/
matlab_install.m
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matlab_install.m
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function matlab_install(SuiteSparse_path)
% Matlab function to compile all the c-files to mex in the GPstuff toolbox.
%
% Some of the sparse GP functionalities in the toolbox require
% SuiteSparse toolbox by Tim Davis:
% http://www.cise.ufl.edu/research/sparse/SuiteSparse/current/SuiteSparse/
%
% This package includes the SuiteSparse version 4.4.2.
%
% * To install without SuiteSparse run matlab_install
% * To install with SuiteSparse run matlab_install('SuiteSparseOn')
%
% The function matlab_install compiles the mex-files and prints on
% the screen, which directories should be added to Matlab paths.
% Copyright (c) 2008-2012, 2016 Jarno Vanhatalo
% Copyright (c) 2016 Eero Siivola
% This software is distributed under the GNU General Public
% License (version 3 or later); please refer to the file
% License.txt, included with the software, for details.
if nargin < 1
SuiteSparse_path = [];
fprintf('\n The path to the SuiteSparse package is not provided. \n')
fprintf('\n Installing GPstuff without compactly supported covariance functions. \n')
fprintf(' You are not able to use the following covariance functions: \n')
fprintf(' gpcf_ppcs0 \n gpcf_ppcs1 \n gpcf_ppcs2 \n gpcf_ppcs3 \n\n\n')
elseif strcmp(SuiteSparse_path, 'SuiteSparseOn')
cdir = pwd;
cd SuiteSparse % Change this to correspond your own settings!
SuiteSparse_path = path_spaces([pwd '/']);
% Compile SuiteSparse
fprintf('Compiling SuiteSparse. This may take a while \n \n')
SuiteSparse_install(false);
paths{1} = SuiteSparse_path;
paths{2} = [SuiteSparse_path 'UMFPACK/MATLAB'];
paths{3} = [SuiteSparse_path 'CHOLMOD/MATLAB'];
paths{4} = [SuiteSparse_path 'AMD/MATLAB'];
paths{5} = [SuiteSparse_path 'COLAMD/MATLAB'];
paths{6} = [SuiteSparse_path 'CCOLAMD/MATLAB'];
paths{7} = [SuiteSparse_path 'CAMD/MATLAB'];
paths{8} = [SuiteSparse_path 'CXSparse/MATLAB/Demo'];
paths{9} = [SuiteSparse_path 'CXSparse/MATLAB/CSparse'];
paths{10} = [SuiteSparse_path 'LDL/MATLAB'];
paths{11} = [SuiteSparse_path 'BTF/MATLAB'];
paths{12} = [SuiteSparse_path 'KLU/MATLAB'];
paths{13} = [SuiteSparse_path 'SPQR/MATLAB'];
paths{14} = [SuiteSparse_path 'RBio/RBio'];
paths{15} = [SuiteSparse_path 'MATLAB_Tools'];
paths{16} = [SuiteSparse_path 'MATLAB_Tools/Factorize'];
paths{17} = [SuiteSparse_path 'MATLAB_Tools/MESHND'];
paths{18} = [SuiteSparse_path 'MATLAB_Tools/LINFACTOR'];
paths{19} = [SuiteSparse_path 'MATLAB_Tools/find_components'];
paths{20} = [SuiteSparse_path 'MATLAB_Tools/GEE'];
paths{21} = [SuiteSparse_path 'MATLAB_Tools/shellgui'];
paths{22} = [SuiteSparse_path 'MATLAB_Tools/waitmex'];
paths{23} = [SuiteSparse_path 'MATLAB_Tools/spqr_rank'];
paths{24} = [SuiteSparse_path 'MATLAB_Tools/spqr_rank/SJget'];
paths{25} = [SuiteSparse_path 'MATLAB_Tools/UFcollection'];
paths{26} = [SuiteSparse_path 'MATLAB_Tools/SSMULT'];
paths{27} = [SuiteSparse_path 'MATLAB_Tools/dimacs10'];
paths{28} = [SuiteSparse_path 'MATLAB_Tools/spok'];
paths{29} = [SuiteSparse_path 'MATLAB_Tools/sparseinv'];
cd(cdir)
fprintf('Compiling GPstuff. This may take a while \n \n')
else
error('Unknown input argument. See help matlab_install for usage.')
end
% Go to diag/ and compile the mex-functions
fprintf('\n Compiling files in diag.\n \n')
cd('diag')
diag_install
cd('..')
% Go to dist/ and compile the mex-functions
fprintf('\n Compiling files in dist.\n \n')
cd('dist')
dist_install
cd('..')
% Go to gp/ and compile the mex-functions
fprintf('\n Compiling files in gp.\n \n')
cd('gp')
gp_install(SuiteSparse_path)
cd('..')
% Go to mc/ and compile the mex-functions
fprintf('\n Compiling files in mc. \n \n')
cd('mc')
mc_install
cd('..')
PP = pwd;
S{1} = [PP '/diag'];
S{2} = [PP '/dist'];
S{3} = [PP '/gp'];
S{4} = [PP '/mc'];
S{5} = [PP '/misc'];
S{6} = [PP '/optim'];
S{7} = [PP '/tests'];
fprintf ('\n The following paths have been added. You may wish to add them\n') ;
fprintf ('permanently, using the MATLAB pathtool command or copying the below\n') ;
fprintf ('lines to your startup.m file. \n\n');
for i = 1:length(S)
addpath(S{i});
fprintf ('addpath %s\n', S{i}) ;
end
if nargin==1
fprintf ('\n')
for k = 1:length (paths)
fprintf ('addpath %s\n', paths {k}) ;
end
end
end
function path = path_spaces(path)
% Build correct path if path includes spaces
space_ind=strfind(path, ' ');
path=strrep(path, ' ', ''' ');
space_ind=space_ind+length(space_ind);
for i=1:length(space_ind)
indd=strfind(path(space_ind(i):end), '/');
path=[path(1:space_ind(i)+indd(1)-2) '''/' path(space_ind(i)+indd(1):end)];
space_ind=space_ind+1;
end
end