Product Backlog - Mei

Mei-Hui Su's Project/Product Backlog

Project/Product Backlog

1. UCVM, SFCVM running on frontier
2. UCVM, continue adding ci to more cvms
3. UCVM, move CVMH and CENCAL to be pluggable models
4. UCVM, upgrade CENCAL to newer version
5. UCVM, study LSU model blending code
6. UCVM, find replacement(pyGMT) to matplotlib used in the plotting scripts because matplotlib's Basemap is not being supported in python3
7. UCVMC, setup remote GitHub runner for UCVM's GitHub actions
8. UCVMC, survey different kinds of unittest/regrssion testing platforms in C/bash/python
9. UCVMC, explore Valgrind as memory leak tool and perhaps coverage tools
10. UCVMC, explore gcov, and prof as coverage tool
11. UCVMC, need to make UCVMC work with python3, mainly plotting and config/build scripts - with docker setup
12. CTM, study the CTM python code from Liz Hearn
13. UCVMC, add watermark on ucvm_web's viewer part (Look at Edric's leaflet overlay for CGM web)
14. WEB, status review for CFM, UCVM, GFM
15. UCVMC, design/test out continuous integration testing framework on github for ucvmc.
16. UCVMC, prepare Plotly usage example to the group
17. UCVMC, internal GTL for cvms5/cca is different from external elygtl:ely, https://scec.usc.edu/scecpedia/UCVM_cca/cvms5_comparing_builtin-gtl_vs_elygtl:ely
18. CFM, update CFM db/tb schema after science group fix the excel page ands typo/conflicts/missing data
19. UCVMC, config dumping tool
20. UCVMC,learn the tools used in https://ds.iris.edu/ds/products/emc-desktoptools/. paraview for desktop
21. UCVMC,refine sop & doc steps for generating ucvm.e

LOST

1. GFM+CRM, add Moho search option
2. UCVMC, user reports UCVM used for simulation SPECFEM3D seems to be causing segfaults (ctape@alaska.edu)>> ?? no segfault ??https://scec.usc.edu/scecpedia/UCVM_elevation_vs_depth,_model_boundary

