Minor tweaks

4 files changed, 5 insertions, 8 deletions

diff --git a/guix.scm b/guix.scm
index b46b832..2bc02ef 100644
--- a/guix.scm
+++ b/guix.scm
@@ -251,6 +251,4 @@ provides a standard linear mixed model resolver with application in
 genome-wide association studies (GWAS).")
     (license license:gpl3)))
 
-
-
-gemma-git
+pangemma-shell-git
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 1ef3990..12e4edb 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -96,7 +96,7 @@ void LMM::CopyToParam(PARAM &cPar) {
   cPar.time_UtX = time_UtX;
   cPar.time_opt = time_opt;
 
-  cPar.ng_test = ng_test;
+  cPar.ng_test = ng_test; // number of markers tested
 
   return;
 }
@@ -1723,7 +1723,6 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
 
     gsl_matrix_set_zero(Xlarge);
     for (size_t i = 0; i < l; i++) {
-      ProgressBar("GWA compute   ", i, l - 1);
       // for each snp batch item extract transformed genotype:
       gsl_vector_view UtXlarge_col = gsl_matrix_column(UtXlarge, i);
       gsl_vector_safe_memcpy(Utx, &UtXlarge_col.vector);
@@ -1851,7 +1850,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
   }
 
   batch_compute(c % msize);
-  ProgressBar("Computed      ", num_snps - 1, num_snps - 1);
+  ProgressBar("Reading SNPS", num_snps - 1, num_snps - 1);
   // cout << "Counted SNPs " << c << " sumStat " << sumStat.size() << endl;
   cout << endl;
   checkpoint_nofile("end-lmm-analyze");
diff --git a/src/lmm.h b/src/lmm.h
index 736c679..596c11b 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -30,7 +30,7 @@
 
 using namespace std;
 
-#define LMM_BATCH_SIZE 20000 // used for batch processing
+#define LMM_BATCH_SIZE 5000 // used for batch processing
 
 class FUNC_PARAM {
 
diff --git a/test/performance/releases.org b/test/performance/releases.org
index ff18287..082cdde 100644
--- a/test/performance/releases.org
+++ b/test/performance/releases.org
@@ -7,7 +7,7 @@ Measurements taken on a recent AMD Ryzen 7 3700X 8-Core Processor @2.195GHz.
 
 We are facing a time regression.
 
-premake5 gmake2 && make verbose=1 config=release -j 8 gemma && time LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./build/bin/Release/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check -debug
+premake5 gmake2 && make verbose=1 config=release -j 8 gemma && time LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./build/bin/Release/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
 
 With openblas 0.3.21 we go a bit faster. Still 10% behind though, there is room for tweaking. It may actually be a new SSD. I want to run some bigger files first.