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Merge pull request #1250 from veg/develop
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2.5.23 rc
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@spond
spond authored Nov 18, 2020
2 parents d502052 + 7fc3fc5 commit fe085e1
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Showing 6 changed files with 49 additions and 68 deletions.
49 changes: 34 additions & 15 deletions res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -396,12 +396,26 @@ fel.site_patterns = alignments.Extract_site_patterns ((fel.filter_specification[
// alpha = alpha_scaler * branch_length
// beta = beta_scaler_test * branch_length or beta_nuisance_test * branch_length

utility.ForEach (fel.case_respecting_node_names, "_node_",
'_node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
_beta_scaler = fel.scaler_parameter_names[_node_class_];
fel.apply_proportional_site_constraint ("fel.site_tree", _node_, fel.alpha, fel.beta, fel.alpha.scaler, _beta_scaler, (( fel.final_partitioned_mg_results[terms.branch_length])[fel.partition_index])[_node_]);
');
fel.lengths_by_class = {};

for (_node_; in; fel.case_respecting_node_names) {
_node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
_beta_scaler = fel.scaler_parameter_names[_node_class_];
fel.lengths_by_class[_node_class_] += fel.apply_proportional_site_constraint ("fel.site_tree", _node_, fel.alpha, fel.beta, fel.alpha.scaler, _beta_scaler, (( fel.final_partitioned_mg_results[terms.branch_length])[fel.partition_index])[_node_]);
}

fel.ignorable = {};
for (fel.t; in; fel.branches.testable) {
if ( fel.lengths_by_class[fel.t] == 0) {
fprintf(stdout, "\n-------\n", io.FormatLongStringToWidth(
">[WARNING] The cumulative branch length in the _" + fel.t + "_ class is 0.
Rates along these branches are not identifiable; testing will not be formally conducted (all p-values set to 1).", 72),
"\n-------\n");
fel.ignorable [fel.scaler_parameter_names[fel.t]] = 1;
} else {
fel.ignorable [fel.scaler_parameter_names[fel.t]] = 0;
}
}


// create the likelihood function for this site
Expand All @@ -424,7 +438,7 @@ fel.queue = mpi.CreateQueue ({"LikelihoodFunctions": {{"fel.site_likelihood"}},
"Models" : {{"fel.site.mg_rev"}},
"Headers" : {{"libv3/all-terms.bf","libv3/tasks/ancestral.bf", "libv3/convenience/math.bf"}},
"Functions" : {{"fel.apply_proportional_site_constraint"}},
"Variables" : {{"terms.fel.test_keys","fel.permutations", "fel.alpha","fel.beta","fel.alpha.scaler","terms.fel.permutation","fel.final_partitioned_mg_results","fel.srv","fel.site_tested_classes","fel.scaler_parameter_names","fel.branches.testable","fel.branches.has_background","fel.alpha.scaler","terms.fel.pairwise","fel.branch_class_counter","fel.report.test_count", "fel.p_value","fel.site.permutations"}}
"Variables" : {{"terms.fel.test_keys","fel.permutations","fel.ignorable","fel.alpha","fel.beta","fel.alpha.scaler","terms.fel.permutation","fel.final_partitioned_mg_results","fel.srv","fel.site_tested_classes","fel.scaler_parameter_names","fel.branches.testable","fel.branches.has_background","fel.alpha.scaler","terms.fel.pairwise","fel.branch_class_counter","fel.report.test_count", "fel.p_value","fel.site.permutations"}}
});


Expand Down Expand Up @@ -644,6 +658,8 @@ function fel.apply_proportional_site_constraint (tree_name, node_name, alpha_par
`node_name`.`alpha_parameter` := (`alpha_factor`) * fel.branch_length__;
`node_name`.`beta_parameter` := (`beta_factor`) * fel.branch_length__;
");

return fel.branch_length;
}
//----------------------------------------------------------------------------------------

Expand Down Expand Up @@ -724,8 +740,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
');
}



snapshot = estimators.TakeLFStateSnapshot (lf);
alternative = estimators.ExtractMLEs (lf, model_mapping);
alternative [utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
Expand Down Expand Up @@ -757,8 +771,8 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
} else {
for (_gname_; in; ^"fel.branches.testable") {
_pname_ = (^"fel.scaler_parameter_names")[_gname_];
if (_pname_ != ref_parameter) {
^_pname_ := ^ref_parameter;
if (_pname_ != ref_parameter && (^"fel.ignorable")[_pname_] == 0) {
parameters.SetConstraint (_pname_,ref_parameter, "");
}
}
}
Expand All @@ -773,12 +787,17 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
for (v2 = v + 1; v2 < testable; v2+=1) {
v1n = (^"fel.branches.testable")[v];
v2n = (^"fel.branches.testable")[v2];

estimators.RestoreLFStateFromSnapshot (lf_id, snapshot);
parameters.SetConstraint ((^"fel.scaler_parameter_names")[v1n],(^"fel.scaler_parameter_names")[v2n], "");
Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
pairwise[v1n + "|" + v2n] = estimators.ExtractMLEs (lf, model_mapping);
(pairwise[v1n + "|" + v2n])[utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];

if ((^"fel.ignorable")[(^"fel.scaler_parameter_names")[v1n]] || (^"fel.ignorable")[(^"fel.scaler_parameter_names")[v2n]]) {
//console.log (v1n + "|" + v2n + " is ignorable");
(pairwise[v1n + "|" + v2n]) = alternative;
} else {
parameters.SetConstraint ((^"fel.scaler_parameter_names")[v1n],(^"fel.scaler_parameter_names")[v2n], "");
Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
pairwise[v1n + "|" + v2n] = estimators.ExtractMLEs (lf, model_mapping);
(pairwise[v1n + "|" + v2n])[utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
}
}
}
} else {
Expand Down
8 changes: 6 additions & 2 deletions src/core/batchlanhelpers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -68,14 +68,18 @@ _String const _HYGenerateANameSpace () {
//____________________________________________________________________________________

void _HYClearANameSpace (const _String& nm) {
/*BufferToConsole("Deleting key: ");
BufferToConsole(nm.get_str());
NLToConsole();
ObjectToConsole(&_HY_HBL_Namespaces);
NLToConsole();*/
_HY_HBL_Namespaces.Delete(nm);
}

