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	tfile_scanner_mcmc_starter.m - cosmo - front and backend for Markov-Chain Monte…
	git clone git://src.adamsgaard.dk/cosmo
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	tfile_scanner_mcmc_starter.m (5983B)
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	1 %% file_scanner_mcmc_starter.m
	2 % This file is started by run.sh.
	3 % The script watches an input folder (infolder) for input files generat…
	4 % by the web interface. The content of the input files is used to start
	5 % calls to the MCMC functions.
	6 %
	7
	8 %% folder and file configuration
	9
	10 % folder containing input files from web interface ("uploadhistory.php")
	11 % and status file
	12 infolder = '~/cosmo/input';
	13
	14 % folder containing input files from web interface while their contents …
	15 % being used by matlab
	16 waitfolder = '~/cosmo/wait';
	17
	18 % outfolder: folder for generated plots
	19 outfolder = '/var/www/html/output/';
	20
	21 [status, hostname] = system('hostname');
	22 if ~isempty(strfind(hostname, 'flaptop')) \|\| ...
	23 ~isempty(strfind(hostname, 'adc-server')) % laptop or desktop
	24 infolder = '~/src/cosmo/input';
	25 outfolder = 'output/';
	26 end
	27
	28 % uniquely identifying file name prefix for input files
	29 prefix = 'cosmo_';
	30
	31 % archivefolder: folder where completed input files are archived. This
	32 % folder should be outside of the webserver document root so others cann…
	33 % access this information
	34 archivefolder = '~/cosmo/archive';
	35
	36 % folder containing matlab scripts to path
	37 matlab_scripts_folder = 'm_pakke2014maj11/';
	38
	39 %% general settings
	40 debug = true; % show debugging output to matlab console
	41
	42 % output graphics formats
	43 graphics_formats = {'fig', 'png', 'pdf'};
	44
	45 % show figures after they are generated in addition to saving them,
	46 % values: 'on' or 'off'
	47 %show_figures = 'on';
	48 show_figures = 'off';
	49
	50 % number of MCMC walkers
	51 %n_walkers = 2;
	52
	53 %% initialization
	54 addpath(matlab_scripts_folder);
	55
	56 % make sure multiple matlab processes to not launch at the exact same ti…
	57 pause(rand()*4.0);
	58
	59 disp('Entering main loop, waiting for input from web interface...');
	60
	61 %% main loop
	62 while 1
	63
	64 try
	65
	66 % detect all files in infolder starting with prefix
	67 infiles = dir(strcat(infolder, '/', prefix, '*'));
	68
	69 % sort files according to modification time
	70 [sorteddates, sortidx] = sort([infiles.datenum]);
	71 infiles = infiles(sortidx);
	72
	73 % process files sequentially
	74 for i = 1:length(infiles);
	75
	76 % read full file name and path
	77 infile = strcat(infolder, '/', infiles(i).name);
	78
	79 % move to waitfolder
	80 movefile(infile, waitfolder);
	81 waitfile = strcat(waitfolder, '/', infiles(i).name);
	82
	83 idstring = strsplit(infile, '_');
	84 id = idstring(2);
	85 statusfile = char(strcat(infolder, '/status_', id));
	86 diary(char(strcat(infolder, '/log_', id)));
	87
	88 if debug
	89 disp(infile);
	90 disp(strcat('Simulation id: ', id));
	91 end
	92
	93 % read file and save data to local scope
	94 [sample_id, name, email, lat, long, ...
	95 be_conc, al_conc, c_conc, ne_conc, ...
	96 be_uncer, al_uncer, c_uncer, ne_uncer, ...
	97 zobs, ...
	98 be_prod_spall, al_prod_spall, c_prod_spall, ne_prod_spal…
	99 be_prod_muons, al_prod_muons, c_prod_muons, ne_prod_muon…
	100 rock_density, ...
	101 epsilon_gla_min, epsilon_gla_max, ...
	102 epsilon_int_min, epsilon_int_max, ...
	103 t_degla_min, t_degla_max, ...
	104 record, ...
	105 record_threshold_min, record_threshold_max, ...
	106 nwalkers] ...
	107 = import_php_file(waitfile, 1, 1); % only read first line
	108
	109 % run inversion
	110 [Ss, save_file] = mcmc_inversion(matlab_scripts_folder, debu…
	111 nwalkers, outfolder, ...
	112 be_conc, al_conc, c_conc, ne_conc, ...
	113 be_uncer, al_uncer, c_uncer, ne_uncer, ...
	114 zobs, ...
	115 be_prod_spall, al_prod_spall, c_prod_spall, ne_prod_spal…
	116 be_prod_muons, al_prod_muons, c_prod_muons, ne_prod_muon…
	117 rock_density, ...
	118 epsilon_gla_min, epsilon_gla_max, ...
	119 epsilon_int_min, epsilon_int_max, ...
	120 t_degla_min, t_degla_max, ...
	121 record, ...
	122 record_threshold_min, record_threshold_max, ...
	123 statusfile, id);
	124
	125 fid = fopen(statusfile, 'w');
	126 fprintf(fid, 'Generating plots and output files');
	127 fclose(fid);
	128
	129 % generate plots
	130 %CompareWalks2(Ss, save_file)
	131 generate_plots(Ss, matlab_scripts_folder, ...
	132 save_file, graphics_formats, show_figures, ...
	133 sample_id, name, email, lat, long, ...
	134 be_conc, al_conc, c_conc, ne_conc, ...
	135 be_uncer, al_uncer, c_uncer, ne_uncer, ...
	136 zobs, ...
	137 be_prod_spall, al_prod_spall, c_prod_spall, ne_prod_spal…
	138 be_prod_muons, al_prod_muons, c_prod_muons, ne_prod_muon…
	139 rock_density, ...
	140 epsilon_gla_min, epsilon_gla_max, ...
	141 epsilon_int_min, epsilon_int_max, ...
	142 t_degla_min, t_degla_max, ...
	143 record, ...
	144 record_threshold_min, record_threshold_max, ...
	145 nwalkers);
	146
	147 % close all figures
	148 close all;
	149
	150 % delete or archive the file so it is not processed again
	151 %delete(infile)
	152 %movefile(infile, archivefolder);
	153 movefile(char(strcat(waitfolder, '/cosmo_', id)), archivefol…
	154
	155 fid = fopen(statusfile, 'w');
	156 fprintf(fid, 'Computations complete');
	157 fclose(fid);
	158
	159 disp(['Computations complete, id = ' id]);
	160
	161 diary off;
	162
	163 %keyboard
	164 end
	165
	166 catch E
	167 disp(E.message)
	168 exit(1) % quit matlab on error
	169 end
	170
	171 % sleep in order to reduce system load
	172 pause(5)
	173
	174 % for debugging purposes; ends loop after first iteration
	175 %break
	176
	177 end