DONE

1. PBR, prototype a PBR web tool for Xiaofeng
2. GRD, new web dashboard/CPD
3. CSM, new web dashboard
4. CGM, adding new INSAR tracks
5. UCVM, create a new software stack for SFCVM/geomodelgrids
6. CFM, add separate models, CFM6.0 preferred/alternative/rupture set in addition to CFM5.3
7. CFM, add copy-to-clipboard action to plot3D's share link call
8. CFM, add map expansion option
9. CFM, allow external KML/KMZ files be ingest as an overlay layer over the map
10. CFM, allow user upload of traces to support CFM6.0 fault review process
11. UCVM, add tapering interpolation method
12. UCVM, add San Jacinto Fault Zone velocity model(sjfz)
13. UCVM, change largefiles location to Globus online collection at CARC (/project/scec_608/public/ucvm)
14. UCVM, add 9 new basin models from Andreas/Harvard group
15. UCVM, add ci to cvms models in GitHub
16. UCVM, work on getting release for upcoming UCVM release, retest on CARC
17. UCVM, link Github runner from ucvm_plotting to UCVM
18. UCVM, test out docker setup for python2/ucvm/ucvm_plotting
19. UCVM, rework get_largefiles.py to pick up path/config info from setup.list instead of current hardwired method.
20. CFM, extend the REST API to allow ingesting of 'external' gocad tsurf file and displaying it on plot3D
21. CFM, add 'sharing link' option to plot3D, implement command option/REST API, to CFM viewer.
22. CGM, add surface plot for INSAR's velocity data given a boundary
23. CGM, add 2d view of INSAR data, add time series plot for INSAR data (calling python pkg)
24. CGM, add GNSS time series data hosted at MIT with plotly plot
25. CGM, flesh out GNSS data access, add INSAR data
26. CGM, trimmed out CFM part of code out of CGM_view 1.0, rework some search logic
27. CFM, add seismicity data to 3dPlot vtk viewer as point scatter plots
28. CFM, add seismicity data to map base leaflet as pixi overlay - Hauksson, Ross, and significant faults layers
29. CM, update UCVM part of code with new UCVM+ucvm_plotting code bases
30. UCVM, reactivated and updated the Utah velocity model, WH
31. UCVM, add 2 new basin velocity models from LSU, (SSIP Imperial Valley, SSIP Coachella Valley)
32. CFM, release CFM viewer with CFM5.3, plus many updates to viewer functions, ie. fault search filtering, strike and dip search option
33. UCVM, split the plotting out to different github repository to simplify the UCVM's dependency python3. --https://github.com/SCECcode/ucvm_plotting
34. USC, test out USC discovery/endeavour slurm/sbatch/srun/mpirun with UCVM's mpi code
35. UCVM, Elnaz TACC/ucvm2etree_extract_MPI was having problem. It turns out global variable for zrange needs to be initalized when using intel mpi compiler on Frontera.
36. GFM, add 3d viewer to GFM viewer
37. CRM/CXM viewer tool to do shp file -> Geojson conversion with postgis -> convert data for CTM, CRM
38. CM+UCVM, create CM viewer with integrated 2d mapview with CFM/GFM/CTM, and ucvm viewer capability
39. GFM+CRM, update GFM with CRM and a new viewer setup
40. GFM, process the shp CRM_polygons_Plesch_Mar_7_2019 from Liz Hearn (CRM pqsql schema)
41. CFM, expand 3d viewer to include surface california shoreline+border as reference orientation
42. CFM, expand 3d viewer to include surface trace/blind for faults
43. CFM, expand 3d viewer to have a orientation axes marker
44. CFM, expand 3d viewer to allow user selectable color picker for each 3D fault representation
45. CFM, expand 3d viewer to include toggle option for surface/wireframe
46. UCVMC, extract geometry geoJson for the 2D area from CRM_polygons_Plesch_Mar_7_2019 and create an optional layer over UCVMC viewer
47. CFM, VTK.js has some updates, need to bring that in, look into vtkOrientationMarkerWidget for CFM_web
48. UCVMC, test GitHub actions and runner for continuous integration setup for ucvm build
49. CFM, on fixing the mixing blindness in a fault - array of blinds at OBJECT_tb
50. CFM, extract geometry geoJson of faults from CFM5.2 into a standalone external file and code ingest leaflet groupLayer that can be reused with any leaflet based scec viewers
51. UCVMC, review various places where vs30/Wallis is used in ucvm/models
52. UCVMC, adding Cencal & CCA06 to Moho's ucvm_web
53. UCVMC, trace the UCVM VS30 values that differ from Rob Grave's VS30 list. interpolation vs nearest point:https://scec.usc.edu/scecpedia/UCVM_VS30_etree_map_(Wills_2015)_UCVM%27s_interpolation#vs30_etree_map
54. UCVMC, add a new model for UCVMC, Albacore, Southern California Offshore velocity model, kohler@caltech.edu, Daniel.bowden@erdw.ethz.ch
55. UCVMC, a list of elevations for elevation-based profile script in generated meta file
56. UCVMC, branch cleanup on UCVMC -- only Master, forGFM, withSVM, forPython3 left
57. UCVMC, verify UCVM's CVMS4.26 profile plots matches with Billy's averaging profile plot with EnJui's CVM4SI26_slices. Also, tested with PO Chan's set of CVMS4.26 dataset.
58. UCVMC, make a mini dockerized UCVM image with cvms, cvms5, and cvmh1511 git@github.com:SCECcode/ucvm_docker.git
