Open zemogle opened 8 years ago
Running line_profiler and profiling every function in evolve.py has yeilded the following:
line_profiler
evolve.py
Timer unit: 1e-06 s Total time: 0.059587 s File: evolve.py Function: load_sfh at line 96 Line # Hits Time Per Hit % Time Line Contents ============================================================== 96 @profile 97 def load_sfh(self): 98 ''' 99 takes in input SFH file and extend backwards to start from 1e-3 Gyr 100 ''' 101 2 6 3.0 0.0 try: 102 2 48635 24317.5 81.6 vals = np.loadtxt(self.SFH_file) 103 2 6 3.0 0.0 scale = [1e-9,1e9] # Gyr conversions for time, SFR 104 2 74 37.0 0.1 sfh = vals*scale # converts time in Gyr and SFR in Msun/Gyr 105 # extrapolates SFH back to 0.001Gyr using SFH file and power law (gamma) 106 2 9273 4636.5 15.6 final_sfh = f.extra_sfh(sfh, self.gamma) 107 2 1593 796.5 2.7 self.sfh = np.array(final_sfh) 108 except: 109 logger.error("File '%s' will not parse" % self.SFH_file) 110 self.sfh = None Total time: 0.559438 s File: evolve.py Function: sfr at line 112 Line # Hits Time Per Hit % Time Line Contents ============================================================== 112 @profile 113 def sfr(self, t): 114 ''' 115 define sfr as function to look up nearest sfr value at any specified time 116 ''' 117 42898 20311 0.5 3.6 try: 118 42898 509412 11.9 91.1 vals = find_nearest(self.sfh,t) 119 42898 29715 0.7 5.3 return vals[1] 120 except: 121 logger.error("No SFH yet") Total time: 95.0901 s File: evolve.py Function: gas_metal_dust_mass at line 123 Line # Hits Time Per Hit % Time Line Contents ============================================================== 123 @profile 124 def gas_metal_dust_mass(self, sn_rate): 125 ''' 126 Calculates the gas, metal and dust mass from stars 127 note mass is only ejected after stars die ie when 128 t - taum (where taum is lifetime of star) > 0 129 ''' 130 # initialize 131 2 2 1.0 0.0 mg = self.gasmass_init 132 2 2 1.0 0.0 mstars = 0 133 2 2 1.0 0.0 md = 0 134 2 2 1.0 0.0 md_all = 0 135 2 2 1.0 0.0 md_stars = 0 136 2 2 1.0 0.0 md_gg = 0 137 2 2 1.0 0.0 metals = 0 138 2 1 0.5 0.0 prev_t = 1e-3 139 2 1 0.5 0.0 metals_pre = 0 140 2 2 1.0 0.0 mstars_list = [] 141 2 2 1.0 0.0 z = [] 142 2 2 1.0 0.0 z_lookup = [] 143 2 2 1.0 0.0 sfr_list = [] 144 2 2 1.0 0.0 sfr_lookup = [] 145 2 2 1.0 0.0 all_results = [] 146 # Limit time to less than tend 147 2 4 2.0 0.0 time = self.sfh[:,0] 148 2 33 16.5 0.0 time = time[time < self.tend] 149 2 21 10.5 0.0 now = datetime.now() 150 # TIME integral 151 3263 6748 2.1 0.0 for item, t in enumerate(time): 152 3262 5910 1.8 0.0 r_sn = sn_rate [item] 153 3262 4627 1.4 0.0 metallicity = metals/mg 154 155 # start appending arrays for needing later 156 3262 6703 2.1 0.0 z.append([t,metallicity]) 157 3262 1423655 436.4 1.5 z_lookup = np.array(z) 158 3262 90205 27.7 0.1 sfr_list.append([t,self.sfr(t)]) 159 3262 1225041 375.5 1.3 sfr_lookup = np.array(sfr_list) 160 161 ''' 162 STARS: dM_stars = sfr(t) * dt 163 ''' 164 3262 77753 23.8 0.1 