Hi all,
I would like to multithread that script, to detect structure from multilocus
genetic data :
>library(Geneland)
>
>geno = read.table("cot966gen_test.txt") #the file is show after
>MCMC(geno.dip.codom = geno, varnpop=T, npopmax=20, spatial = F, nit=100000,
>thinnin=100, path.mcmc="./")
>PostProcessChain(path.mcmc="./", nxdom=100, nydom=100, burnin=200)
I have an 8 cores computer, and since I have to compute that bit on a thousand
of line like that :
209 209 217 217 180 180 154 154 181 181
192 192 -9 -9 211 211 -9 -9 160 160
-9 -9
-9 -9 -9 -9 254 254 140 140 181 181
-9 -9 -9 -9 211 211 158 158 160 160
158 146
209 209 223 223 348 348 186 186 -9 -9
-9 -9 -9 -9 -9 -9 -9 -9 154 154
146 146
212 212 291 291 218 218 170 170 187 187
194 194 190 190 214 208 152 152 158 158
155 155
209 209 -9 -9 180 180 150 150 185 185
-9 -9 -9 -9 211 211 152 152 -9 -9
155 155
212 212 209 209 234 234 166 166 187 187
-9 -9 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 205 205 236 236 164 164 187 187
194 194 183 183 214 214 163 163 160 160
155 155
212 212 203 203 238 236 164 164 187 187
-9 -9 179 179 -9 -9 -9 -9 -9 -9
-9 -9
212 212 203 203 236 236 164 164 187 187
194 194 -9 -9 214 214 165 165 160 160
155 155
212 212 209 209 236 234 164 164 187 187
194 194 179 179 -9 -9 -9 -9 -9 -9
-9 -9
212 212 205 205 236 236 166 166 -9 -9
-9 -9 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 -9 -9 180 180 147 147 181 181
-9 -9 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 -9 -9 180 180 147 147 181 181
198 198 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 209 209 234 234 166 166 187 187
-9 -9 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 209 209 234 234 166 166 187 187
-9 -9 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 209 209 236 236 166 166 187 187
194 194 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 207 207 236 236 164 164 -9 -9
194 194 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 212 205 205 238 238 164 164 187 187
-9 -9 -9 -9 -9 -9 -9 -9 160 160
155 155
212 212 209 207 234 234 164 164 187 187
194 194 183 183 -9 -9 -9 -9 -9 -9
-9 -9
-9 -9 -9 -9 -9 -9 166 166 -9 -9
194 194 183 183 -9 -9 -9 -9 -9 -9
-9 -9
212 212 209 205 234 234 164 164 187 187
194 194 179 179 214 214 165 165 160 160
155 155
212 212 205 205 234 234 164 164 187 187
194 194 183 183 214 214 163 163 160 160
155 155
212 212 209 209 236 236 166 166 187 187
194 194 -9 -9 -9 -9 -9 -9 -9 -9
-9 -9
212 209 -9 -9 180 180 150 147 187 187
-9 -9 -9 -9 211 211 158 154 -9 -9
155 155
209 209 207 207 328 328 184 184 181 181
-9 -9 -9 -9 211 211 165 165 -9 -9
155 155
212 212 253 253 212 212 168 150 187 181
-9 -9 -9 -9 208 208 160 160 -9 -9
155 146
212 212 -9 -9 230 224 178 178 193 193
194 194 -9 -9 208 208 158 158 160 158
155 155
212 212 -9 -9 232 224 150 150 197 189
-9 -9 -9 -9 208 208 160 160 158 158
155 155
209 209 219 215 194 194 162 162 193 193
192 192 161 161 208 208 163 160 154 154
155 146
212 212 251 251 222 222 164 164 183 183
194 194 -9 -9 208 208 160 160 158 158
155 155
-9 -9 293 251 -9 -9 -9 -9 195 195
192 192 -9 -9 -9 -9 -9 -9 154 154
146 146
212 212 293 249 232 212 178 176 183 183
-9 -9 -9 -9 208 208 156 152 158 158
155 155
209 209 217 197 256 192 160 160 189 183
192 192 -9 -9 208 208 -9 -9 154 154
155 146
209 209 223 197 238 200 206 206 183 183
-9 -9 198 198 208 208 165 165 154 154
155 146
212 212 249 249 218 218 -9 -9 183 183
194 194 190 169 -9 -9 -9 -9 -9 -9
155 146
212 212 -9 -9 224 224 164 164 193 193
-9 -9 -9 -9 208 208 165 160 158 158
155 146
209 209 217 213 304 212 182 182 195 195
192 192 -9 -9 208 208 165 165 154 154
155 146
209 209 238 219 266 248 188 188 183 183
192 192 -9 -9 -9 -9 -9 -9 -9 -9
146 146
209 209 243 223 254 200 162 162 183 183
192 192 -9 -9 -9 -9 -9 -9 154 154
146 146
212 212 247 247 228 224 210 210 183 183
-9 -9 -9 -9 208 208 158 158 158 158
155 155
It will take a while. So I want to multithread all that, but I don't know how.
I read things on the multicore package, but I don't know how to use it here, or
snow packages, so I would really appreciate a bit of help...
So, does anyone know about Geneland and multithreading ?
Thanks,
Aurélien Chateigner
PhD Student
Institut de Recherche sur la Biologie de l'Insecte
UMR CNRS 6035
Université François Rabelais de Tours
Faculté des Sciences et Techniques
Avenue Monge - Parc Grandmont
37200 TOURS (FRANCE)
http://irbi.univ-tours.fr/
aurelien.chateig...@gmail.com
Phone: +33 (0)2 47 36 73 83
+33 (0)6 84 88 72 91
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