add README

README.txt

+-------------------------------------------------
+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. 
+
+

search_O1.m

@@ -7,7 +7,7 @@ function search_O1(freq,idx)
 % ========
 % Input:
 %     freq - Start frequency for all the parallel jobs
-%     idx  - Condor job index
+%     idx  - Condor job offset index
 %     Note: Start frequency for each sub-job: freq + idx
 %
 % Output: