Peter RochfordCSS-Dynamac Inc.

NOAA/NOS/NCCOS SeminarJuly 29, 2015

• A set of services and Information Technology (IT) framework provided by the National Centers for Environmental Prediction (NCEP) which enables NOAA employees and their partners to share ideas, collaborate, engage in software development, and conduct applied research.

• VLab communities allow users with common interest to collaborate using tools like forums, blogs, wikis, document libraries, web forms, and workflows.

• VLab Development Services provide users with integrated project management, issue tracking, software repositories, continuous integration, and code review tools.

Virtual Lab (VLab)

• NOAA scientists tend to develop their own software.• Software sharing would be more productive for everyone• Lack central common software repository for sharing• Use of different versions of software invites inconsistency in

results and creates problems in having the latest features• Sharing across NOAA branches is problematic because of

different networks: e.g. CO-OPS, COAST, MMAP• Sharing with academic collaborators is problematic because

they don’t have access to NOAA computer networks

• Solution must be easy for scientists to use if software projects are to be supported and involvement naturally grows

Software Sharing Problem

National Centers for Coastal Ocean Science

(NCCOS)Director: Mary Erickson

Deputy Director: Steven Thur

Office of Coast Survey (OCS)

Director: Rear Adm. Gerd Glang

Deputy Director: Kathryn Ries

Center for Operational Products and Services

(CO-OPS)Director: Richard Edwing

National Ocean Service (NOS)

Line Office

Program Office

Center for Coastal Monitoring and Assessment (CCMA)

Director: Dr. Mark Monaco

Division Office

Coastal Ocean Assessment, Status, and Trends (COAST)

Chief: Dr. Greg Piniak

Coast Survey Development Lab (CSDL)

Chief: Capt. Richard BrennanDep. Chief: Maureen Kenny

Marine Modeling & Analysis (MMAP)

Chief: Dr. Ed Myers (acting)

Oceanographic Division (OD)Chief: Pat burke (acting)

Dep. Chief: Adria Schneck-Scottl (acting)

Planning Monitoring & Analysis BranchChief: Carolyn Lindley

Branch Office

• Use VLab established by NOAA/NCEP (located in SSMC2)• VLab is web accessible and requires no IT approval process• Anyone with a NOAA email address and password can

access VLab. Accounts can be created for outside partners.

• Provides a software project infrastructure for creation and collaboration on projects using Redmine

• Supports source code configuration control using Git or Subversion (svn)

• Users can commit and update source code from/to their local platform

• Issues with software can be issued, tracked, and resolved

• NWS provides User Help for VLab• NWS does daily backups of software projects

Software Sharing Solution: VLab

• A ROMS Tools project has already been created in VLab1. ROMS Utilities

1.1 roms_dates (Available)• Reports date and time of data in a Regional Ocean

Modeling System (ROMS) history, restart, and station files. (Written in Fortran 2003. Available.)

1.2 roms_mld (Under development)• Calculates a mixed layer depth (MLD) from

temperature and salinity profiles in a ROMS history file. (Written in Fortran 2003.)

2. ROMS Toolbox (Available)• A collection of Matlab functions for scientific analysis

and visualization of data from ROMS.

MMAP Projects in VLab (1)

3. Skill Metrics Toolbox (Available)• A collection of Matlab functions for scientific analysis

and visualization of model forecast skill• Skill metric functions• Pattern diagrams: target diagram, Taylor diagram

4. Operational Forecast Skill Assessment (Proposed)• National Ocean Service (NOS) package for

evaluation of nowcast/forecast models that support navigational and environmental applications in U.S. Coastal waters. (Written in Fortran 77, 90, & 2003.)

• CSDL uses for hindcast evaluation• CO-OPS uses for nowcast/forecast evaluation• Requires merging and validation of multiple versions

• Other folders can be easily added, subprojects created, or new projects other than ROMS Tools created

MMAP Projects in VLab (2)

• Reads the history file and reports the times and dates of the time series of records

• Example:% roms_dates history_001.nc 2001-01-01

Reference Date: 2001-01-01 00:00:00Record Date Time Julian Day Ocean Time Time Steps 1 12-Aug-2008 12:00:00 3146.5 4725259200 108360

2 13-Aug-2008 00:00:00 3147.0 4725302400 108720

3 13-Aug-2008 12:00:00 3147.5 4725345600 109080

4 14-Aug-2008 00:00:00 3148.0 4725388800 109440

5 14-Aug-2008 12:00:00 3148.5 4725432000 109800

6 15-Aug-2008 00:00:00 3149.0 4725475200 110160

roms_dates

Matlab command:>> doc ‘ROMS Toolbox’

Matlab command:>> doc ‘Skill Metrics Toolbox’

• Provides a different summary of pattern statistics for overall model skill assessment: correlation, standard deviation, & centered root-mean-square deviation (RMSD)

Taylor Diagram

• Provides a summary of pattern statistics for overall model skill assessment: bias & unbiased RMSD (uRMSD)

Target Diagram

• Login to VLab Development Services: • Screen Name: NOAA email address, e.g. peter.rochford• Password: “NOAA email password”

• Await approval from project administrator (Peter Rochford)

• Login to VLab again and click on the "Projects" link at the top left of the web page to see the available projects.

• Scroll down and select the  "ROMS Tools" project. If the page appears then you can download software to your local platform using Subversion (svn).

• To see what software is currently available, select the "Repository" tab. The "ROMS Utilities" folder will appear on the top left. Select desired folder. You will then see a list of files that you can individually download if desired.

Accessing ROMS Tools Project (1)

• To download acomplete folder use svn. For example, to download the roms_dates folder to a Linux platform:

svn co https://vlab.ncep.noaa.gov/svn/roms-tools/ROMS\ Utilities/roms_dates roms_dates \

--username peter.rochford

• You will be prompted for your NOAA email password and then asked whether to include your unencrypted password in the local svn database. Simply answer "no" for the latter.

• If successful, you will have a "roms_dates" folder created with the Fortran 2003 code for building the roms_dates utility.

Accessing ROMS Tools Project (2)

• VLab provides a convenient web-accessible infrastructure for sharing software within MMAP, across NOAA branches (CO-OPS, COAST, MMAP), and with non-NOAA collaborators

• VLab provides capability for a central common software repository with software configuration control

• Almost immediately accessible to anyone with a NOAA email account

• Very easy and short learning curve for scientists to use

• Success requires involvement and support of MMAP scientists

Summary

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