README.md

README

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+# 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
+```