info
    • DONE: MC ENSO perform two portrait plots RMSE, non-RMSE - add description in metric collection file
    • [TODO:Yann]: give Jiwoo me code to plot dive down diagnostics

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lee1043 commented Jul 13, 2020

Closing this issue for house cleaning

@lee1043 lee1043 closed this as completed Jul 13, 2020
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