Add floating point hardware checking for Intel on GNU compilers

When using the -check function (the default) it is enabled for Kinship
computation and LM/LMM up to individual SNP computation. This means
there can no longer be NaN values for matrices that are reused for every
SNP, but it is possible to have NaN for individual SNPs.

Fixes #161

1 files changed, 17 insertions, 0 deletions

diff --git a/src/gemma.cpp b/src/gemma.cpp
index 809cd8e..a183edc 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1624,6 +1624,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
   clock_t time_begin, time_start;
   time_begin = clock();
 
+  if (is_check_mode()) enable_segfpe(); // fast NaN checking
+
   // Read Files.
   cout << "Reading Files ... " << endl;
   cPar.ReadFiles();
@@ -1882,6 +1884,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
     enforce_msg(G, "allocate G"); // just to be sure
 
     time_start = clock();
+
     cPar.CalcKin(G);
 
     cPar.time_G = (clock() - time_start) / (double(CLOCKS_PER_SEC) * 60.0);
@@ -1909,6 +1912,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
     VARCOV cVarcov;
     cVarcov.CopyFromParam(cPar);
 
+    if (is_check_mode()) disable_segfpe(); // fast NaN checking
+
     if (!cPar.file_bfile.empty()) {
       cVarcov.AnalyzePlink();
     } else {
@@ -2022,6 +2027,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
     VARCOV cVarcov;
     cVarcov.CopyFromParam(cPar);
 
+    if (is_check_mode()) disable_segfpe(); // fast NaN checking
+
     if (!cPar.file_bfile.empty()) {
       cVarcov.AnalyzePlink();
     } else {
@@ -2048,6 +2055,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
 
       gsl_vector_view Y_col = gsl_matrix_column(Y, 0);
 
+      if (is_check_mode()) disable_segfpe(); // fast NaN checking
+
       if (!cPar.file_gene.empty()) {
         cLm.AnalyzeGene(W,
                         &Y_col.vector); // y is the predictor, not the phenotype
@@ -2754,6 +2763,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
           LMM cLmm;
           cLmm.CopyFromParam(cPar);
 
+          if (is_check_mode()) disable_segfpe(); // fast NaN checking
+
           gsl_vector_view Y_col = gsl_matrix_column(Y, 0);
           gsl_vector_view UtY_col = gsl_matrix_column(UtY, 0);
 
@@ -2770,6 +2781,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
           }
           else {
             // BIMBAM analysis
+
             if (cPar.file_gxe.empty()) {
               cLmm.AnalyzeBimbam(U, eval, UtW, &UtY_col.vector, W,
                                  &Y_col.vector, cPar.setGWASnps);
@@ -2785,6 +2797,8 @@ void GEMMA::BatchRun(PARAM &cPar) {
           MVLMM cMvlmm;
           cMvlmm.CopyFromParam(cPar);
 
+          if (is_check_mode()) disable_segfpe(); // fast NaN checking
+
           if (!cPar.file_bfile.empty()) {
             if (cPar.file_gxe.empty()) {
               cMvlmm.AnalyzePlink(U, eval, UtW, UtY);
@@ -3107,6 +3121,9 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
   outfile << "##" << endl;
   outfile << "## GEMMA Version    = " << version << " (" << date << ")" << endl;
   outfile << "## Build profile    = " << GEMMA_PROFILE << endl ;
+  #ifdef __GNUC__
+  outfile << "## GCC version      = " << __GNUC__ << "." << __GNUC_MINOR__ << "." << __GNUC_PATCHLEVEL__ << endl;
+  #endif
   outfile << "## GSL Version      = " << GSL_VERSION << endl;
   outfile << "## Eigen Version    = " << EIGEN_WORLD_VERSION << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION << endl;
 #ifdef OPENBLAS