From 806a01c27a1fd366c120820de0c38caea1d4cdcd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 26 Nov 2025 12:01:37 +0100
Subject: openblas speed on par

---
 src/lmm.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

(limited to 'src/lmm.cpp')

diff --git a/src/lmm.cpp b/src/lmm.cpp
index 87b9e1e..fb3a255 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -55,6 +55,7 @@
 using namespace std;
 
 void LMM::CopyFromParam(PARAM &cPar) {
+  checkpoint_nofile("lmm-copy-from-param");
   a_mode = cPar.a_mode;
   d_pace = cPar.d_pace;
 
@@ -91,6 +92,7 @@ void LMM::CopyFromParam(PARAM &cPar) {
 }
 
 void LMM::CopyToParam(PARAM &cPar) {
+  checkpoint_nofile("lmm-copy-to-param");
   cPar.time_UtX = time_UtX;
   cPar.time_opt = time_opt;
 
@@ -105,6 +107,7 @@ void LMM::WriteFiles() {
 
   file_str = path_out + "/" + file_out;
   file_str += ".assoc.txt";
+  checkpoint("lmm-write-files",file_str.c_str());
 
   ofstream outfile(file_str.c_str(), ofstream::out);
   if (!outfile) {
@@ -1668,6 +1671,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   bool process_gwasnps = gwasnps.size();
   if (process_gwasnps)
     debug_msg("Analyze subset of SNPs (LOCO)");
+  checkpoint_nofile("start-lmm-analyze");
 
   // Calculate basic quantities.
   size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2;
@@ -1704,6 +1708,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   auto batch_compute = [&](size_t l) { // using a C++ closure
     // Compute SNPs in batch, note the computations are independent per SNP
     // debug_msg("enter batch_compute");
+    checkpoint_nofile("\nstart-batch_compute");
     gsl_matrix_view Xlarge_sub = gsl_matrix_submatrix(Xlarge, 0, 0, inds, l);
     gsl_matrix_view UtXlarge_sub =
         gsl_matrix_submatrix(UtXlarge, 0, 0, inds, l);
@@ -1763,6 +1768,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
       sumStat.push_back(SNPs);
     }
     // debug_msg("exit batch_compute");
+    checkpoint_nofile("end-batch_compute");
   };
 
   const auto num_snps = indicator_snp.size();
@@ -1847,6 +1853,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   ProgressBar("Reading SNPs", num_snps - 1, num_snps - 1);
   // cout << "Counted SNPs " << c << " sumStat " << sumStat.size() << endl;
   cout << endl;
+  checkpoint_nofile("end-lmm-analyze");
 
   gsl_vector_safe_free(x);
   gsl_vector_safe_free(x_miss);
-- 
cgit 1.4.1