`Location`

NCWCP Building, 5830 UNIVERSITY RESEARCH CT, COLLEGE PARK, MD 20740

Atrium 4552-4553: May 7, 9-11, 14, 17-18
Atrium 2552-2553: May 8, 15-16

If you do not have a CAC card, please contact Sandra Claar or gvernier.

First day, May 7th

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 repository`

sea-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

Prerequisite & `Homework`

In a nutshell

You 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
Basic understanding of cmake and ctest.
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.
wiki from Nov 2017 UFO hackathon

Build and test the soca-bundle: TO DO before May 7

Start by making a directory in which to put all of your hackathon code and build.

$ mkdir marine-ufo
$ cd marine-ufo

Clone the soca-bundle

$ git clone -b develop https://github.com/JCSDA/soca-bundle.git

What will be in the bundle (after issuing ecbuild in the build process):

IODA: Interface for Observation Data Access. Currently only contains a nice netcdf wrapper, provided by the GMAO.
CRTM: Community Radiative Transfer Model.
OOPS: Object Oriented Prediction System.
UFO: Unified Forward Operator.
SOCA: JEDI encapsulation of MOM6-SIS2

On Theia

Building

Start by making a directory in which to put all of your hackathon code and build.

$ cd ./soca-bundle/scripts/
$ ./build_socab.sh

If the configuration and built went OK, things should lokk like this

$ cd ..
$ tree -L 1
.
├── build
├── CMakeLists.txt
├── crtm
├── eckit
├── fckit
├── ioda
├── LICENSE
├── oops
├── README.md
├── scripts
├── soca
└── ufo

Testing

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/

Get an interactive session

$ qsub -I -l procs=16 -l walltime=08:00:00 -A marine-cpu -N soca-test
$ cd ./build

Load the modules

$ 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

Start the unit testing

$ ctest

In Singularity containers

Building

Install singularity. See http://singularity.lbl.gov/ or Install Singularity on Mac OS X
cd into the marine-ufo directory
Download the image
Checkout the latest singularity image
```
$ singularity pull shub://JCSDA/singularity
```

Start the singularity container

Start the singularity container

$ singularity shell -e /path/to/singularity/image/JCSDA-singularity-master-latest.simg

Download the pre-built mom6-sis2-fms libraries:

create a directory /1-level-above-soca-bundle/mom6-sis2-fms
Download the two tarballs and mom6 executable, untar in the above directory

Your directory structure should look like this:

Start the singularity container

.
├── 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:

Start the singularity container

.
├── 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

Testing

cd into ./build and run the ctest

Current status (04/30/2018) of the unit testing under singularity:

Start the unit testing

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 Operators`

Each 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 …
I/O software for bufr, netcdf, grib2, ...
Diurnal interface UFO
Interface to vertical interpolation functions (forward and adjoint)
Drifters
Ocean color
Altimeters (e.g. L2 ADT or SSHA)
Along track L2P SST and SSS from GHRSST
Develop code to test if an observation is inside of the domain
Add your favorite observation type ...
DOCUMENT

Tutorial: How to add a UFO

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/

content of marine ufo directory

.
├── gsw                # Equation of state of sea-water <------ OBSOLETE
├── obsop              
├── seaicefraction     # Template for linear UFO
├── seaicethickness    # Template for nonlinear UFO
└── stericheight

Branching/Merging

... 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.

Step-by-step how to implement a UFO

MOVED TO JEDI-DOCS

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:

Class definition from OOPS base classes:
1. ./src/ufo/marine/seaicethickness/ObsSeaIceThickness.h
2. ./src/ufo/marine/seaicethickness/ObsSeaIceThicknessTLAD.h
Fortran/C++ binding:
1. ./src/ufo/marine/seaicethickness/ObsSpace.SeaIceThickness.interface.F90
2. ./src/ufo/marine/seaicethickness/ObsSeaIceThickness.interface.F90
Low level fortran implementation of the classes’ methods (where most of your work will be):
1. Observation operators:
  1. ./src/ufo/marine/seaicethickness/ufo_seaicethick_mod.F90
2. Observation
  1. ./src/ufo/marine/seaicethickness/ufo_obs_seaicethick_mod.F90
Edit ./src/ufo/Fortran.hto finish defining the c-binding
Add the obs operators (NL, TLM & AD) to:
1. ./src/ufo/instantiateLinearObsOpFactory.h
2. ./src/ufo/instantiateObsOperatorFactory.h
Edit ./src/ufo/ObsSpace.cc
Implement the unit tests:
1. Edit ./test/CMakeLists.txt
2. Add or edit the appropriate .json file in ./test/testinput/

Page tree

Marine UFO Hackathon (May 7-18, 2018)

Location

First day, May 7th

Status of UFO repository

Prerequisite & Homework

In a nutshell

Build and test the soca-bundle: TO DO before May 7

On Theia

Building

Testing

In Singularity containers

Building

Testing

Scope of the Hackathon: Implement marine related Unified Forward Operators

Tutorial: How to add a UFO

Branching/Merging

Step-by-step how to implement a UFO

MOVED TO JEDI-DOCS

`Location`

`Status of UFO repository`

Prerequisite & `Homework`

`Scope of the Hackathon: Implement marine related Unified Forward Operators`