Installation of ArgoRT

This Argo Realtime Processing system is a collection of directories and files.


Directory structure

In the following, SOURCE refers to the directory from which you are 
to download the system.

Set up your processing area to match the structure of SOURCE. That is:

Make a processing directory (refer to here as ARGO_RT). Either recursively
copy SOURCE to ARGO_RT, or setup and populate the subdirectories 

   argos_downloads/
   cal_data/
   docs/
   export/
   matfiles/
   netcdf/
   src/
   reports/
   run_logs/
   spreadsheet/
   tesac/
   workfiles/
   work/

(If saving netcdf Profile files after exporting, could have subdirectories for
 each float in netcdf/.)

See ArgoRT directories for details.

The Argo master spreadsheet, called masterargo.xls, must not be 
restructured at all! It must record all floats that are to be processed
(if they are not in this database they will not be processed!

Also establish a separate web directory (most likely not within the above area),
with structure as in SOURCE/web/,   ie with subdirectories:
   doc/
   floats/
   processing/
   templates/
	
Populate these directories from those in SOURCE.
   
Set protection in web areas so that all is public-viewable (hence web-viewable)




                   
Modifications to code

Paths

In set_argo_sys_params edit paths to:
- your processing directory name in variable  .root_dir  
- root web directory name in variable  .web_dir
- root URL in variable  .www_root

System tuning is by modification to other fields
in that file.


Modify hardcoded paths in  
    argo_cron
    ftp_get_argos

Also ensure that the ranges of Argos IDs in ftp_get_argos covers
all oue floats.

Modify hardcoded paths and passwords in shell script 
    writeGDAC

Modify paths and Matlab licenses or command in:
    run_rt_argo.sh
    run_web_report.sh


Processing records file
Create a new processing records variable and file in ARGO_RT:
  Manually create an empty file: 
     >> PROC_RECORDS = [];
     >> fnm = [argo_root_dir 'Argo_proc_records'];
     >> save(fnm,'PROC_RECORDS');
OR
  Generate a new one from existing matfiles using 
  proc_recs_rebuild 
  

Master Spreadsheet

Assuming the Excel spreadsheet argomaster.xls has been generated or
copied, save a csv versions of sheet 2 (call it argomaster.csv) and 
of sheet 4 (call it argomaster_cal.csv) in ARGO_RT/spreadsheet/


Bathymetry data

The name and path of the netcdf bathymetry file is hardcoded in 
get_ocean_depth.m. 
Modify, or change this function altogether as needed to obtain bathymetry
information (which is used to check that the float is not in an impossibly
shallow location.)


Calibration Reference data

Review load_ctd_refset.m.  This code
has some arbitrary variable names and organisation, and could warrant 
a revamp.   




Run Scheduling - cron

Modify paths and review run times in 
   argo_cron

There is one "cron table" on any machine for any one user. To examine it 
for the present user and machine, type
    crontab -l
 
(Note:  The line
   5 5,11,17,23 * * *  /home/dunn/Argo_netcdf/src/run_rt_argo.sh
means run that script at 5.05, 11.05, 17.05 and 23.05, every day.)

run_web_report.sh should run at a convenient time for operators 
to look at the updated page, once per day only (preferably only on days
when operators will), since the page only shows reports generated since 
the last time the page was updated.

When ready to activate the system, load the cron table:
  crontab argo_cron
and check with 
  crontab -l


Note: If there need to be other jobs in the cron table then 
argo_cron and the other cron entry files should be concatonated and 
submitted with crontab.




Matlab

Matlab license numbers and commands need to be altered in run scripts 
(see Paths above).

For all ArgoRT work, cd to ARGO_RT (or maybe a subdirectory of it). 
Invoke Matlab and set up paths. Eg
   addpath src
   
This and other routine Matlab setup can be placed in a startup.m file
in your ~/matlab/ directory.

-v6 matfiles
Some matfiles are saved with -v6 for backwards compatibility. This
ought to be unnecessary (why would you go back to v6?), so feel free to
make the decision and remove all instances of -v6.


                          

System Tuning

Most system tuning is achieved by editing file set_argo_sys_params. The purpose of each parameter is described in that file.

Operator Training

After installing the web-based documentation, all pages of System Documentation (except the Source Code pages) should be read by those involved with the system. This is not because it is any good, but because snippets of information are scattered throughout both the Operator and Programmer pages, (including, for example, in "File Types").

Updated 17-Nov-2006 JRD