SeaDAS Installation Instructions

SeaDAS 6.2 Installation Instructions

INSTALLATION NOTES:

Do not install a new version of SeaDAS "on top of" an old version. Instead, before installing SeaDAS remove or move any previous versions and also disable any lines in your shell initialization files that set up the old SeaDAS environment (e.g. "export SEADAS=old/path/to/seadas", setenv SEADAS old/path/to/seadas", "source old/path/to/seadas/config/seadas.env").

If you encounter difficulties downloading the large distribution files you can download them in 10MB pieces and then join them back together. See the FAQ for instructions.

Do not install or run SeaDAS as the root user. Doing so is a security hazard and may also lead to functionality problems. To install one version of SeaDAS to be shared by multiple users, see the SeaDAS shared installation page.

If you are NOT using runtime SeaDAS, IDL must be installed on your computer along with its high resolution coastline database (found under IDL's Custom Installation section), and the "idl" command must also be in your path (i.e. typing "idl" in an xterm window should start an IDL session).

Mac OS X users must have X11 installed in order to use SeaDAS. To determine if X11 is installed on your computer, look for the "Applications/Utilities/X11" application. If it is not present, please install X11 from your OS X Installation Disc. The installation instructions below should be done in an X11 window, not in the "Terminal" application window.

Some Linux distributions(e.g. Ubuntu) come without csh initially installed. The seadas_setup script and other data processing scripts require csh in order to run successfully. If you do not have csh installed, you must install it yourself prior to SeaDAS installation. You can determine if you have csh installed by either running the command "which csh" or "ls /bin/csh". If you have root permission on your computer, try "yum install csh" or "sudo apt-get install csh", otherwise ask your system administrator to install csh.

Step

What To Do

How To Do It

In an xterm window, create a SeaDAS root directory and enter that directory (name it anything you like):

> mkdir seadas6.2
> cd seadas6.2

ftp the compressed SeaDAS tar files into your new directory (mirrors may take a while to host a new SeaDAS version):

USA:
samoa.gsfc.nasa.gov
(dir: seadas/seadas)

UK:
seadasuk.pml.ac.uk
(dir: seadas/seadas6.2)

Brazil:
orion.io.usp.br
(dir: pub/seadas)

Japan:
odyssey.fish.hokudai.ac.jp
(dir: SeaDAS_v6.2)

Australia:
ftp.marine.csiro.au
(dir: mirror/samoa.gsfc.nasa.gov/seadas/seadas_6.2)

> ftp samoa.gsfc.nasa.gov

anonymous

user@hostname

binary

cd seadas/seadas

get seadas_xxx.tar.gz (where xxx is linux, macintel, or macppc)

get seadas_idl_rt.tar.gz (optional for runtime SeaDAS)

get seadas_processing.tar.gz (required for data processing)

get seadas_seawifs.tar.gz (optional for SeaWiFS processing)

get seadas_modisa.tar.gz (optional for Aqua processing)

get seadas_modist.tar.gz (optional for Terra processing)

get seadas_meris.tar.gz (optional for MERIS processing)

get seadas_octs.tar.gz (optional for OCTS processing)

get seadas_czcs.tar.gz (optional for CZCS processing)

get seadas_dem_modis.tar.gz (optional for terrain correction)

quit

Uncompress and extract the SeaDAS tar files:

> gunzip -c seadas_xxx.tar.gz | tar xvf -
> gunzip -c seadas_idl_rt.tar.gz | tar xvf -
> gunzip -c seadas_processing.tar.gz | tar xvf -
> etc...

Run the SeaDAS setup program from within the SeaDAS home directory (execute the command './config/seadas_setup' or './config/seadas_setup -em') and click on the Okay button.

NOTE: You must have csh installed before running seadas_setup!

If you have IDL installed with a *FULL* license:
> ./config/seadas_setup

OR

If you are using runtime SeaDAS:
> ./config/seadas_setup -em

Activate the Seadas setup just created:

> source config/seadas.env

If you are running under csh or tcsh, execute:
> rehash

If you are a Mac OS X user, execute:
> limit stacksize unlimited (for csh or tcsh)
> ulimit -Ss unlimited (for bash)

Depending on your shell, add the following line to the end of your .cshrc, .tcshrc, or .bashrc file, where "PATH_TO_SEADAS" is the full directory path of your seadas directory (e.g. /home/zaphod/seadas6.2):

Add this text to one of your shell init files:

     source PATH_TO_SEADAS/config/seadas.env

If you are a Mac OS X user, also add the line:
     limit stacksize unlimited (for csh or tcsh)
OR
     ulimit -Ss unlimited (for bash)

Start SeaDAS.

> seadas (if you have IDL installed)

OR

> seadas -em (to use runtime SeaDAS)

Depending on your disk space, you may want to remove the compressed tar files:

> rm *.gz (optionally do this if SeaDAS is working)

Check periodically for new SeaDAS updates. You do not need to install any updates if you have just installed SeaDAS, since the updates are included in the main tar file distributions. Updates can be downloaded from the SeaDAS distribution directory via anonymous ftp from samoa.gsfc.nasa.gov.

