diff options
| -rw-r--r-- | guix.scm | 4 | ||||
| -rw-r--r-- | src/lmm.cpp | 5 | ||||
| -rw-r--r-- | src/lmm.h | 2 | ||||
| -rw-r--r-- | test/performance/releases.org | 2 |
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. |