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-------------------------------------------------
README - Instructions to run the scripts on Atlas
-------------------------------------------------
The scripts need to be compiled on a head node with Matlab license. 
Run the compiled executable file on execute nodes.


1. Files to compile
-------------------
The following files need to be put in the same directory for compiling.
Project scripts:
    - search_O1.m (main script)
    - viterbi_colFLT.m
    - argmax.m
    - binaryfilter.m
    - readfstats.m
Matlab functions:
    - bestblk.m
    - col2im.m
    - colfilt.m
    - fcnchk.m
    - im2col.m
    - mkconstarray.m

2. Instruction to compile
-------------------------
NOTE: To run jobs with Condor, one can NOT use the default path (/tmp/) for 
Matlab's lock files and must specify the number of cores Matlab will use on 
the nodes as it will otherwise try to run on all available ones. 

The solution is described in wiki: https://wiki.atlas.aei.uni-hannover.de/foswiki/bin/view/ATLAS/MatlabUnderCondor

EXAMPLE:
Run the command in the directory where the .m scripts are:

/opt/matlab/default/bin/mcc -mv -R singleCompThread -R nojvm -R nodesktop -R nosplash -o <executable file name> <main script>.m 

3. Files to deploy
------------------
    - <executable file> (from last step)
    - atlas-matlab-init
    - Condor submission file <name>.sub

EXAMPLE: (Run manually)
atlas-matlab-init <executable file name> <parameter1, parameter2, ...> 

EXAMPLE: (Run as Condor jobs)
Refer to sample submission file viterbi_search.sub

4. Notes
--------
The main script search_O1.m is an example of the search. The parameters can 
be adjusted according to the requirement of different searches. For the purpose
of parallel search, the frequency band is separated into 1-Hz sub-bands and this script takes two parameters.

Parameter 1 - start frequency for all the parallel jobs
Parameter 2 - Job offset index

EXAMPLE:
./search_O1 100 0 - Search a 1-Hz sub-band from 100 to 101 Hz.
./search_O1 100 1 - Search a 1-Hz sub-band from 101 to 102 Hz.