README.txt 1.5 KB
Newer Older
Ling Sun's avatar
Ling Sun committed
1
2
3
4
5
6
7
8
9
10
11
-------------------------------------------------
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:
12
    - run_search.m (main script)
Ling Sun's avatar
Ling Sun committed
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
    - 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