On Fri, Jul 30, 2021 at 10:42:49PM +0200, Pjotr Prins wrote: > ASSERT:expected:<2247> but was:<2246>
Builds on my machine now, waiting for Salsa CI before uploading. Thanks a lot for your quick support Andreas. > is a round off :/. Can you comment out that line? I can resend the > patch tomorrow otherwise. > > Pj. > > On Fri, Jul 30, 2021 at 10:08:45PM +0200, Andreas Tille wrote: > > Dear Pjotr, > > > > thanks a lot for your input. I've applied your changes but there is one > > remaining failure. I've attached the build log. Did I possibly made some > > mistake when merging your patch? > > > > Kind regards > > > > Andreas. > > > > On Fri, Jul 30, 2021 at 12:29:57PM +0200, Pjotr Prins wrote: > > > Dear Andreas, > > > > > > I have merged the reproducible patch from the Debian source tree and > > > changed/disabled some other tests (attached). The problem is that > > > different AMD64 CPUs together with OpenBlas simply give different > > > results (mostly SIMD differences). > > > > > > I tested the current tests on both Intel and AMD that I have and these > > > tests pass right now. > > > > > > If one is left that still fails, simply disable it. > > > > > > I'll revamp the GEMMA testing soon. I have to. > > > > > > Attached > > > > > > Pj. > > > > > > > > From f90317c64e80c94ba0b5f644d3dc4f502677f8e8 Mon Sep 17 00:00:00 2001 > > > From: Pjotr Prins <pjotr.publi...@thebird.nl> > > > Date: Fri, 30 Jul 2021 05:01:55 -0500 > > > Subject: [PATCH] Merging the test changes from the Debian tree and > > > changing > > > some other tests to enhance reproducibility. > > > > > > --- > > > Makefile | 4 ++-- > > > test/dev_test_suite.sh | 10 +++++----- > > > test/test_suite.sh | 20 ++++++++++---------- > > > 3 files changed, 17 insertions(+), 17 deletions(-) > > > > > > diff --git a/Makefile b/Makefile > > > index 0cf3097..499b325 100644 > > > --- a/Makefile > > > +++ b/Makefile > > > @@ -201,8 +201,8 @@ ifdef WITH_LAPACK > > > endif > > > endif > > > > > > -HDR = $(wildcard src/*.h) ./src/version.h > > > -SOURCES = $(wildcard src/*.cpp) > > > +HDR = $(sort $(wildcard src/*.h)) ./src/version.h > > > +SOURCES = $(sort $(wildcard src/*.cpp)) > > > > > > # all > > > OBJS = $(SOURCES:.cpp=.o) > > > diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh > > > index 676e0b3..c596679 100755 > > > --- a/test/dev_test_suite.sh > > > +++ b/test/dev_test_suite.sh > > > @@ -79,7 +79,7 @@ testBXDLMMLikelihoodRatio() { > > > > > > outfn=output/$outn.assoc.txt > > > assertEquals "73180" `wc -w < $outfn` > > > - assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' > > > $outfn` > > > + #assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' > > > $outfn` > > > } > > > > > > testBXDLMM9LikelihoodRatio() { > > > @@ -96,7 +96,7 @@ testBXDLMM9LikelihoodRatio() { > > > > > > outfn=output/$outn.assoc.txt > > > assertEquals "80498" `wc -w < $outfn` > > > - assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' > > > $outfn` > > > + #assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' > > > $outfn` > > > } > > > > > > testCenteredRelatednessMatrixissue188() { > > > @@ -113,7 +113,7 @@ testLMMissue188() { > > > $gemma $gemmaopts -b data/issue188/2000 -lmm 2 -k > > > output/$outn.cXX.txt -maf 0.01 -o $outn -n 1 > > > assertEquals 0 $? > > > outfn=output/$outn.assoc.txt > > > - assertEquals "338154001.76" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + #assertEquals "338154001.76" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > } > > > > > > testCenteredRelatednessMatrixKLOCO1() { > > > @@ -147,7 +147,7 @@ testUnivariateLinearMixedModelLOCO1() { > > > 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` > > > + #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > } > > > > > > testPlinkCenteredRelatednessMatrixKLOCO1() { > > > @@ -188,7 +188,7 @@ testPlinkUnivariateLinearMixedModelLOCO1() { > > > 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` > > > + #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > } > > > > > > > > > diff --git a/test/test_suite.sh b/test/test_suite.sh > > > index cc244c0..892faa4 100755 > > > --- a/test/test_suite.sh > > > +++ b/test/test_suite.sh > > > @@ -27,7 +27,7 @@ testBslmm2() { > > > -gk 1 -o $outn > > > assertEquals 0 $? > > > outfn=output/$outn.cXX.txt > > > - assertEquals "579.50" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + assertEquals "580" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum > > > += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` > > > } > > > > > > testBslmm3() { > > > @@ -76,7 +76,7 @@ testBslmm5() { > > > -o $outn -seed 100 > > > assertEquals 0 $? > > > outfn=output/$outn.prdt.txt > > > - assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + # assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > } > > > > > > testCenteredRelatednessMatrixKFullLOCO1() { > > > @@ -88,7 +88,7 @@ testCenteredRelatednessMatrixKFullLOCO1() { > > > assertEquals 0 $? > > > outfn=output/$outn.cXX.txt > > > assertEquals "1940" `wc -l < $outfn` > > > - assertEquals "2246.49" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + assertEquals "2247" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum > > > += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` > > > } > > > > > > testUnivariateLinearMixedModelFullLOCO1() { > > > @@ -106,7 +106,7 @@ testUnivariateLinearMixedModelFullLOCO1() { > > > assertEquals 0 $? > > > outfn=output/$outn.assoc.txt > > > assertEquals "951" `wc -l < $outfn` > > > - assertEquals "267507852.03" `perl -nle 'foreach $x (split(/\s+/,$_)) > > > { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + # assertEquals "267507852.03" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > } > > > > > > testCenteredRelatednessMatrixK() { > > > @@ -118,7 +118,7 @@ testCenteredRelatednessMatrixK() { > > > assertEquals "1940" `wc -l < $outfn` > > > assertEquals "3763600" `wc -w < $outfn` > > > assertEquals "0.335" `head -c 5 $outfn` > > > - assertEquals "1119.60" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + assertEquals "1120" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum > > > += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` > > > } > > > > > > testUnivariateLinearMixedModel() { > > > @@ -134,7 +134,7 @@ testUnivariateLinearMixedModel() { > > > assertEquals 0 $? > > > outfn=output/mouse_hs1940_CD8_lmm.assoc.txt > > > assertEquals "129228" `wc -w < $outfn` > > > - assertEquals "4038540440.81" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > + # assertEquals "4038540440.81" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > } > > > > > > testLinearMixedModelPhenotypes() { > > > @@ -149,7 +149,7 @@ testLinearMixedModelPhenotypes() { > > > > > > outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt > > > assertEquals "139867" `wc -w < $outfn` > > > - assertEquals "4029037056.58" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > + # assertEquals "4029037056.58" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > } > > > > > > testPlinkStandardRelatednessMatrixK() { > > > @@ -161,7 +161,7 @@ testPlinkStandardRelatednessMatrixK() { > > > -gk 2 -o $testname > > > assertEquals 0 $? > > > assertEquals "427" `wc -l < $outfn` > > > - assertEquals "-358.05" `perl -nle 'foreach $x (split(/\s+/,$_)) { > > > $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' > > > $outfn` > > > + assertEquals "-358" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum > > > += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` > > > } > > > > > > # Test for https://github.com/genetics-statistics/GEMMA/issues/58 > > > @@ -178,8 +178,8 @@ testPlinkLinearMixedModelCovariates() { > > > -o $testname > > > assertEquals 0 $? > > > outfn=output/$testname.assoc.txt > > > - assertEquals "223243" `wc -l < $outfn` > > > - assertEquals "89757159113.94" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > + # assertEquals "223243" `wc -l < $outfn` > > > + # assertEquals "89757159113.94" `perl -nle 'foreach $x > > > (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { > > > printf "%.2f",$sum }' $outfn` > > > } > > > > > > shunit2=`which shunit2` > > > -- > > > 2.21.0 > > > > > > > > > -- > > http://fam-tille.de > > -- http://fam-tille.de