LocationNCWCP Building, 5830 UNIVERSITY RESEARCH CT, COLLEGE PARK, MD 20740
If you do not have a CAC card, please contact Sandra Claar or gvernier.
For those of you without a CAC card/access to the building inside the security gates: We will meet at the main entrance of the NCWCP building between 8:50-9:00 am.
Status of UFO repositorysea-ice fraction: Will be used as a template/example for the development of linear UFO's.
sea-ice thickness: Will be used as a template/example for the development of nonlinear UFO’s
CRTM based
Radio sonde
The Thermodynamic Equation of Seawater - 2010 is included in the ufo repository
HomeworkYou will need a laptop with Singularity installed.
If you decide to run/build outside of singularity, there will be some support for those of you who have access to Theia (contact Rahul Mahajan or Stylianos Flampouris) and Discover (contact Dan Holdaway).
Access to the JEDI repositories and singularity image: contact Yannick Tremolet and ask for access to the JEDI bundle.
Compiling issues sorted before the start of the hackathon.
Basic knowledge of git so we can all work together efficiently.
We will use ZenHub to manage the hackathon
Observation files for the UFO you want to work on.
Interpolated model fields needed for the UFO you will be implementing. We will try to provide a prototype JEDI encapsulation of MOM6-SIS2.
$ mkdir marine-ufo $ cd marine-ufo |
$ git clone -b develop https://github.com/JCSDA/soca-bundle.git |
What will be in the bundle (after issuing ecbuild in the build process):
$ cd ./soca-bundle/scripts/ $ ./build_socab.sh |
$ cd .. $ tree -L 1 . ├── build ├── CMakeLists.txt ├── crtm ├── eckit ├── fckit ├── ioda ├── LICENSE ├── oops ├── README.md ├── scripts ├── soca └── ufo |
git-lfs is not installed on Theia, you will need to manually link to the files in:
/scratch4/NCEPDEV/ocean/scrub/Guillaume.Vernieres/JEDI/soca/data/latest/
$ qsub -I -l procs=16 -l walltime=08:00:00 -A marine-cpu -N soca-test $ cd ./build |
$ source ../scripts/jedi_env_theia.sh $ module list Currently Loaded Modules: 1) intel/18.1.163 2) impi/5.1.2.150 3) hdf5/1.8.14 4) netcdf/4.3.0 5) cmake/3.9.0 6) boost/1.64-intel-18.1.163 7) eigen/3.3.4 |
$ ctest |
Download the image
$ singularity pull shub://JCSDA/singularity |
Start the singularity container
$ singularity shell -e /path/to/singularity/image/JCSDA-singularity-master-latest.simg |
Your directory structure should look like this:
.
├── JCSDA-singularity-master-latest.simg
├── mom6-sis2-fms
│ ├── include
│ ├── libfms.a
│ ├── libmom6.a
│ ├── marine_include.tar
│ ├── marinelibs.tar
│ └── MOM6
└── soca-bundle
├── CMakeLists.txt
├── LICENSE
├── README.md
└── scripts
|
cd into scripts and run: ./build_socab_sing.sh
The above should have cloned all the repositories and build all the applications. Your directory structure should now look like:
.
├── JCSDA-singularity-master-latest.simg
├── mom6-sis2-fms
│ ├── include
│ ├── libfms.a
│ ├── libmom6.a
│ ├── marine_include.tar
│ ├── marinelibs.tar
│ └── MOM6
└── soca-bundle
├── build
├── CMakeLists.txt
├── crtm
├── eckit
├── fckit
├── ioda
├── LICENSE
├── oops
├── README.md
├── scripts
├── soca
└── ufo
|
cd into ./build and run the ctest
Current status (04/30/2018) of the unit testing under singularity:
gvernier:test$ ctest
Test project /home/gvernier/Sandboxes/soca/soca-bundle-test/build/soca/test
Start 1: test_soca_truth
1/17 Test #1: test_soca_truth .................. Passed 2.81 sec
Start 2: test_soca_forecast
2/17 Test #2: test_soca_forecast ............... Passed 3.09 sec
Start 3: test_soca_makeobs3d
3/17 Test #3: test_soca_makeobs3d .............. Passed 71.89 sec
Start 4: test_soca_geometry
4/17 Test #4: test_soca_geometry ............... Passed 0.31 sec
Start 5: test_soca_linearmodel
5/17 Test #5: test_soca_linearmodel ............ Passed 51.90 sec
Start 6: test_soca_state
