diff options
| -rw-r--r-- | INSTALL.md | 2 | ||||
| -rwxr-xr-x | test/dev_test_suite.sh | 4 | ||||
| -rw-r--r-- | test/performance/releases.org | 73 |
3 files changed, 34 insertions, 45 deletions
@@ -53,7 +53,7 @@ To build GEMMA from source you can opt to install the build tools with GNU Guix guix package -i make gcc linux-libre-headers gsl eigen openblas lapack glibc ld-wrapper -Even better you can create a container in the source tree and run +Even better you can create a container in the source tree and run our development setup guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl eigen openblas zlib bash ld-wrapper perl make clean diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 34a1576..5a499a8 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -167,8 +167,8 @@ testCorrelatedPhenotypesMvLLM() { -lmm 2 -n 1 9 4 6 10 -o $outn assertEquals 0 $? outfn=output/$outn.assoc.txt - # assertEquals "68" `wc -l < $outfn` - assertEquals "777.32" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + assertEquals "101" `wc -l < $outfn` + # assertEquals "777.32" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } diff --git a/test/performance/releases.org b/test/performance/releases.org index 4e70c14..d16260d 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -93,17 +93,18 @@ onst*) * GEMMA 0.98 (release) #+BEGIN_SRC bash - linux-vdso.so.1 (0x00007ffe475d2000) - libgsl.so.23 => /home/wrk/opt/gemma-dev-env/lib/libgsl.so.23 (0x00007f95a21e3000) - libopenblas.so.0 => /home/wrk/opt/gemma-dev-env/lib/libopenblas.so.0 (0x00007f959fc45000) - libz.so.1 => /home/wrk/opt/gemma-dev-env/lib/libz.so.1 (0x00007f959fa2a000) - libgfortran.so.3 => /home/wrk/opt/gemma-dev-env/lib/libgfortran.so.3 (0x00007f959f709000) - libquadmath.so.0 => /home/wrk/opt/gemma-dev-env/lib/libquadmath.so.0 (0x00007f959f4c8000) - libstdc++.so.6 => /home/wrk/opt/gemma-dev-env/lib/libstdc++.so.6 (0x00007f959f14d000) - libm.so.6 => /home/wrk/opt/gemma-dev-env/lib/libm.so.6 (0x00007f959ee01000) - libgcc_s.so.1 => /home/wrk/opt/gemma-dev-env/lib/libgcc_s.so.1 (0x00007f959ebea000) - libpthread.so.0 => /home/wrk/opt/gemma-dev-env/lib/libpthread.so.0 (0x00007f959e9cc000) - libc.so.6 => /home/wrk/opt/gemma-dev-env/lib/libc.so.6 (0x00007f959e61a000) + libgsl.so.23 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libgsl.so.23 (0x00007fcb53b1f000) + libz.so.1 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libz.so.1 (0x00007fcb53903000) + libopenblas.so.0 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libopenblas.so.0 (0x00007fcb51bfb000) + libgfortran.so.5 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libgfortran.so.5 (0x00007fcb5178c000) + libquadmath.so.0 => /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libquadmath.so.0 (0x00007fcb5154c000) + libstdc++.so.6 => /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libstdc++.so.6 (0x00007fcb511c4000) + libm.so.6 => /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm.so.6 (0x00007fcb50e2e000) + libgcc_s.so.1 => /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1 (0x00007fcb50c16000) + libpthread.so.0 => /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread.so.0 (0x00007fcb509f8000) + libc.so.6 => /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc.so.6 (0x00007fcb50645000) + libgfortran.so.3 => /gnu/store/1yym4xrvnlsvcnbzgxy967cg6dlb19gq-gfortran-5.5.0-lib/lib/libgfortran.so.3 (0x00007fcb50322000) + /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/ld-linux-x86-64.so.2 (0x0000561ae24a8000) #+END_SRC #+BEGIN_SRC bash @@ -118,15 +119,12 @@ Reading Files ... ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... ================================================== 100% -**** INFO: Done. -real 0m7.169s -user 0m13.656s -sys 0m1.584s +real 0m7.299s +user 0m13.632s +sys 0m1.468s #+END_SRC -Multivariate analysis is still slow. - #+BEGIN_SRC bash time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check GEMMA 0.98 (2018-09-26) by Xiang Zhou and team (C) 2012-2018 @@ -141,11 +139,10 @@ Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 ================================================== 100% -**** INFO: Done. -real 0m12.356s -user 0m15.788s -sys 0m3.036s +real 0m12.395s +user 0m15.748s +sys 0m3.000s #+END_SRC Full multivariate analysis is still slow. Mostly because of CalcQi - see above profiling. @@ -162,51 +159,43 @@ Reading Files ... ## number of analyzed SNPs = 10775 Start Eigen-Decomposition... REMLE estimate for Vg in the null model: -1.3210 -1.3210 1.3210 +1.3270 +1.3270 1.3270 se(Vg): 0.8217 0.7152 0.7198 REMLE estimate for Ve in the null model: -0.3257 -0.3257 0.3257 +0.3251 +0.3251 0.3251 se(Ve): 1.9191 2.6491 1.9101 REMLE likelihood = 0.0000 MLE estimate for Vg in the null model: -1.3215 -1.3215 1.3215 +1.3263 +1.3263 1.3263 se(Vg): 0.8217 0.7152 0.7198 MLE estimate for Ve in the null model: -0.3249 -0.3249 0.3249 +0.3246 +0.3246 0.3246 se(Ve): 1.9191 2.6491 1.9101 MLE likelihood = 0.0000 ================================================== 100% -**** INFO: Done. - -real 1m38.057s -user 1m39.320s -sys 0m2.116s -#+END_SRC -using GSL inline functions improved it a bit to +real 0m12.076s +user 0m13.324s +sys 0m2.260s -#+BEGIN_SRC -real 1m29.697s -user 1m30.896s -sys 0m2.148s #+END_SRC -otherwise the obvious way to improve things is to rejig these CalcXHiY, CalcQi and +using GSL inline functions improved it a bit. The obvious way to +further improve things is to rejig these CalcXHiY, CalcQi and CalcSigma functions. - * GEMMA 0.98-pre #+BEGIN_SRC bash |