59. UCVMC, needs some Z25/Z10 data for some models with GTL https://scec.usc.edu/scecpedia/UCVM_z1,z2.5_for_CCA06_with_GTL,_CVM-S4.26.M01
60. UCVMC, viewer that allow user to query for UCVMC material property and initiate the plotting capability in UCVMC/utilities(git@github.com:SCECcode/UCVM_web.git)
61. UCVMC, add Elevation query mode to ucvm2mesh, ucvm2mesh_mpi, ucvm2mesh_mpi_layer, (currently on branch -forGFM). User needs to include cvmh as part of cvmlist and let UCVM's model tiling to set the property values for in-air, in-water properly,ucvmlist=cvmsi,cvmh. Note: if region is outside of cvmh area, then no data would exists for those regions. In configuration file, specify querymode=ELEVATION
62. CFM, add simple 3d viewer (using vtk.js) to selected faults
63. SVM, Elnas has requested generation of 3 new etrees, https://scec.usc.edu/scecpedia/UCVM_svm_etree and new data is at https://scec.usc.edu/scecpedia/UCVM_svmgtl_and_elygtl
64. GFM, viewer that allow user to query for GFM material property + plotting capability(https://github.com/SCECcode/GFM_web.git)
65. GFM, geological features decorated model -- update vx-lite with new g model files
66. CFM, study web page accessibility, https://www.w3.org/TR/wai-aria-practices, study ui write-up, https://www.smashingmagazine.com/06/designing-perfect-accordion-checklist/
67. CFM, prep the core CFM code for the new CFM data release (Edric has been updating and maintaining UI per user's requests) -- CFM5.2-Fault_ID_preferred_final.xlsx, CFM52_db, nonblind, blind native ts files
68. UCVMC, SVM GTL from Caltech (https://scec.usc.edu/scecpedia/UCVM_svmgtl_and_elygtl) and (https://scec.usc.edu/scecpedia/UCVM_svmgtl)
69. UCVMC,review and update the GitHub UCVMC's wiki pages
70. UCVMC,tied up loose ends and tests for UCVM V19.4,add examples directory for program and plots examples
71. UCVMC, generate etree for Garner Valley, CA for elnaz@caltech.edu, https://scec.usc.edu/scecpedia/UCVM_etree_for_Garner_Valley
72. UCVMC, add plot_elevation_profile.py and plot_elevation_cross_section.py,(ctape@alaska.edu) https://scec.usc.edu/scecpedia/UCVM_elevation_vs_depth,_model_boundary
73. CFM, document CFM dashboard in github and transfer to SCEC space
74. CFM, streamline the preprocessing of CFM database -- xlsx file to Postgres db
75. UCVMC, generate plots for USGS CVM doc -- http://hypocenter.usc.edu/research/ucvmc/USGS-CVM-plot.tar.gz
76. CFM, add analytic tracking to the dashboard -- Edric/google
77. CFM, add latlon search option with direct location selection on the map area
78. CFM, add highlighting of faults on the viewer part in addition to be from the table
79. CFM, add group download(zip) of multiple faults geo data and meta data
80. UCVMC, final set of plot/data for jplet@cpp.edu, 400+ 1d plots in http://hypocenter.usc.edu/research/ucvmc_result/pomona4.tar.gz, cross section plots in http://hypocenter.usc.edu/research/ucvmc_result/pomona3.tar.gz
81. CFM, update cfm dashboard(add dip search, add 'key' trigger to keywordTxt, change latlon search to 4 inputs)
82. CFM, add download function to CFM dashboard (on popup window)
83. CFM, stash the CFM5.2 dataset at asperity's /var/www/html/CFM5_preferred/native, 500m, 1000m
84. CFM, refine end-to-end setup of new CFM dashboard to server/client test environment
85. CFM, setup initial CFM db host over at AWS, http://asperity.scec.org/CFM/web/cfm_view.html
86. UCVMC, first set of plot/data for jplet@cpp.edu. https://scec.usc.edu/scecpedia/UCVMC_basin_depth_study,_poly_tech,_Pomona
87. UCVMC, support jpolet@cpp.edu's group with cross_section and depth_profile processing (added metadata/data output to depth_profile.py) https://scec.usc.edu/scecpedia/UCVMC_how_to_plot_cross_section_and_depth_profile
88. CFM, gather and define the functions needed for the leaflet CFM viewers and study leaflet api and start building up the viewer utilities
89. UCVMC, update 1d grid reference data for UCVMC acceptance test
90. CFM, add the linkup in js for the leaflet viewer and postgis' geoJSON geometry trace info
91. CFM, add php/js to extract geoJSON for target fault object during query and track them to be sent to the viewer
92. CFM, translate shapesfiles from release tarball into postgis db sql script and ingest into backend db
93. CFM, explore and code a leaflet viewer with canned geoJSON data
94. CFM, code php/java scripts/html page for queries with user input:query by region (with on the fly region list extracted from backend db via php), query by a range of strike value(with on the fly min/max strike range, extracted from the backend db via php), query by keyword(full text search from postgres db on object name, can be expanded in the future per request); query by latlon (within 0.0001 precision, a small roi box is created and used postgis to make overlap check)
95. CFM, preprocess the excel from CFM5_release_2017, define db/tb schema and ingest the information into postgres db.