6/17 Test #6: test_soca_state ..................***Exception: SegFault 0.70 sec
Start 7: test_soca_modelaux
7/17 Test #7: test_soca_modelaux ............... Passed 0.19 sec
Start 8: test_soca_model
8/17 Test #8: test_soca_model .................. Passed 1.67 sec
Start 9: test_soca_increment
9/17 Test #9: test_soca_increment .............. Passed 2.23 sec
Start 10: test_soca_errorcovariance
10/17 Test #10: test_soca_errorcovariance ........***Exception: SegFault 3.02 sec
Start 11: test_soca_localization
11/17 Test #11: test_soca_localization ........... Passed 0.27 sec
Start 12: test_soca_obserrorcov
12/17 Test #12: test_soca_obserrorcov ............ Passed 0.08 sec
Start 13: test_soca_hofx
13/17 Test #13: test_soca_hofx ................... Passed 69.12 sec
Start 14: test_soca_3dvar
14/17 Test #14: test_soca_3dvar .................. Passed 112.80 sec
Start 15: test_soca_3dvarfgat
15/17 Test #15: test_soca_3dvarfgat ..............***Failed 206.50 sec
Start 16: test_soca_4denvar
16/17 Test #16: test_soca_4denvar ................***Failed 0.32 sec
Start 17: test_soca_dirac
17/17 Test #17: test_soca_dirac ..................***Failed 0.28 sec
71% tests passed, 5 tests failed out of 17
Label Time Summary:
boost = 60.37 sec (9 tests)
executable = 60.37 sec (9 tests)
script = 466.80 sec (8 tests)
soca = 527.18 sec (17 tests)
Total Test time (real) = 527.20 sec
The following tests FAILED:
6 - test_soca_state (SEGFAULT)
10 - test_soca_errorcovariance (SEGFAULT)
15 - test_soca_3dvarfgat (Failed)
16 - test_soca_4denvar (Failed)
17 - test_soca_dirac (Failed)
Errors while running CTest
|
Possible JEDI-Model interface available for the Hackathon
Instead of using pre-interpolated model fields at observation locations, we might be able to use the following model/JEDI interfaces:
MOM6/SIS2 (soca, provided in the bundle)
FV3GFS
WW3
Scope of the Hackathon: Implement marine related Unified Forward OperatorsEach UFO will require the development of the nonlinear, linearized and adjoint operators.
Tentative to do list for the hackathon (in no particular order):
Nonlinear mapping of insitu temperature and salinity as a function of temperature (potential or conservative) and salinity(practical/absolute).
Jacobians of GSW-TEOS10
TLM/AD of insitu temperature and salinity
Readers for Argo, CTD, XBT, arrays, moorings …
Diurnal interface UFO
Interface to vertical interpolation functions (forward and adjoint)
Drifters
Altimeters (e.g. L2 ADT or SSHA)
Along track L2P SST and SSS from GHRSST
Add your favorite observation type ...
The ufo repository is part of the JEDI bundle and should be under ./code/jedi-bundle/ufo/
Most (all) of your work will be saved under ~/code/jedi-bundle/ufo/src/ufo/marine/
. ├── gsw # Equation of state of sea-water <------ OBSOLETE ├── obsop ├── seaicefraction # Template for linear UFO ├── seaicethickness # Template for nonlinear UFO └── stericheight |
... more on that later.
NOW IS A GOOD TIME TO CREATE YOUR OWN BRANCH: Branch out of feature/marine and call it something like feature/marine-myufo.
This tutorial example is based on a simple, yet, nonlinear observing operator for sea-ice thickness. If your UFO is linear, use the sea-ice fraction UFO as a template.
The sea-ice thickness operator takes as input sea-ice fraction and thickness of each sea-ice categories, interpolated at the observation locations, and outputs the weighted average thickness.
Nonlinear: $h(c_1,...,c_{N_c}, h_1,...,h_{N_c}) = \sum\limits_{n=1}^{n=N_c} c_n h_n$ |
Linearized around $c^{traj}, h^{traj}$: $\delta h(\delta c_1,...,\delta c_{N_c}, \delta h_1,...,\delta h_{N_c}) = \sum\limits_{n=1}^{n=N_c} (c_n^{traj} \delta h_n + h_n^{traj} \delta c_n)$ |
Adjoint
$
\begin{align}
\delta \hat{c_n} = \delta \hat{c_n} + h_n^{traj} \delta h \\
\delta \hat{h_n} = \delta \hat{h_n} + c_n^{traj} \delta h
\end{align} $ $n=1,...,N_c$ |
Copy & edit the following files and rename them appropriately: