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

2 files changed, 10 insertions, 7 deletions

diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 0d3d8a0..ad743ff 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -14,6 +14,7 @@ testBXDStandardRelatednessMatrixKSingularError() {
            -c ../example/BXD_covariates.txt \
            -a ../example/BXD_snps.txt \
            -gk \
+           -no-check \
            -o $outn
     assertEquals 22 $? # should show singular error
 }
@@ -56,7 +57,7 @@ testBXDLMMLikelihoodRatio() {
            -c ../example/BXD_covariates2.txt \
            -a ../example/BXD_snps.txt \
            -k ./output/BXD.cXX.txt \
-           -lmm 2 -maf 0.1 \
+           -lmm 2 -no-check -maf 0.1 \
            -o $outn
     assertEquals 0 $?
 
@@ -89,7 +90,7 @@ testUnivariateLinearMixedModelLOCO1() {
            -a ../example/mouse_hs1940.anno.txt \
            -k ./output/mouse_hs1940_LOCO1.cXX.txt \
 	   -snps ../example/mouse_hs1940_snps.txt -lmm \
-	   -nind 400 \
+	   -nind 400 -no-check \
            -o $outn
     assertEquals 0 $?
     grep "total computation time" < output/$outn.log.txt
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 7af33aa..faddd43 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -8,7 +8,7 @@ testBslmm1() {
     $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
            -p ../example/mouse_hs1940.pheno.txt \
            -n 2 -a ../example/mouse_hs1940.anno.txt \
-           -bslmm \
+           -bslmm -no-check \
            -o $outn -w 1000 -s 10000 -seed 1
     assertEquals 0 $?
     outfn1=output/$outn.hyp.txt
@@ -39,7 +39,7 @@ testBslmm3() {
            -a ../example/mouse_hs1940.anno.txt \
            -bslmm \
            -o $outn \
-           -w 1000 -s 10000 -seed 1
+           -w 1000 -s 10000 -seed 1 -no-check
     assertEquals 0 $?
     outfn=output/$outn.hyp.txt
     # assertEquals "291" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",100*$sum }' $outfn`
@@ -54,7 +54,7 @@ testBslmm4() {
            -emu ./output/mouse_hs1940_CD8_bslmm.log.txt \
            -ebv ./output/mouse_hs1940_CD8_bslmm.bv.txt \
            -k ./output/mouse_hs1940_CD8_train.cXX.txt \
-           -predict \
+           -predict -no-check \
            -o $outn
     assertEquals 0 $?
     outfn=output/$outn.prdt.txt
@@ -98,7 +98,7 @@ testUnivariateLinearMixedModelFullLOCO1() {
 	   -loco 1 \
            -a ../example/mouse_hs1940.anno.txt \
            -k ./output/mouse_hs1940_full_LOCO1.cXX.txt \
-	   -lmm \
+	   -lmm -no-check \
            -o $outn
     assertEquals 0 $?
     grep "total computation time" < output/$outn.log.txt
@@ -142,7 +142,8 @@ testLinearMixedModelPhenotypes() {
            -n 1 6 \
            -a ../example/mouse_hs1940.anno.txt \
            -k ./output/mouse_hs1940.cXX.txt \
-           -lmm -o mouse_hs1940_CD8MCH_lmm
+           -lmm -no-check \
+           -o mouse_hs1940_CD8MCH_lmm
     assertEquals 0 $?
 
     outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
@@ -172,6 +173,7 @@ testPlinkLinearMixedModelCovariates() {
            -lmm 1 \
            -maf 0.1 \
            -c $datadir/HLC_covariates.txt \
+           -no-check \
            -o $testname
     assertEquals 0 $?
     outfn=output/$testname.assoc.txt