ocssw  V2019
Introduction

This contains science processing software used within OBPG. It is provided here with NO SUPPORT. For fully supported code, please use the binaries distributed with SeaDAS https://seadas.gsfc.nasa.gov/

OCSSW_bash.env (OCSSW.env for csh) is provided for setting needed environment variables to build the software.

REQUIREMENTS:

  • gcc (4.5 or higher)
  • g++ (matching gcc version)
  • gfortran (matching gcc version)
  • zlib
  • csh
  • tcsh
  • unzip
  • git
  • cmake
  • bison
  • flex
  • libX11-devel
  • wget

additional known OS-specific requirements

  • Ubuntu 16.04
    • zlib1g-dev
  • CentOS 7
    • glibc-static
    • libgfortran-static
    • zlib-static
    • gmp-static
    • libjpeg-turbo-static
    • libstdc++-static
  • Mac:
    • libX11 can be installed by XQuartz

Building the code

CMake is used for the build system with a CMakeLists.txt file in each directory.

Here are the steps needed to build using bash, cmake and make:

  1. Get a copy of the ocssw source git repository
$ git clone https://oceandata.sci.gsfc.nasa.gov/ocssw/ocssw-src.git [optional target directory name]

Note: OBPG staff developers with access to the deveopment repository can do the following instead:

git clone https://oceandata.sci.gsfc.nasa.gov/rcs/obpg/ocssw.git [optional target directory name]
or when on OBPG internal network, with ssh key in gitlab:
git clone git@oceanrcs101:obpg/ocssw.git
cd ocssw
git submodule init
git submodule update
  1. Setup environment variables (usually in ~/.bashrc)
$ export CC=gcc
$ export CXX=g++
$ export FC=gfortran
$ export OCSSWROOT=$HOME/ocssw
$ export OCSSW_DEBUG=1 #set to 0 if not debugging
$ source $OCSSWROOT/OCSSW_bash.env
  1. Grab the third party library sources and put them in opt
$ cd $OCSSWROOT/opt
$ wget https://oceandata.sci.gsfc.nasa.gov/ocssw/opt-src.tar
$ tar -xvf opt-src.tar

Note: OBPG staff developers can use the get_lib3_src.sh script to obtain these

  1. Build and install the third party libs

    Note: You may want to remove $OCSSWROOT/opt/bin, $OCSSWROOT/opt/lib, and $OCSSWROOT/opt/include

$ cd $OCSSWROOT/opt/src
$ export OCSSW_DEBUG=0 #probably do not want to debug these
$ # you may want to remove $OCSSWROOT/opt/bin, $OCSSWROOT/opt/lib, and $OCSSWROOT/opt/include prior to:
$ ./BuildIt
  1. Create build directory and run cmake

    CMake allows for out-of-source-tree builds. Make a directory for this and run cmake within it, e.g.:

$ cd <ocssw source directory> (e.g. $OCSSWROOT/ocssw-src)
$ mkdir build
$ cd build
$ cmake ..

Note: There are a few options you can give to cmake to control what extra software is built:

BUILD_VIIRS_L1 - Build VIIRS L1 code
(not yet open source)
BUILD_HISTORICAL - Build the historical code
(e.g. old seawifs binaries no longer needed)
BUILD_MISC - Build non-essential code
BUILD_AHMAD_FRASER - Build the AF radiative transfer code
(not distributed)
BUILD_ALL - Build everything we got
The "cmake .." command is run like this to use one or more of these options:
cmake .. -DBUILD_HISTORICAL=ON -DBUILD_MISC=ON
Please be aware that not all the code required for these options
is available in the externally accessible source repository
  1. Build the OCSSW binaries
$ cd <ocssw build directory> (e.g. $OCSSWROOT/ocssw-src/build)
$ export OCSSW_DEBUG=1 #could be set to 0 if not debugging
$ make -j 20
  1. Install binaries into $OCSSWROOT/bin
$ make install
  1. Grab all the data trees

    See https://oceandata.sci.gsfc.nasa.gov/ocssw/ for manual installation or use install_ocssw.py or the SeaDAS GUI

    Note: OBPG staff developers can use the following:

$ cd <cmake build directory>
$ make update #This command will take a LONG time

IDE setup

NetBeans

Here are the steps needed to use NetBeans for programming and debugging:

