Preparing for release

2 files changed, 33 insertions, 44 deletions

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