openMP_checker

.gitignore

@@ -6,4 +6,3 @@
 *.o
 .DS_Store
 *.Rmd
-Makevars

R/BacGWES.R

@@ -243,7 +243,8 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
   ######## Welcome message ########
   {
     timestamp()
-    cat("\n ***** This is LDWeaver", as.character(packageVersion(pkg = "LDWeaver")), " *****")
+    cat("\n ***** This is LDWeaver", as.character(packageVersion(pkg = "LDWeaver")), " *****\n")
+    test_openmp()
     if(ncores > 1) cat(paste("\n\n Performing GWES analysis on:", dset, " - using", ncores, "cores\n\n"))
     if(ncores == 1) cat(paste("\n\n Performing GWES analysis on:", dset, "\n\n"))
     if(perform_SR_analysis_only) cat("Only short-range analysis requested. \n")

R/RcppExports.R

@@ -37,6 +37,10 @@
     .Call('_LDWeaver_extractRef', PACKAGE = 'LDWeaver', file)
 }
 
+test_openmp <- function() {
+    invisible(.Call('_LDWeaver_test_openmp', PACKAGE = 'LDWeaver'))
+}
+
 .readFasta <- function(file, pos_len) {
     .Call('_LDWeaver_readFasta', PACKAGE = 'LDWeaver', file, pos_len)
 }

R/performPopulationStuctureCorrection.R

@@ -52,20 +52,20 @@ estimate_Hamming_distance_weights = function(snp.dat, threshold = 0.1, mega_dset
 
     }
   } else {
-    snpmat_t = as(snp.dat$snp.matrix_A, 'dgCMatrix')
+    snpmat_t = as(snp.dat$snp.matrix_A, 'lgeMatrix')
     # shared.snps = MatrixExtra::crossprod((snpmat_t))
     shared.snps = crossprod((snpmat_t))
 
-    snpmat_t = as(snp.dat$snp.matrix_C, 'dgCMatrix')
+    snpmat_t = as(snp.dat$snp.matrix_C, 'lgeMatrix')
     shared.snps = shared.snps + crossprod((snpmat_t))
 
-    snpmat_t = as(snp.dat$snp.matrix_G, 'dgCMatrix')
+    snpmat_t = as(snp.dat$snp.matrix_G, 'lgeMatrix')
     shared.snps = shared.snps + crossprod((snpmat_t))
 
-    snpmat_t = as(snp.dat$snp.matrix_T, 'dgCMatrix')
+    snpmat_t = as(snp.dat$snp.matrix_T, 'lgeMatrix')
     shared.snps = shared.snps + crossprod((snpmat_t))
 
-    snpmat_t = as(snp.dat$snp.matrix_N, 'dgCMatrix')
+    snpmat_t = as(snp.dat$snp.matrix_N, 'lgeMatrix')
     shared.snps = shared.snps + crossprod((snpmat_t))
 
     hdw = 1/( Matrix::colSums( (snp.dat$nsnp - shared.snps) < thresh) + 1)

src/Makevars

@@ -0,0 +1,13 @@
+CXX_STD=CXX11
+
+CXX1X=$(shell ${R_HOME}/bin/R CMD config CXX11)
+
+PKG_LIBS = $(shell $(R_HOME)/bin/Rscipt.exe -e "Rcpp:::LdFlags()") -lz
+
+ifeq ($(shell $(CXX1X) -fopenmp -E -xc++ - 2>&1 >/dev/null && echo 'true'), true)
+  PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -DARMA_64BIT_WORD
+  PKG_LIBS=$(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+else
+  PKG_CXXFLAGS=-DARMA_64BIT_WORD
+  PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+endif

src/RcppExports.cpp

@@ -129,6 +129,15 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// test_openmp
+void test_openmp();
+RcppExport SEXP _LDWeaver_test_openmp() {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    test_openmp();
+    return R_NilValue;
+END_RCPP
+}
 // readFasta
 List readFasta(std::string file, int pos_len);
 RcppExport SEXP _LDWeaver_readFasta(SEXP fileSEXP, SEXP pos_lenSEXP) {
@@ -152,6 +161,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_LDWeaver_extractAlnParam", (DL_FUNC) &_LDWeaver_extractAlnParam, 4},
     {"_LDWeaver_extractSNPs", (DL_FUNC) &_LDWeaver_extractSNPs, 4},
     {"_LDWeaver_extractRef", (DL_FUNC) &_LDWeaver_extractRef, 1},
+    {"_LDWeaver_test_openmp", (DL_FUNC) &_LDWeaver_test_openmp, 0},
     {"_LDWeaver_readFasta", (DL_FUNC) &_LDWeaver_readFasta, 2},
     {NULL, NULL, 0}
 };

src/openMP_tester.cpp

@@ -0,0 +1,16 @@
+#include <Rcpp.h>
+#ifdef _OPENMP
+#include <omp.h>
+// [[Rcpp::plugins(openmp)]]
+#endif
+
+
+// [[Rcpp::export]]
+void test_openmp() {
+#ifdef _OPENMP
+  int nthreads = omp_get_max_threads();
+  Rcpp::Rcout << "with OpenMP support - system supports up to: " << nthreads << " cores" << std::endl;
+#else
+  Rcpp::Rcout << "without OpenMP support - WARNING! Some functions will run slower..." << std::endl;
+#endif
+}