/Applications/BioNetGen/Perl2/BNG2.pl
BioNetGen version 2.0.48
readFile::Reading from file toy-jim.bngl
Read 16 parameters.
Read 5 species.
Adding P as allowed state of component Y of molecule K
Read 8 reaction rule(s).
Read 9 observable(s).
WARNING: Removing old network file toy-jim.net.
Iteration 0: 5 species 0 rxns 0.00e+00 CPU s
Iteration 1: 8 species 3 rxns 0.00e+00 CPU s
Iteration 2: 12 species 12 rxns 2.00e-02 CPU s
Iteration 3: 17 species 29 rxns 6.00e-02 CPU s
Iteration 4: 18 species 51 rxns 1.40e-01 CPU s
Iteration 5: 24 species 58 rxns 4.00e-02 CPU s
Iteration 6: 25 species 97 rxns 1.60e-01 CPU s
Iteration 7: 25 species 101 rxns 1.00e-02 CPU s
Cumulative CPU time for each rule
Rule 1: 8 reactions 4.00e-02 CPU s 5.00e-03 CPU s/rxn
Rule 2: 20 reactions 1.20e-01 CPU s 6.00e-03 CPU s/rxn
Rule 3: 36 reactions 1.20e-01 CPU s 3.33e-03 CPU s/rxn
Rule 4: 28 reactions 8.00e-02 CPU s 2.86e-03 CPU s/rxn
Rule 5: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn
Rule 6: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn
Rule 7: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn
Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn
Total : 101 reactions 3.90e-01 CPU s 3.86e-03 CPU s/rxn
Wrote network to toy-jim.net.
CPU TIME: generate_network 0.5 s.
Network simulation using ODEs
Wrote network to toy-jim_equil.net.
Running run_network on Steve-2.home
full command: "/Applications/BioNetGen/bin/run_network" -o "toy-jim_equil" -e -p cvode -a 1e-10 -r 1e-08 -b -c -g "toy-jim_equil.net" "toy-jim_equil.net" 100 10
run_network 1.5
Read 16 parameters
Read 25 species
Read 101 reaction(s)
101 reaction(s) have nonzero rate
Read 9 group(s) from toy-jim_equil.net
Initialization took 0.00 CPU seconds
Propagating with cvode using GMRES
time n_steps n_deriv_calls
100.00 199 462 RMS change in concentrations=3.6e-02.
200.00 211 494 RMS change in concentrations=8.4e-11. Steady state reached.
Time course of concentrations written to file toy-jim_equil.cdat.
Time course of groups written to file toy-jim_equil.gdat.
Propagation took 0.00e+00 CPU seconds
Final network file written to toy-jim_equil_end.net
Program times: 0.00 CPU s 0.00 clock s
Updating species concentrations from toy-jim_equil.cdat
CPU TIME: simulate_ode 0.0 s.
Set concentration of species L(r) to value 1
Wrote SBML to toy-jim.xml.
CPU TIME: writeSBML 0.0 s.
Wrote M-file toy-jim.m.
CPU TIME: writeMfile 0.0 s.
Network simulation using ODEs
Wrote network to toy-jim_kinetics.net.
Running run_network on Steve-2.home
full command: "/Applications/BioNetGen/bin/run_network" -o "toy-jim_kinetics" -e -p cvode -a 1e-10 -r 1e-08 -g "toy-jim_kinetics.net" "toy-jim_kinetics.net" 1 120
run_network 1.5
Read 16 parameters
Read 25 species
Read 101 reaction(s)
101 reaction(s) have nonzero rate
Read 9 group(s) from toy-jim_kinetics.net
Initialization took 0.00 CPU seconds
Propagating with cvode using dense LU
time n_steps n_deriv_calls
1.00 38 75
2.00 49 90
3.00 60 101
4.00 70 136
5.00 78 145
6.00 85 152
7.00 92 159
8.00 99 166
9.00 104 172
10.00 109 177
11.00 114 182
12.00 118 186
13.00 122 216
14.00 125 219
15.00 128 222
16.00 131 225
17.00 133 228
18.00 135 230
19.00 137 232
20.00 139 234
21.00 141 236
22.00 143 238
23.00 145 240
24.00 147 242
25.00 149 244
26.00 151 246
27.00 153 249
28.00 154 250
29.00 155 251
30.00 157 253
31.00 158 254
32.00 159 255
33.00 161 257
34.00 162 258
35.00 163 259
36.00 165 261
37.00 166 262
38.00 167 263
39.00 169 265
40.00 170 266
41.00 171 267
42.00 173 294
43.00 174 296
44.00 174 296
45.00 175 297
46.00 176 298
47.00 177 299
48.00 178 300
49.00 179 301
50.00 180 302
51.00 181 303
52.00 182 304
53.00 182 304
54.00 183 305
55.00 184 306
56.00 185 307
57.00 186 308
58.00 187 309
59.00 188 310
60.00 189 311
61.00 189 311
62.00 190 312
63.00 191 313
64.00 192 314
65.00 193 315
66.00 194 316
67.00 194 316
68.00 195 318
69.00 196 319
70.00 196 319
71.00 197 320
72.00 197 320
73.00 198 321
74.00 198 321
75.00 199 322
76.00 200 323
77.00 200 323
78.00 201 324
79.00 201 324
80.00 202 325
81.00 203 326
82.00 203 326
83.00 204 327
84.00 204 327
85.00 205 328
86.00 206 329
87.00 206 329
88.00 207 330
89.00 207 330
90.00 208 331
91.00 208 331
92.00 209 332
93.00 210 333
94.00 210 333
95.00 211 334
96.00 211 334
97.00 212 336
98.00 212 336
99.00 212 336
100.00 213 337
101.00 213 337
102.00 213 337
103.00 214 338
104.00 214 338
105.00 215 339
106.00 215 339
107.00 215 339
108.00 216 340
109.00 216 340
110.00 217 341
111.00 217 341
112.00 217 341
113.00 218 342
114.00 218 342
115.00 218 342
116.00 219 343
117.00 219 343
118.00 220 344
119.00 220 344
120.00 220 344
Time course of concentrations written to file toy-jim_kinetics.cdat.
Time course of groups written to file toy-jim_kinetics.gdat.
Propagation took 1.00e-02 CPU seconds
Final network file written to toy-jim_kinetics_end.net
Program times: 0.01 CPU s 0.00 clock s
Updating species concentrations from toy-jim_kinetics.cdat
CPU TIME: simulate_ode 0.1 s.
Finished processing file toy-jim.bngl
CPU TIME: total 0.7 s.