diff options
Diffstat (limited to 'test')
| -rwxr-xr-x | test/dev_test_suite.sh | 48 | ||||
| -rw-r--r-- | test/src/unittests-math.cpp | 117 | ||||
| -rwxr-xr-x | test/test_suite.sh | 6 |
3 files changed, 165 insertions, 6 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 0fc4423..284c9aa 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -11,7 +11,8 @@ testBXDStandardRelatednessMatrixKSingularError() { -c ../example/BXD_covariates.txt \ -a ../example/BXD_snps.txt \ -gk \ - -debug -o $outn + -debug \ + -o $outn assertEquals 22 $? # should show singular error } @@ -44,7 +45,7 @@ testBXDLMMLikelihoodRatio() { assertEquals 0 $? outfn=output/$outn.assoc.txt - assertEquals "80498" `wc -w < $outfn` + assertEquals "73180" `wc -w < $outfn` assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } @@ -83,6 +84,49 @@ testUnivariateLinearMixedModelLOCO1() { assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } +testPlinkCenteredRelatednessMatrixKLOCO1() { + return 0 + outn=mouse_hs1940_Plink_LOCO1 + rm -f output/$outn.* + $gemma -bfile ../example/mouse_hs1940 \ + -a ../example/mouse_hs1940.anno.txt \ + -snps ../example/mouse_hs1940_snps.txt \ + -nind 400 \ + -loco 1 \ + -gk \ + -debug \ + -o $outn + assertEquals 0 $? + grep "total computation time" < output/$outn.log.txt + outfn=output/$outn.cXX.txt + assertEquals 0 $? + assertEquals "400" `wc -l < $outfn` + assertEquals "0.312" `head -c 5 $outfn` + assertEquals "71.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + + +testPlinkUnivariateLinearMixedModelLOCO1() { + return 0 + outn=mouse_hs1940_CD8_Plink_LOCO1_lmm + rm -f output/$outn.* + $gemma -bfile ../example/mouse_hs1940 \ + -n 1 \ + -loco 1 \ + -k ./output/mouse_hs1940_Plink_LOCO1.cXX.txt \ + -a ../example/mouse_hs1940.anno.txt \ + -snps ../example/mouse_hs1940_snps.txt -lmm \ + -nind 400 \ + -debug \ + -o $outn + assertEquals 0 $? + grep "total computation time" < output/$outn.log.txt + assertEquals 0 $? + outfn=output/$outn.assoc.txt + assertEquals "68" `wc -l < $outfn` + assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + shunit2=`which shunit2` if [ -x "$shunit2" ]; then diff --git a/test/src/unittests-math.cpp b/test/src/unittests-math.cpp index ac4c180..757c2dc 100644 --- a/test/src/unittests-math.cpp +++ b/test/src/unittests-math.cpp @@ -1,14 +1,23 @@ #include <catch.hpp> #include <iostream> #include "gsl/gsl_matrix.h" -#include "mathfunc.h" +#include <cblas.h> + #include <algorithm> #include <limits> #include <numeric> +#include "debug.h" +#include "mathfunc.h" +#include "fastblas.h" +#include "fastopenblas.h" + using namespace std; TEST_CASE( "Math functions", "[math]" ) { + debug_set_debug_mode(true); + debug_set_no_check_mode(false); + debug_set_strict_mode(true); double data[] = { 2,-1, 0, -1, 2,-1, 0,-1, 2}; @@ -51,3 +60,109 @@ TEST_CASE( "Math functions", "[math]" ) { REQUIRE (std::isnan(v3[2])); REQUIRE(has_nan(v3)); } + +TEST_CASE("cblas_dgemm", "[math]") { + double *A, *B, *C; + int m, n, k, i, j; + double alpha, beta; + + printf ("\n This example computes real matrix C=alpha*A*B+beta*C using \n" + " Intel(R) MKL function dgemm, where A, B, and C are matrices and \n" + " alpha and beta are double precision scalars\n\n"); + + m = 2000, k = 200, n = 1000; + printf (" Initializing data for matrix multiplication C=A*B for matrix \n" + " A(%ix%i) and matrix B(%ix%i)\n\n", m, k, k, n); + alpha = 1.0; beta = 0.0; + + printf (" Allocating memory for matrices aligned on 64-byte boundary for better \n" + " performance \n\n"); + A = (double *)malloc( m*k*sizeof( double )); + B = (double *)malloc( k*n*sizeof( double )); + C = (double *)malloc( m*n*sizeof( double )); + + printf (" Intializing matrix data \n\n"); + for (i = 0; i < (m*k); i++) { + A[i] = (double)(i+1); + } + + for (i = 0; i < (k*n); i++) { + B[i] = (double)(-i-1); + } + + for (i = 0; i < (m*n); i++) { + C[i] = 0.0; + } + + printf (" Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface \n\n"); + assert(m==2000); + assert(k==200); + assert(n==1000); + //cblas_dgemm(CblasRowMajor, CblasNoTrans, CblasNoTrans, + // m, n, k, alpha, A, k, B, n, beta, C, n); + fast_cblas_dgemm(CblasRowMajor, CblasNoTrans, CblasNoTrans, + m, n, k, alpha, A, k, B, n, beta, C, n); + + REQUIRE(trunc(C[0]) == -2666620100.0 ); + REQUIRE(trunc(C[1]) == -2666640200.0 ); + REQUIRE(trunc(C[2003]) == -10627000400.0 ); + +} + +TEST_CASE("fast_dgemm", "[math]") { + double *A, *B, *C; + int m, n, k, i, j; + double alpha, beta; + + printf ("\n This example computes real matrix C=alpha*A*B+beta*C using \n" + " Intel(R) MKL function dgemm, where A, B, and C are matrices and \n" + " alpha and beta are double precision scalars\n\n"); + + m = 2000, k = 200, n = 1000; + printf (" Initializing data for matrix multiplication C=A*B for matrix \n" + " A(%ix%i) and matrix B(%ix%i)\n\n", m, k, k, n); + alpha = 1.0; beta = 0.0; + + printf (" Allocating memory for matrices aligned on 64-byte boundary for better \n" + " performance \n\n"); + A = (double *)malloc( m*k*sizeof( double )); + B = (double *)malloc( k*n*sizeof( double )); + C = (double *)malloc( m*n*sizeof( double )); + + printf (" Intializing matrix data \n\n"); + for (i = 0; i < (m*k); i++) { + A[i] = (double)(i+1); + } + + for (i = 0; i < (k*n); i++) { + B[i] = (double)(-i-1); + } + + for (i = 0; i < (m*n); i++) { + C[i] = 0.0; + } + + printf (" Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface \n\n"); + // cblas_dgemm(CblasRowMajor, CblasNoTrans, CblasNoTrans, + // m, n, k, alpha, A, k, B, n, beta, C, n); + // eigenlib_dgemm(const char *TransA, const char *TransB, const double alpha, + // const gsl_matrix *A, const gsl_matrix *B, const double beta, + // gsl_matrix *C) { + gsl_matrix *AM = gsl_matrix_safe_alloc(m,k); // rows x cols + gsl_matrix *BM = gsl_matrix_safe_alloc(k,n); + gsl_matrix *CM = gsl_matrix_calloc(m,n); + + fast_copy(AM,A); + fast_copy(BM,B); + fast_copy(CM,C); + fast_dgemm("N","N",alpha,AM,BM,beta,CM); + printf ("\n Computations completed.\n\n"); + A = AM->data; + B = BM->data; + C = CM->data; + + REQUIRE(trunc(C[0]) == -2666620100.0 ); + REQUIRE(trunc(C[1]) == -2666640200.0 ); + REQUIRE(trunc(C[2003]) == -10627000400.0 ); + +} diff --git a/test/test_suite.sh b/test/test_suite.sh index 350fc27..dc6053a 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -62,7 +62,7 @@ testUnivariateLinearMixedModel() { assertEquals "4038540440.86" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } -testMultivariateLinearMixedModel() { +testLinearMixedModelPhenotypes() { $gemma -g ../example/mouse_hs1940.geno.txt.gz \ -p ../example/mouse_hs1940.pheno.txt \ -n 1 6 \ @@ -92,8 +92,8 @@ testPlinkStandardRelatednessMatrixK() { # Test for https://github.com/genetics-statistics/GEMMA/issues/58 # fixed GSLv2 NaN's that appeared with covariates. -testPlinkMultivariateLinearMixedModel() { - testname=testPlinkMultivariateLinearMixedModel +testPlinkLinearMixedModelCovariates() { + testname=testPlinkLinearMixedModelCovariates datadir=../example $gemma -bfile $datadir/HLC \ -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \ |