diff options
| -rw-r--r-- | README.md | 8 | ||||
| -rw-r--r-- | doc/developers/profiling.md | 30 | ||||
| -rw-r--r-- | src/mvlmm.cpp | 6 |
3 files changed, 40 insertions, 4 deletions
diff --git a/README.md b/README.md index da231f3..022801b 100644 --- a/README.md +++ b/README.md @@ -116,15 +116,15 @@ a typical example would be ```sh # compute Kinship matrix -gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ +gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt \ -gk -o mouse_hs1940 # run univariate LMM -gemma -g ../example/mouse_hs1940.geno.txt.gz \ - -p ../example/mouse_hs1940.pheno.txt -n 1 -a ../example/mouse_hs1940.anno.txt \ +gemma -g ./example/mouse_hs1940.geno.txt.gz \ + -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm ``` -Above example files can be downloaded from +Above example files are in the git repo and can be downloaded from [github](https://github.com/genetics-statistics/GEMMA/tree/master/example). ### Debugging and optimization diff --git a/doc/developers/profiling.md b/doc/developers/profiling.md new file mode 100644 index 0000000..0d26453 --- /dev/null +++ b/doc/developers/profiling.md @@ -0,0 +1,30 @@ +# Profiling + +gperftools (formerly the Google profiler) is included in the .guix-dev +startup script. Compile gemma for profiling: + + make clean + make profile + +Run the profiler + + env CPUPROFILE=/tmp/prof.out ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -gk -o mouse_hs1940 + pprof ./bin/gemma /tmp/prof.out + +and `top` shows + +``` +Welcome to pprof! For help, type 'help'. +(pprof) top +Total: 720 samples + 103 14.3% 14.3% 103 14.3% dgemm_kernel_ZEN + 39 5.4% 19.7% 79 11.0% ____strtod_l_internal + 37 5.1% 24.9% 53 7.4% __printf_fp_l + 36 5.0% 29.9% 36 5.0% __sched_yield + 34 4.7% 34.6% 34 4.7% __strlen_avx2 + 31 4.3% 38.9% 31 4.3% __strspn_sse42 + 26 3.6% 42.5% 116 16.1% ReadFile_geno + 25 3.5% 46.0% 26 3.6% _int_malloc + 23 3.2% 49.2% 23 3.2% gsl_vector_set + 18 2.5% 51.7% 18 2.5% __strcspn_sse42 +``` diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp index 4b8db05..51ed901 100644 --- a/src/mvlmm.cpp +++ b/src/mvlmm.cpp @@ -3666,6 +3666,8 @@ void MVLMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, t_last++; } for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) { + cout << snpInfo[t].rs_number << endl; + if (t % d_pace == 0 || t == snpInfo.size() - 1) { ProgressBar("Reading SNPs", t, snpInfo.size() - 1); } @@ -3752,6 +3754,10 @@ void MVLMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, gsl_matrix_set_zero(Xlarge); for (size_t i = 0; i < l; i++) { + double t = (double(clock()-time_start)/(double(CLOCKS_PER_SEC))); + printf("%.2f ",t); + if (i>10) exit(1); + cout << i << "," << l << endl; gsl_vector_view UtXlarge_col = gsl_matrix_column(UtXlarge, i); gsl_vector_memcpy(&X_row.vector, &UtXlarge_col.vector); |