dmstars = self.sfr(t) 165 166 ''' 167 GAS: dMg = (-sfr(t) + e(t) + inflows(t) - outflows(t)) * dt 168 set up astration, inflow, outflow components 169 ''' 170 3262 56955 17.5 0.1 gas_ast = self.sfr(t) 171 3262 62668 19.2 0.1 gas_inf = f.inflows(self.sfr(t), self.inflows['xSFR']) 172 3262 61147 18.7 0.1 gas_out = f.outflows(self.sfr(t), self.outflows['xSFR']) 173 174 ''' 175 METALS: dMz = (-Z*sfr(t) + ez(t) + Z*inflows(t) - Z*outflows(t)) * dt 176 set up astration, inflow and outflow components 177 ''' 178 3262 59347 18.2 0.1 metals_ast = f.astration(metals,mg,self.sfr(t)) 179 3262 4713 1.4 0.0 if self.outflows['metals']: 180 1864 33706 18.1 0.0 metals_out = metallicity*f.outflows(self.sfr(t), self.outflows['xSFR']) 181 else: 182 1398 1638 1.2 0.0 metals_out = 0. 183 3262 59859 18.4 0.1 metals_inf = self.inflows['metals']*f.inflows(self.sfr(t), self.inflows['xSFR']) 184 185 ''' 186 DUST: dMd = (-Md/Mg*sfr(t) + ed(t) + Md/Mg*inflows(t) - Md/Mg*outflows(t) 187 - (1-f)*Md/t_destroy + f(1-Md/Mg)*Md/t_graingrowth) * dt 188 set up astration, inflows, outflows, destruction, grain growth components 189 ''' 190 3262 4479 1.4 0.0 if self.outflows['dust']: 191 1864 33644 18.0 0.0 mdust_out = (md/mg)*f.outflows(self.sfr(t), self.outflows['xSFR']) 192 else: 193 1398 1647 1.2 0.0 mdust_out = 0. 194 3262 59203 18.1 0.1 mdust_inf = self.inflows['dust']*f.inflows(self.sfr(t), self.inflows['xSFR']) 195 3262 55883 17.1 0.1 mdust_ast = f.astration(md,mg,self.sfr(t)) 196 197 3262 81253 24.9 0.1 mdust_gg, t_gg = f.graingrowth(self.choice_dust[2], self.epsilon,mg, self.sfr(t), metallicity, md, self.coldfraction) 198 3262 22796 7.0 0.0 mdust_des, t_des = f.destroy_dust(self.choice_des, self.destroy_ism, mg, r_sn, md, self.coldfraction) 199 200 ''' 201 Get ejected masses from stars when they die 202 gas_ej = e(t): ejected gas mass from stars of mass m at t = taum 203 metals_stars = ez(t): ejected metal mass from stars of mass m at t = taum (fresh + recycled) 204 mdust_stars = ed(t): ejected dust mass from stars of mass m at t = taum (fresh + recycled) 205 ''' 206 gas_ej, metals_stars, mdust_stars = \ 207 3262 88276663 27062.1 92.8 f.mass_integral(self.choice_dust, self.reduce_sn, t, metallicity, sfr_lookup, z_lookup, self.imf) 208 209 ''' 210 integrate over time for gas, metals and stars (mg, metals, md) 211 ''' 212 3262 12345 3.8 0.0 dmg = -gas_ast + gas_ej + gas_inf - gas_out 213 3262 7334 2.2 0.0 dmetals = -metals_ast + metals_stars + metals_pre + metals_inf - metals_out 214 3262 7084 2.2 0.0 ddust = -mdust_ast + mdust_stars + mdust_inf - mdust_out + mdust_gg - mdust_des 215 # dust_source_all separates out the dust sources (Md vs t) wihtout including sinks (Astration etc) 216 # and grain growth separately (this is the Md vs time contributed by dust sources) 217 3262 4919 1.5 0.0 dust_source_all = mdust_stars + mdust_gg 218 3262 4751 1.5 0.0 dt = t - prev_t # calculate next time step 219 3262 4068 1.2 0.0 prev_t = t 220 3262 5564 1.7 0.0 mstars += dmstars*dt 221 