From 19ac4f91105d03762e71d8af6c60e33030d7f254 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Mon, 2 Oct 2023 17:02:53 -0600
Subject: [PATCH] Removing extra mem allocation+copy in geese::likelihood

---
 include/barry/model-meat.hpp                    |  2 +-
 .../models/geese/geese-meat-likelihood.hpp      | 17 ++++++++---------
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/include/barry/model-meat.hpp b/include/barry/model-meat.hpp
index 11bbbd408..78b00dcbd 100644
--- a/include/barry/model-meat.hpp
+++ b/include/barry/model-meat.hpp
@@ -101,7 +101,7 @@ inline double likelihood_(
     double numerator = 0.0;
     
     // Computing the numerator
-    for (size_t j = 0u; j < params.size(); ++j)
+    for (size_t j = 0u; j < n_params; ++j)
         numerator += *(stats_target + j) * params[j];
 
     if (!log_)
diff --git a/include/barry/models/geese/geese-meat-likelihood.hpp b/include/barry/models/geese/geese-meat-likelihood.hpp
index 27616d4e8..ca55f9d60 100644
--- a/include/barry/models/geese/geese-meat-likelihood.hpp
+++ b/include/barry/models/geese/geese-meat-likelihood.hpp
@@ -14,7 +14,7 @@ inline void pset_loop(
     const std::vector<std::vector<bool>> & states,
     const std::vector< PhyloArray > & psets,
     const std::vector<double> & psets_stats,
-    std::vector< std::vector< size_t > > & locations,
+    const std::vector< std::vector< size_t > > & locations,
     const std::vector<geese::Node *> & node_offspring
 ) 
 {
@@ -73,17 +73,11 @@ inline void pset_loop(
     if (off_mult < 0.0)
         return;
 
-    // Multiplying by P(x|x_n), the transition probability
-    std::vector< double > temp_stats;
-    temp_stats.reserve(par0.size());
-    for (auto p = 0u; p < par0.size(); ++p)
-        temp_stats.push_back(psets_stats[par0.size() * n + p]);
-
     // Use try catch in the following line
     try {
 
         off_mult *= barry::likelihood_(
-            &temp_stats[0u],
+            &psets_stats[par0.size() * n],
             par0,
             norm_const_i,
             par0.size(),
@@ -223,8 +217,13 @@ inline double Geese::likelihood(
 
             // Setting the probability at the node
             node.subtree_prob[s] = 0.0;
+            auto & nsp = node.subtree_prob[s];
+            #if defined(_OPENMP) || defined(__OPENMP)
+            #pragma omp simd reduction(+:nsp)
+            #endif
             for (size_t n = 0u; n < psets.size(); ++n)
-                node.subtree_prob[s] += totprob_n[n];
+                nsp += totprob_n[n];
+
 
         }