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profiling (don't merge!) #25

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profiling (don't merge!) #25

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7725b9a
Example using `vprof` for running w/ RecombCollector
ashander Apr 26, 2017
d2a4803
Use line_profiler
ashander Apr 26, 2017
e8c4f74
Add timing for whole sim
ashander Apr 26, 2017
44f22e5
Added more profiling in wrapper
ashander Apr 26, 2017
32a6fd1
fixup! Added more profiling in wrapper
ashander Apr 26, 2017
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148 changes: 148 additions & 0 deletions devel/prof.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,148 @@
Wrote profile results to test_arg_recorder_with_wf.py.lprof
Timer unit: 1e-06 s

Total time: 0.565759 s
File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
Function: add_individual at line 26

Line # Hits Time Per Hit % Time Line Contents
==============================================================
26 @profile
27 def add_individual(self, name, time, population=msprime.NULL_POPULATION,
28 is_sample=False):
29 '''Add a new individual.
30 We need to add individuals when they are *born*,
31 rather than the first time they reproduce, to ensure
32 that records are output in order by birth time of the parent.
33 '''
34 101240 72447 0.7 12.8 if name not in self:
35 101240 58303 0.6 10.3 self[name] = (msprime.Node(time=time, population=population,
36 101240 297613 2.9 52.6 name=name, is_sample=is_sample), [])
37 101240 137396 1.4 24.3 self.num_nodes = max(self.num_nodes, 1+int(name))

Total time: 7.5774 s
File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
Function: add_record at line 39

Line # Hits Time Per Hit % Time Line Contents
==============================================================
39 @profile
40 def add_record(self, left, right, parent, children):
41 '''
42 Add records corresponding to a reproduction event in which children (a
43 tuple of IDs) inherit from parent (a single ID) on the interval
44 [left,right).
45 '''
46 # unneeded but helpful for debugging
47 150314 120881 0.8 1.6 if parent not in self.keys():
48 raise ValueError("Parent " + str(parent) +
49 "'s birth time has not been recorded with " +
50 ".add_individual().")
51 # time = self[parent][0]
52 150314 79151 0.5 1.0 new_rec = msprime.Edgeset(
53 150314 71103 0.5 0.9 parent=parent,
54 150314 66660 0.4 0.9 children=children,
55 150314 65861 0.4 0.9 left=left,
56 150314 325604 2.2 4.3 right=right)
57 150314 6848145 45.6 90.4 merge_records(new_rec, self[parent][1])

Total time: 4.08047 s
File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
Function: merge_records at line 142

Line # Hits Time Per Hit % Time Line Contents
==============================================================
142 @profile
143 def merge_records(new, existing):
144 '''
145 Incorporate a new record (l,r,x,c,t[x])
146 into a list of existing ones (a,b,x,C,t[x]) sorted on left endpoint.
147 Keeping them in sorted order simplifies the procedure
148 (makes it so we don't have to split the new record).
149 '''
150 150314 101369 0.7 2.5 k = 0
151 150314 87001 0.6 2.1 cur_left = new.left
152 # print("MR: -----")
153 # print("adding", new)
154 # print(" to", existing)
155 308472 241009 0.8 5.9 while (k < len(existing)) and (cur_left < new.right):
156 158158 124833 0.8 3.1 left = existing[k].left
157 158158 93386 0.6 2.3 right = existing[k].right
158 158158 90150 0.6 2.2 parent = existing[k].parent
159 158158 96347 0.6 2.4 children = existing[k].children
160 # print("k:",k)
161 # print("existing:",existing[k])
162 # print("cur_left:",cur_left)
163 158158 92653 0.6 2.3 if new.parent != parent:
164 raise ValueError("Trying to merge records with different parents.")
165 158158 85414 0.5 2.1 if right <= cur_left:
166 # no overlap
167 # print("no overlap")
168 15534 8903 0.6 0.2 k += 1
169 15534 7404 0.5 0.2 continue
170 142624 77301 0.5 1.9 if cur_left < left:
171 # print("dangling left")
172 15409 10416 0.7 0.3 existing.insert(k, msprime.Edgeset(
173 15409 7887 0.5 0.2 left=cur_left,
174 15409 16021 1.0 0.4 right=min(new.right, left),
175 15409 7897 0.5 0.2 parent=parent,
176 15409 43180 2.8 1.1 children=new.children))
177 15409 15864 1.0 0.4 cur_left = min(new.right, left)
178 15409 9449 0.6 0.2 k += 1
179 15409 7490 0.5 0.2 continue
180 127215 393801 3.1 9.7 combined_children = tuple(sorted(children+new.children))
181 127215 87066 0.7 2.1 combined_rec = msprime.Edgeset(
182 127215 67410 0.5 1.7 left=cur_left,
183 127215 234108 1.8 5.7 right=min(new.right, right),
184 127215 73773 0.6 1.8 parent=new.parent,
185 127215 312244 2.5 7.7 children=combined_children)
186 127215 78337 0.6 1.9 if cur_left == left:
187 # print("equal left")
188 105571 67860 0.6 1.7 if new.right < right:
189 # print("overlap right")
190 21590 13336 0.6 0.3 mod_rec = msprime.Edgeset(
191 21590 12284 0.6 0.3 left=new.right,
192 21590 11592 0.5 0.3 right=right,
193 21590 11575 0.5 0.3 parent=parent,
194 21590 149418 6.9 3.7 children=children)
195 21590 19858 0.9 0.5 existing[k] = combined_rec
196 21590 13557 0.6 0.3 k += 1
197 21590 20224 0.9 0.5 existing.insert(k, mod_rec)
198 21590 13962 0.6 0.3 k += 1
199 else:
200 # print("dangling right")
201 83981 71541 0.9 1.8 existing[k] = combined_rec
202 83981 55980 0.7 1.4 k += 1
203 else:
204 # here we know that left < cur_left < right
205 # print("overlap left")
206 21644 13649 0.6 0.3 mod_rec = msprime.Edgeset(
207 21644 11864 0.5 0.3 left=left,
208 21644 11487 0.5 0.3 right=cur_left,
209 21644 11471 0.5 0.3 parent=parent,
210 21644 93849 4.3 2.3 children=children)
211 21644 20146 0.9 0.5 existing[k] = mod_rec
212 21644 13783 0.6 0.3 k += 1
213 21644 20156 0.9 0.5 existing.insert(k, combined_rec)
214 21644 13301 0.6 0.3 k += 1
215 21644 14807 0.7 0.4 if new.right < right:
216 # print("overlap right")
217 existing.insert(k, msprime.Edgeset(
218 left=new.right,
219 right=right,
220 parent=parent,
221 children=children))
222 k += 1
223 127215 110940 0.9 2.7 cur_left = min(new.right, right)
224 # add whatever's left at the end
225 150314 101572 0.7 2.5 if cur_left < new.right:
226 82579 60579 0.7 1.5 existing.insert(k, msprime.Edgeset(
227 82579 47194 0.6 1.2 left=cur_left,
228 82579 50544 0.6 1.2 right=new.right,
229 82579 47932 0.6 1.2 parent=new.parent,
230 82579 428151 5.2 10.5 children=new.children))
231 # print("getting")
232 # for x in existing:
233 # print(" ", x)
234 150314 77143 0.5 1.9 return None

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