10.

If you want to rebuild the SeaDAS application on your system and you have the proper C and Fortran compilers, follow the instructions in the REBUILDING SEADAS NOTES section below.

11.

If you want to share SeaDAS among multiple users follow the instructions on the SeaDAS shared installation page.

REBUILDING SEADAS NOTES:

ONLY perform these steps if you are rebuilding SeaDAS, and the proper compilers are installed on your system.

Required compilers:

SeaDAS can be rebuilt with either the free gcc/g++/gfortran compilers, or the Intel C and Fortran compilers (The SeaDAS Linux and Intel Mac distributions are built with gcc, g++, and ifort.) Though the Intel compilers are not free (an exception being the Linux non-commercial license), they will likely provide processing speed gains. Contact us for gfortran vs. ifort benchmarks.

Intel Compilers:

http://software.intel.com/en-us/intel-compilers/
http://software.intel.com/en-us/articles/non-commercial-software-development/

If using gfortran, the currently supported versions are:

Linux: gfortran 4.5
Intel Mac: gfortran 4.5
PPC Mac: gfortran 4.4

Current gfortran binary distributions can be downloaded here:

http://gcc.gnu.org/wiki/GFortran

STEPS TO BUILD A SEADAS PROCESSING BINARY:

Install SeaDAS.

Check to make sure the compilers you want to use are configured via the OCSSW_CC, OCSSW_CXX, and OCSSW_FC environment variables, e.g.:
   $ env |grep OCSSW_
   OCSSW_CC=gcc
   OCSSW_CXX=g++
   OCSSW_FC=ifort

NOTE: If you choose to use a different compiler (and possibly version of a compiler) than was used for the distribution you may need to first rebuild any libraries used by the program. In this situation it might be simplest to just rebuild the entire SeaDAS package with your chosen compiler (see the next section, STEPS TO BUILD THE ENTIRE SEADAS PACKAGE).

For linux, you may want to set GCC_TUNE environment variable, e.g.:
   export GCC_TUNE="-mtune=opteron"
   OR
   export GCC_TUNE="-mtune=core2"

If you are using gfortran (as opposed to Intel fortran), then you must switch the $SEADAS/src/lib3/ symbolic link from the ifortran prebuilt libs to the gfortran prebuilt libs. To switch to the gfortran lib3's, execute these commands:
   cd $SEADAS/src
   tar xvfz lib3.linux_gfortran.tar.gz    (this creates the lib3_gfortran directory)
   rm lib3
   ln -s lib3_gfortran lib3

All SeaDAS processing programs and libraries are stored under the $SEADAS/src/build/src/ directory. To build a particular binary, change into that program's directory, e.g.:
   cd $SEADAS/src/build/src/l2gen
   make clean
   make

In this example the l2gen directory actually contains the code for various binaries, and all will be built when only 'make' is executed. To build only the l2gen binary you would issue the command:
   make -f l2gen.mk

If your binary compiles successfully, you can then copy it into the $SEADAS/bin/ directory. BACKUP THE ORIGINAL BINARY FIRST!
cp l2gen $SEADAS/bin
To modify an existing algorithm for l2gen you can alter that specific algorithm's code. If you want to add an entirely NEW product, consult $SEADAS/src/build/src/l2gen/HOWTO_Add_a_product.txt.

STEPS TO BUILD THE ENTIRE SEADAS PACKAGE:

WARNING: The steps below will remove all the distributed binaries and libraries before regenerating them. Backup the $SEADAS/bin/ and $SEADAS/src/build/lib/ directories before compiling!

Install SeaDAS.

Check to make sure the compilers you want to use are configured via the OCSSW_CC, OCSSW_CXX, and OCSSW_FC environment variables, e.g.:
   $ env |grep OCSSW_
   OCSSW_CC=gcc
   OCSSW_CXX=g++
   OCSSW_FC=ifort

Next make sure the correct Fortran compiler (matching OCSSW_FC) and flags are uncommented in the $SEADAS/config/build/*.cf file for your platform. The files are linux.cf, macosx_intel.cf, macosx_ppc.cf.

If you are using gfortran (as opposed to Intel fortran), then you must switch the $SEADAS/src/lib3/ symbolic link from the ifortran prebuilt libs to the gfortran prebuilt libs. To switch to the gfortran lib3's, execute these commands:
   cd $SEADAS/src
   tar xvfz lib3.linux_gfortran.tar.gz    (this creates the lib3_gfortran directory)
   rm lib3
   ln -s lib3_gfortran lib3

For linux, you may want to set GCC_TUNE environment variable, e.g.:
   export GCC_TUNE="-mtune=opteron"
   OR
   export GCC_TUNE="-mtune=core2"

Build the entire SeaDAS package:
cd $SEADAS
./config/build_seadas

Check the final lines of the build script's stdout to make sure the expected number of bins/libs were created. If there was a problem check the makesrc.out and makesdssrc.out build log files.

Curator: OceanColor Webmaster

Authorized by: gene carl feldman

Updated: 05 January 2011