Why matlab is taking long time for data analysis on linux server

I am trying to execute the below codes but it is taking long time

    s = shaperead('grid_area2000.shp');
N = length(s);
for i = 1:N
    plot(s(i).X,s(i).Y)
    hold on
end
lat = xlsread('lat.xlsx');
long = xlsread('long.xlsx');
 [X ,Y] = meshgrid(long,lat); 
data = load('testdata.mat');
 [nx,ny,d] = size(data);
iwant = cell(d,N);
for j = 1:d
    A = data(:,:,j);
    for k = 1:N
        idx = inpolygon(X(:),Y(:),s(k).X,s(k).Y);
        iwant(j,k) = A(idx);
    end
end

The properties of data (940*420*10) and shapefile(both X and Y are 1*614035) MATLAB version is 2014a, my system configure is 1Tkb disk and 16Gb RAM, server configure

   Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                6
On-line CPU(s) list:   0-5
Thread(s) per core:    1
Core(s) per socket:    6
座：                 1
NUMA 节点：         1
厂商 ID：           GenuineIntel
CPU 系列：          6
型号：              79
型号名称：        Intel(R) Xeon(R) CPU E5-2603 v4 @ 1.70GHz
步进：              1
CPU MHz：             1200.093
BogoMIPS：            3395.97
虚拟化：           VT-x
L1d 缓存：          32K
L1i 缓存：          32K
L2 缓存：           256K
L3 缓存：           15360K
NUMA 节点0 CPU：    0-5

What is wrong with my system/server or data and command? How can I fix it? Thank you in advance for any sort of help.