96. UCVMC,generate the tiled v1000 data that Kevin needed for https://github.com/kevinmilner/cybershake-analysis/tree/master/study_18_8/hazard_maps#study-188-hazard-maps, they are left with https://scec.usc.edu/scecpedia/Bay_Area_Velocity_Model_Z2.5_data#Bay_Area_Velocity_Model
97. CFM,study requirements for work on SCEC Community Fault Model,start with postgres db, postgis extension, php service, javascript, leaflet, tile service from open street map.
98. UCVMC,define the json blob for material properties used in plotting scripts, define import and export to file format, rpretell@ucdavis.edu, https://scec.usc.edu/scecpedia/LA_Vertical_Profiles#Result
99. UCVMC,look into updating Wills' map in UCVMC, https://scec.usc.edu/scecpedia/Wills_Map, ucvm.e
100. UCVMC,work to make Rob Grave's mesh generating code to work for him (tweak Rob's directory and Scott's https://source.usc.edu/svn/cybershake/import/trunk/UCVM)
101. UCVMC,doc how to process .bin file generated from plotting script or ucvm basin_query call, https://scec.usc.edu/scecpedia/UCVMC_How_to_process_bin_data
102. UCVMC,translate pbs/hpc/ucvm2mesh to slurm calls
103. (No work done)Generate large (100M+ point) AWP mesh using ucvmc and ucvmp and compare(Scott said ucvmp can not generate big mesh since it does not have mpi flavor to it)
104. UCVMC,Bay Area velocity model's z2.5 plots for Kevin -- different tiling order of cca/cencal/cvms5 , https://scec.usc.edu/scecpedia/Bay_Area_Velocity_Model_Z2.5_data#Result
105. UCVMC,updated cca06 crossing data for Kevin (fuzzy edge problem compare to UCVM python version, a bug found by Scott in CCA06 C version), nwo includes two sets, one without GTL and the other with GTL, https://scec.usc.edu/scecpedia/Final_CCA06_Crossings_Result
106. Doc how La Habra mesh is made with ucvm2mesh_mpi_layer, https://scec.usc.edu/scecpedia/UCVMC_La_Habra_mesh_generation#ucvm2mesh_mpi_layer
107. UCVMC,Generated various plots highlight CS17.3-H, https://scec.usc.edu/scecpedia/UCVMC_CS17.3-H_plots#Plots
108. UCVMC,Registered new Central California Basin Model from Havard. CS17.3-H with ELY GTL
109. UCVMC,built a useable UCVMC installation on Titan, /lustre/atlas/proj-shared/geo112/ucvm_18_5/
110. UCVMC,made UCVMC statically linkable and the plugin models worked as in dynamically linked UCVMC
111. UCVMC,reworked logic in ucvm2mesh-mpi to have a more 'feasible' compute node requirement for very large mesh like La Habra, ucvm2mesh_mpi_layer, remember to strip result directory when running at blue waters. lfs setstripe -c 4 /path/to/working/directory
112. UCVMC,extract UCVMC cs173 info for Scott's gridpoints (off alittle but okayed by Scott)
113. UCVMC,reworked basin_query tests in slurm on hpc
114. UCVMC,created a pull request to official UCVM-C, fix up each models that is in github -- merged into official UCVMC's dev branch
115. UCVMC,Ran tests tiling cencal+cca+cvms5+bbp1d, the 1d part gets surface gtl
116. UCVMC,Tiled cencal+cca(with gtl)+cvms5(with gtl)+1d tested and verified
117. UCVMC,GTL for CCA06- verified by generating identical plots to CyberShake_Study_18.5
118. UCVMC,Fixed plugin/dynamic loading of modules, Scott's interleaving bug, fixes for cvmsi is also needed for the plugin module. There was the missed case for left-over points in chunking/processing code, fixed that. Also the code was not setup to take more than one dynamic library
119. UCVMC,Setup to run my latest UCVMC on blue water - query works but plotting scripts do not work with BW's installed default pthread library(too old, conflicting with matplotlib's pyplot from Anaconda2)
120. UCVM,Fixed segfaults flagged from a working ucvmc installation on local mac (fixed cs173_final(), cca_final()), (mac gdb installation hints: https://gist.github.com/gravitylow/fb595186ce6068537a6e9da6d8b5b96d)
121. UCVMC,Ran basin_query_mpi on hpc with SLURM
122. UCVMC,Doc projection fix on scecpedia, https://scec.usc.edu/scecpedia/Final_Projection_Review_Result
123. UCVMC,Add the fixed config file into CCA's github, also edits from below(pending moving to scec space): https://github.com/meihuisu/CCA.git
124. UCVMC,Copy the CCA06 data on scec-01/Intensity to hypocenter, change the dependency to hypocenter in the make-data script
125. UCVMC,adding elygtl to CCA06
126. UCVMC,new cs173 github location(pending moving to scec space):https://github.com/meihuisu/cs173.git
127. UCVMC,Register Scott NorCal model into UCVM
 - CS173, compare CS173 plots from ScottC with my version
128. UCVMC,Doc CCA06 Crossing review, https://scec.usc.edu/scecpedia/Final_CCA06_Crossings_Result
129. UCVMC,Update basin_query_mpi to return list of crossing per grid point, also return one crossing output file for each algorithm.
130. UCVMC,To check projection fix, trace processing from en-jui data files to configuration files
131. UCVMC,Cross section plots showing 0-10km depth through CCA06, showing velocity inversions, starting at one end of region at 5km spacing to other end of region. **No need, posted inversion plot in scecpedia**

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