  1. download, build and install OCSSW as described above. Make sure to set OCSSW_DEBUG=0 before building 3rd party libs and setting OCSSW_DEBUG=1 before building OCSSW code.
  2. setup the correct compilers
menu Tools -> Options
select C/C++
select Build Tools tab
Base Directory = /usr/bin
C Compiler = /usr/bin/gcc-5
C++ Compiler = /usr/bin/g++-5
Fortran Compiler = /usr/bin/gfortran-5
Assembler = /usr/bin/as
Make Command = /usr/bin/make
Debugger Command = /usr/bin/gdb
QMake Command = /usr/bin/qmake
CMake Command = /usr/bin/cmake
click OK
  1. load the project into netbeans
menu File -> New Project
select C/C++
select C/C++ Project with Existing Sources
click Next
Folder that contains existing source = $OCSSWROOT
(substitute the real dir for $OCSSWROOT)
Build Host = localhost
Tool Collection = Default GNU
Configuration Mode = Custom
click Next
check Pre-Build Step is Required
Run in Folder = $OCSSWROOT/build
select Predefined Command
Script type = CMake
Script = $OCSSWROOT/CMakeLists.txt
Arguments = (the default is fine)
click Next
(Build Actions)
click Next
(Source Files)
Source File Folders = $OCSSWROOT
(Exclude Pattern)
^(nbproject|.git|opt|share|test|var)$
click Next
(Code Assistance Configuration)
click Next
(Project Name and Location)
click Finish
  1. Setup a run configuration
menu Run -> Set Project Configuration -> Customize...
click Manage Configurations...
click New
New Name = l2gen (or whatever you want)
select l2gen
click Set Active
click OK
select Categories: Build -> Make
Working Directory = build
Build Command = ${MAKE} -j 20
Clean Command = ${MAKE} clean
Build Result = build/src/l2gen/l2gen
select Categories: Run
Run Command = "${OUTPUT_PATH}" par=S2002079035435.L2_MLAC_OC.subpix.par
Run Directory = $OCSSWROOT/test/l2gen/seawifs
Environment =
Build First = checked
Console Type = Internal Terminal
External Terminal Type = Default
click OK

Now you can Run or Debug

  1. Setup OBPG standard code formatting style
select menu Tools->Options
select "Editor" icon on top
select "Formatting" tab
Make sure "Language: All Languages"
Check "Expand Tabs to Spaces"
Number of spaces = 4
for each language (C, C++, C/C++ Headers) change
select Style = K&R
under "Braces Placement" heading
Function Declaration = Same Line

Eclipse

Here are the steps needed to use eclipse for programming and debugging:

  1. download, build and install OCSSW as described above. Make sure to set OCSSW_DEBUG=0 before building 3rd party libs and setting OCSSW_DEBUG=1 before building OCSSW code.
  2. load the project into eclipse
menu File -> New -> C++ Project Project Name:
make up a name for the project
uncheck Use Default
Location Location = $OCSSWROOT (substitute your val for $OCSSWROOT)
Project type:
Makefile Project -> Empty Project
Toolchains = "Linux GCC" for Linux, "MacOSX GCC" for mac
Next Advanced Settings (button)
C/C++ Build (list item)
Builder Settings (tab)
uncheck "Use default build command"
Build Command = make -j 20
uncheck "Generate Makefiles automatically"
Build Location = ${workspace_loc:/ocssw/build}
Click on the OK Button.
Click on the Finish Button.
Wait a long time for the C/C++ Indexer to finish...
  1. make a run configuration to run l2gen
menu Run -> Run Configurations...
select C/C++ Application
click the icon with a plus sign on it
Name = l2gen-run
Main tab C/C++ Application = build/src/l2gen/l2gen
Arguments tab Program arguments = "par=S1997262224952.L2_LAC.par"
uncheck Use default
Working directory = $OCSSWROOT/test/l2gen (substitute your value)
click Apply
click Run
  1. Setup OBPG standard code formatting style
menu Window -> Preferences General -> Editors -> Text Editors Display tab
width = 4
check "Insert spaces for tabs"
C/C++ -> Code Style -> Formatter click "New..." button
Profile name = OCSSW Initialize settings with following profile: K&R [built-in]
click OK
Indentation tab Tab policy:
Spaces only
Indentation size = 4
Tab size = 4
Braces tab Function declaration: Same Line
Line Wrapping tab check "Never join already wrapped lines"
click OK
click Apply
click OK