//____________________________________________________________________________________


void ReadModelList(void)
{
void ReadModelList(void) {
if (templateModelList.empty() == false) return;

_String modelListFile (GetStandardDirectory (HY_HBL_DIRECTORY_TEMPLATE_MODELS) & "models.lst"),
Expand Down
2 changes: 1 addition & 1 deletion src/core/global_things.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ namespace hy_global {
kErrorStringDatasetRefIndexError ("Dataset index reference out of range"),
kErrorStringMatrixExportError ("Export matrix called with a non-polynomial matrix argument"),
kErrorStringNullOperand ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
kHyPhyVersion = _String ("2.5.22"),
kHyPhyVersion = _String ("2.5.23"),

kNoneToken = "None",
kNullToken = "null",
Expand Down
6 changes: 3 additions & 3 deletions src/core/likefunc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4101,6 +4101,9 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
#endif


_variables_changed_during_last_compute = new _SimpleList ();
variables_changed_during_last_compute = new _AVLList (_variables_changed_during_last_compute);

#ifdef __HYPHYMPI__
if (hy_mpi_node_rank == 0) {
#endif
Expand All @@ -4109,9 +4112,6 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
}
#endif

_variables_changed_during_last_compute = new _SimpleList ();
variables_changed_during_last_compute = new _AVLList (_variables_changed_during_last_compute);


bool skipCG = ! CheckEqual (get_optimization_setting (kSkipConjugateGradient, 0.0), 0.0),
keepStartingPoint = ! CheckEqual (get_optimization_setting (kUseLastResults, 0.0), 0.0),
Expand Down
7 changes: 5 additions & 2 deletions src/core/trie.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -344,10 +344,11 @@ bool _Trie::Delete (const _String& key){
emptySlots << history.list_data[k];
payload.list_data[history.list_data[k]] = 0L;
parents.list_data[history.list_data[k]] = -1L;
_SimpleList * parentList = ((_SimpleList**)list_data)[history.list_data[k-1]];
_SimpleList * parentList = ((_SimpleList**)list_data)[k ? history.list_data[k-1] : 0];
unsigned long parentNode = parentList->FindStepping (history.list_data[k],2, 1) - 1;
parentList->Delete (parentNode);
parentList->Delete (parentNode);

DeleteObject (current_list);
((_SimpleList**)list_data)[history.list_data[k]] = nil;
inserted_values--;
Expand Down Expand Up @@ -450,7 +451,9 @@ BaseRef _Trie::toStr(unsigned long) {
}
} else {
_String * this_string = RetrieveStringFromPath(traversal_history, &alph);
(*serialized) << '"' << this_string << "\":" << _String (GetValue (traversal_history.list_data[traversal_history.lLength-2]));
(*serialized) << '"';
(*serialized).AppendNewInstance(this_string);
(*serialized) << "\":" << _String (GetValue (traversal_history.list_data[traversal_history.lLength-2]));
if (doComma) {
(*serialized) << ',';
} else {
Expand Down
45 changes: 0 additions & 45 deletions src/mains/unix.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -694,51 +694,6 @@ void SetStatusLineUser (_String const s) {
#ifndef __UNITTEST__
int main (int argc, char* argv[]) {

/*long N = 1000L;
long repeats = 20L;
long density = 0.25 * RAND_MAX;
auto start = std::chrono::high_resolution_clock::now();
srand(time(0));
_Matrix::switchThreshold = atoi (argv[1]);
printf ("%ld\n", _Matrix::switchThreshold);
for (long i = 0; i < N; i++) {
_Matrix test (61,61,false,true);
test.ForEachCellNumeric([density] (hyFloat& e, long i, long r, long c) -> void {
if (r != c && rand() < density) {
e = genrand_real1 ();
} else {
e = 0.0;
}
});
for (long r = 0; r < 61; r++) {
double s = 0.;
for (long c = 0; c < 61; c++) {
s += test (r, c);
}
test.theData[r*61+r] = -s;
}
test.AmISparse();
//ObjectToConsole(&test);
//printf ("%d\n", test.is_dense());
for (long j = 0; j < repeats; j++) {
DeleteObject (test.Exponentiate());
//return 0;
}
}
auto end = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> elapsed = end - start;
printf ("%15.12g s\n", elapsed.count());
return 0;*/


#ifdef _COMPARATIVE_LF_DEBUG_DUMP
FILE * comparative_lf_debug_matrix_content_file = doFileOpen (_COMPARATIVE_LF_DEBUG_DUMP, "w");
Expand Down

1 comment on commit fe085e1

@kjlevitz
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⚠️ Performance Alert ⚠️

Possible performance regression was detected for benchmark 'Benchmark.js Benchmark'.
Benchmark result of this commit is worse than the previous benchmark result exceeding threshold 2.

Benchmark suite Current: fe085e1 Previous: eca60ff Ratio
CFEL.wbf 152.8584530724549 secs/op (±2.057623%) null secs/op (±0.000000%) Infinity

This comment was automatically generated by workflow using github-action-benchmark.

CC: @klevitz

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