3262 4789 1.5 0.0 mg += dmg*dt # gas mass integral 222 3262 5506 1.7 0.0 if mg <= 0: 223 # exit program if all ISM removed 224 1 18 18.0 0.0 print ('Oops you have no interstellar medium left') 225 1 3 3.0 0.0 break 226 3261 4682 1.4 0.0 metals += dmetals*dt # metal mass integral 227 3261 4636 1.4 0.0 md += ddust*dt # dust mass integral 228 3261 4712 1.4 0.0 md_all += dust_source_all*dt # dust mass sources integral 229 3261 4751 1.5 0.0 md_gg += mdust_gg*dt # dust source from grain growth only 230 3261 4771 1.5 0.0 md_stars += mdust_stars*dt # dust source from stars only 231 3261 1657357 508.2 1.7 Z = zip(*z_lookup) # write metallicity to an array 232 3261 1487612 456.2 1.6 s_f_r = zip(*sfr_lookup) # write SFR lookup array 233 3261 10769 3.3 0.0 if mg <= 0. or metals <=0: # write dust/metals ratio 234 1353 1740 1.3 0.0 dust_to_metals = 0. 235 else: 236 1908 3620 1.9 0.0 dust_to_metals = md/metals 237 3261 5994 1.8 0.0 all_results.append((t, mg, mstars, metals, metallicity, \ 238 3261 114921 35.2 0.1 md, dust_to_metals, self.sfr(t)*1e-9, \ 239 3261 6936 2.1 0.0 md_all, md_stars, md_gg, t_des, t_gg)) 240 # to test code kinks 241 2 108 54.0 0.0 print("Gas, metal and dust mass exterior loop %s" % str(datetime.now()-now)) 242 2 4818 2409.0 0.0 return np.array(all_results) Total time: 2.26193 s File: evolve.py Function: supernova_rate at line 244 Line # Hits Time Per Hit % Time Line Contents ============================================================== 244 @profile 245 def supernova_rate(self): 246 ''' 247 Calculates the SN rate at time t by integrating over mass m 248 ''' 249 # initialize 250 2 4 2.0 0.0 sn_rate_list = [] 251 2 2 1.0 0.0 dm = 0.01 252 2 2 1.0 0.0 prev_t = 1e-3 253 # define time array 254 2 8 4.0 0.0 time = self.sfh[:,0] 255 2 55 27.5 0.0 time = time[time < self.tend] 256 3291 3391 1.0 0.1 for t in time: 257 # need to clear the sn_rates as we don't want them adding up 258 3289 2447 0.7 0.1 sn_rate = 0. 259 3289 2478 0.8 0.1 dsn_rate = 0. 260 3289 2951 0.9 0.1 if t < 0.049: 261 2180 1374063 630.3 60.7 m = lookup_fn(t_lifetime,'lifetime_high_metals',t)[0] 262 else: 263 1109 805 0.7 0.0 m = 9. 264 119825 95893 0.8 4.2 while m < 40.: 265 116536 88941 0.8 3.9 if m > 10.: 266 111744 82717 0.7 3.7 dm = 0.5 267 116536 428777 3.7 19.0 sn_rate += f.initial_mass_function(m, self.imf_type)*dm 268 116536 95611 0.8 4.2 m += dm 269 3289 73646 22.4 3.3 r_sn = self.sfr(t)*sn_rate # units in N per Gyr 270 3289 3470 1.1 0.2 dt = t - prev_t 271 3289 2478 0.8 0.1 prev_t = t 272 3289 3895 1.2 0.2 sn_rate_list.append(r_sn) 273 2 300 150.0 0.0 return np.array(sn_rate_list)
It looks like the unzipping at lines 231 and 232 of gas_metal_dust_mass() are taking most of the time.
gas_metal_dust_mass()
I'll have a look at speeding that up.
Running
line_profilerand profiling every function inevolve.pyhas yeilded the following:It looks like the unzipping at lines 231 and 232 of
gas_metal_dust_mass()are taking most of the time.I'll have a look at speeding that up.