Compiling and running standalone matlab executable.

First, define the paths:

export LD_LIBRARY_PATH=/opt/matlab2012a/bin/glnxa64:/opt/matlab2012a/sys/os/glnxa64:/opt/matlab2012a/runtime/glnxa64/

Compile the .m file

mcc -mv mymatlabfile.m

The matlab compiler generates two execute files: mymatlabfile and run_mymatlabfile.sh

Ignore the shell script generated by matlab. Simply execute ./mymatlabfile 

If you have addpath commands in your .m file, these will cause error while running the standalone executables. To solve this, do the following

if ~isdeployed
    addpath('path1...');
end

If your .m file has input parameters, execute the file in the following way

mymatlabfile para1 para2.

For example, if this is your matlab file

function myprog(num1, num2)

you call the file by

myprog 100 200

Note that the paramters 100 and 200 will be passed as string instead of numbers so you have to modify your .m file:

function myprog(num1, num2)
if isdeployed
    num1 = str2double(num1);
    num2 = str2double(num2);
end

Bash script to run in clusters

#!/bin/bash

# total number = 8677
for i in {1..8599..860}
do
    let j=$i+860-1
    echo "Running $i and $j....."
    srun -c 5 -o output/output$i.txt ./calc_bg_pooling $i $j &
done

echo "Running the last small part....."
srun -c 5 -o output/output8601.txt ./calc_bg_pooling 8601 8677 &
Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: