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rbouckaertrbouckaert
committedMar 21, 2016
reduce impact of logging on timing -- reduce screen logging frequency, comment out trace and tree logs
1 parent e2b99fb commit 2c4ae12

9 files changed

+53
-44
lines changed
 

‎process.pl

+4-4
Original file line numberDiff line numberDiff line change
@@ -29,25 +29,25 @@
2929
print FOUT "#!/bin/bash\n";
3030
print FOUT "mkdir singleThread\n";
3131
print FOUT "cd singleThread\n";
32-
print FOUT "mkdir test_xml\n";
32+
print FOUT "mkdir singleThread/test_xml\n";
3333
doWith(1);
3434
print FOUT "cd ..\n";
3535

3636
print FOUT "mkdir doubleThread\n";
3737
print FOUT "cd doubleThread\n";
38-
print FOUT "mkdir test_xml\n";
38+
print FOUT "mkdir doubleThread/test_xml\n";
3939
doWith(2);
4040
print FOUT "cd ..\n";
4141

4242
print FOUT "mkdir fourThread\n";
4343
print FOUT "cd fourThread\n";
44-
print FOUT "mkdir test_xml\n";
44+
print FOUT "mkdir fourThread/test_xml\n";
4545
doWith(4);
4646
print FOUT "cd ..\n";
4747

4848
print FOUT "mkdir GPU\n";
4949
print FOUT "cd GPU\n";
50-
print FOUT "mkdir test_xml\n";
50+
print FOUT "mkdir GPU/test_xml\n";
5151
doGPU();
5252
print FOUT "cd ..\n";
5353
close FOUT;

‎xml/GTRGI_1.xml

+5-5
Original file line numberDiff line numberDiff line change
@@ -225,7 +225,7 @@
225225
<operators idref="operators"/>
226226

227227
<!-- write log to screen -->
228-
<log id="screenLog" logEvery="1000">
228+
<log id="screenLog" logEvery="10000">
229229
<column label="Posterior" dp="4" width="12">
230230
<posterior idref="posterior"/>
231231
</column>
@@ -244,7 +244,7 @@
244244
</log>
245245

246246
<!-- write log to file -->
247-
<log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
247+
<!-- <log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
248248
<posterior idref="posterior"/>
249249
<prior idref="prior"/>
250250
<likelihood idref="likelihood"/>
@@ -264,16 +264,16 @@
264264
<strictClockBranchRates idref="branchRates"/>
265265
<speciationLikelihood idref="speciation"/>
266266
</log>
267-
267+
-->
268268
<!-- write tree log to file -->
269-
<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
269+
<!-- <logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
270270
<treeModel idref="treeModel"/>
271271
<trait name="rate" tag="rate">
272272
<strictClockBranchRates idref="branchRates"/>
273273
</trait>
274274
<posterior idref="posterior"/>
275275
</logTree>
276-
</mcmc>
276+
--> </mcmc>
277277
<report>
278278
<property name="timer">
279279
<mcmc idref="mcmc"/>

‎xml/GTRGI_2.xml

+6-5
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121

2222

2323
<run id="mcmc" spec="MCMC" chainLength="1000000">
24+
<operatorschedule spec="OperatorSchedule" transform="log"/>
2425
<state id="state" storeEvery="5000">
2526
<tree id="Tree.t:test" name="stateNode">
2627
<taxonset id="TaxonSet.test" spec="TaxonSet">
@@ -138,7 +139,7 @@
138139
<operator id="proportionInvariantScaler.s:test" spec="ScaleOperator" parameter="@proportionInvariant.s:test" scaleFactor="0.5" weight="0.1"/>
139140

140141
<operator id="gammaShapeScaler.s:test" spec="ScaleOperator" parameter="@gammaShape.s:test" scaleFactor="0.5" weight="0.1"/>
141-
142+
<!--
142143
<logger id="tracelog" fileName="test.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
143144
<log idref="posterior"/>
144145
<log idref="likelihood"/>
@@ -156,18 +157,18 @@
156157
<log idref="proportionInvariant.s:test"/>
157158
<log idref="gammaShape.s:test"/>
158159
</logger>
159-
160-
<logger id="screenlog" logEvery="1000">
160+
-->
161+
<logger id="screenlog" logEvery="10000">
161162
<log idref="posterior"/>
162163
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
163164
<log idref="likelihood"/>
164165
<log idref="prior"/>
165166
</logger>
166-
167+
<!--
167168
<logger id="treelog.t:test" fileName="tree.trees" logEvery="1000" mode="tree">
168169
<log id="TreeWithMetaDataLogger.t:test" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test"/>
169170
</logger>
170-
171+
-->
171172
</run>
172173

173174
</beast>

‎xml/GTRG_1.xml

+5-5
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,7 @@
216216
<operators idref="operators"/>
217217

218218
<!-- write log to screen -->
219-
<log id="screenLog" logEvery="1000">
219+
<log id="screenLog" logEvery="10000">
220220
<column label="Posterior" dp="4" width="12">
221221
<posterior idref="posterior"/>
222222
</column>
@@ -235,7 +235,7 @@
235235
</log>
236236

237237
<!-- write log to file -->
238-
<log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
238+
<!-- <log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
239239
<posterior idref="posterior"/>
240240
<prior idref="prior"/>
241241
<likelihood idref="likelihood"/>
@@ -254,16 +254,16 @@
254254
<strictClockBranchRates idref="branchRates"/>
255255
<speciationLikelihood idref="speciation"/>
256256
</log>
257-
257+
-->
258258
<!-- write tree log to file -->
259-
<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
259+
<!-- <logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
260260
<treeModel idref="treeModel"/>
261261
<trait name="rate" tag="rate">
262262
<strictClockBranchRates idref="branchRates"/>
263263
</trait>
264264
<posterior idref="posterior"/>
265265
</logTree>
266-
</mcmc>
266+
--> </mcmc>
267267
<report>
268268
<property name="timer">
269269
<mcmc idref="mcmc"/>

‎xml/GTRG_2.xml

+6-5
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,7 @@
1818

1919

2020
<run id="mcmc" spec="MCMC" chainLength="1000000">
21+
<operatorschedule spec="OperatorSchedule" transform="log"/>
2122
<state id="state" storeEvery="5000">
2223
<tree id="Tree.t:test" name="stateNode">
2324
<taxonset id="TaxonSet.test" spec="TaxonSet">
@@ -130,7 +131,7 @@
130131
<operator id="RateGTScaler.s:test" spec="ScaleOperator" parameter="@rateGT.s:test" scaleFactor="0.5" weight="0.1"/>
131132

132133
<operator id="gammaShapeScaler.s:test" spec="ScaleOperator" parameter="@gammaShape.s:test" scaleFactor="0.5" weight="0.1"/>
133-
134+
<!--
134135
<logger id="tracelog" fileName="test.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
135136
<log idref="posterior"/>
136137
<log idref="likelihood"/>
@@ -147,18 +148,18 @@
147148
<log idref="rateGT.s:test"/>
148149
<log idref="gammaShape.s:test"/>
149150
</logger>
150-
151-
<logger id="screenlog" logEvery="1000">
151+
-->
152+
<logger id="screenlog" logEvery="10000">
152153
<log idref="posterior"/>
153154
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
154155
<log idref="likelihood"/>
155156
<log idref="prior"/>
156157
</logger>
157-
158+
<!--
158159
<logger id="treelog.t:test" fileName="tree.trees" logEvery="1000" mode="tree">
159160
<log id="TreeWithMetaDataLogger.t:test" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test"/>
160161
</logger>
161-
162+
-->
162163
</run>
163164

164165
</beast>

‎xml/GTRI_1.xml

+7-4
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,7 @@
216216
<operators idref="operators"/>
217217

218218
<!-- write log to screen -->
219-
<log id="screenLog" logEvery="1000">
219+
<log id="screenLog" logEvery="10000">
220220
<column label="Posterior" dp="4" width="12">
221221
<posterior idref="posterior"/>
222222
</column>
@@ -235,7 +235,8 @@
235235
</log>
236236

237237
<!-- write log to file -->
238-
<log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
238+
<!--
239+
<log id="fileLog" logEvery="10000" fileName="test.log" overwrite="false">
239240
<posterior idref="posterior"/>
240241
<prior idref="prior"/>
241242
<likelihood idref="likelihood"/>
@@ -254,15 +255,17 @@
254255
<strictClockBranchRates idref="branchRates"/>
255256
<speciationLikelihood idref="speciation"/>
256257
</log>
257-
258+
-->
258259
<!-- write tree log to file -->
259-
<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
260+
<!--
261+
<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
260262
<treeModel idref="treeModel"/>
261263
<trait name="rate" tag="rate">
262264
<strictClockBranchRates idref="branchRates"/>
263265
</trait>
264266
<posterior idref="posterior"/>
265267
</logTree>
268+
-->
266269
</mcmc>
267270
<report>
268271
<property name="timer">

‎xml/GTRI_2.xml

+7-6
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121

2222

2323
<run id="mcmc" spec="MCMC" chainLength="1000000">
24+
<operatorschedule spec="OperatorSchedule" transform="log"/>
2425
<state id="state" storeEvery="5000">
2526
<tree id="Tree.t:test" name="stateNode">
2627
<taxonset id="TaxonSet.test" spec="TaxonSet">
@@ -131,8 +132,8 @@
131132
<operator id="RateGTScaler.s:test" spec="ScaleOperator" parameter="@rateGT.s:test" scaleFactor="0.5" weight="0.1"/>
132133

133134
<operator id="proportionInvariantScaler.s:test" spec="ScaleOperator" parameter="@proportionInvariant.s:test" scaleFactor="0.5" weight="0.1"/>
134-
135-
<logger id="tracelog" fileName="test.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
135+
<!--
136+
<logger id="tracelog" fileName="test.log" logEvery="10000" model="@posterior" sanitiseHeaders="true" sort="smart">
136137
<log idref="posterior"/>
137138
<log idref="likelihood"/>
138139
<log idref="prior"/>
@@ -148,18 +149,18 @@
148149
<log idref="rateGT.s:test"/>
149150
<log idref="proportionInvariant.s:test"/>
150151
</logger>
151-
152-
<logger id="screenlog" logEvery="1000">
152+
-->
153+
<logger id="screenlog" logEvery="10000">
153154
<log idref="posterior"/>
154155
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
155156
<log idref="likelihood"/>
156157
<log idref="prior"/>
157158
</logger>
158-
159+
<!--
159160
<logger id="treelog.t:test" fileName="tree.trees" logEvery="1000" mode="tree">
160161
<log id="TreeWithMetaDataLogger.t:test" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test"/>
161162
</logger>
162-
163+
-->
163164
</run>
164165

165166
</beast>

‎xml/GTR_1.xml

+6-5
Original file line numberDiff line numberDiff line change
@@ -207,7 +207,7 @@
207207
<operators idref="operators"/>
208208

209209
<!-- write log to screen -->
210-
<log id="screenLog" logEvery="1000">
210+
<log id="screenLog" logEvery="10000">
211211
<column label="Posterior" dp="4" width="12">
212212
<posterior idref="posterior"/>
213213
</column>
@@ -226,7 +226,8 @@
226226
</log>
227227

228228
<!-- write log to file -->
229-
<log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
229+
<!--
230+
<log id="fileLog" logEvery="1000" fileName="test.log" overwrite="false">
230231
<posterior idref="posterior"/>
231232
<prior idref="prior"/>
232233
<likelihood idref="likelihood"/>
@@ -244,16 +245,16 @@
244245
<strictClockBranchRates idref="branchRates"/>
245246
<speciationLikelihood idref="speciation"/>
246247
</log>
247-
248+
-->
248249
<!-- write tree log to file -->
249-
<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
250+
<!-- <logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="test.trees" sortTranslationTable="true">
250251
<treeModel idref="treeModel"/>
251252
<trait name="rate" tag="rate">
252253
<strictClockBranchRates idref="branchRates"/>
253254
</trait>
254255
<posterior idref="posterior"/>
255256
</logTree>
256-
</mcmc>
257+
--> </mcmc>
257258
<report>
258259
<property name="timer">
259260
<mcmc idref="mcmc"/>

‎xml/GTR_2.xml

+7-5
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@
1616

1717

1818
<run id="mcmc" spec="MCMC" chainLength="1000000">
19+
<operatorschedule spec="OperatorSchedule" transform="log"/>
1920
<state id="state" storeEvery="5000">
2021
<tree id="Tree.t:test" name="stateNode">
2122
<taxonset id="TaxonSet.test" spec="TaxonSet">
@@ -122,7 +123,8 @@
122123

123124
<operator id="RateGTScaler.s:test" spec="ScaleOperator" parameter="@rateGT.s:test" scaleFactor="0.5" weight="0.1"/>
124125

125-
<logger id="tracelog" fileName="test.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
126+
<!--
127+
<logger id="tracelog" fileName="test.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
126128
<log idref="posterior"/>
127129
<log idref="likelihood"/>
128130
<log idref="prior"/>
@@ -137,18 +139,18 @@
137139
<log idref="rateCG.s:test"/>
138140
<log idref="rateGT.s:test"/>
139141
</logger>
140-
141-
<logger id="screenlog" logEvery="1000">
142+
-->
143+
<logger id="screenlog" logEvery="10000">
142144
<log idref="posterior"/>
143145
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
144146
<log idref="likelihood"/>
145147
<log idref="prior"/>
146148
</logger>
147-
149+
<!--
148150
<logger id="treelog.t:test" fileName="test.trees" logEvery="1000" mode="tree">
149151
<log id="TreeWithMetaDataLogger.t:test" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test"/>
150152
</logger>
151-
153+
-->
152154
</run>
153155

154156
</beast>

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