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* GEMMA performance stats
Below measurements are taken on 4x Intel(R) Core(TM) i7-6770HQ CPU @
2.60GHz with hyperthreading and 16 GB RAM with warmed up memory
buffers.
Between 0.96 and 0.97 a speed regression was [[https://github.com/genetics-statistics/GEMMA/issues/136][reported]] which resulted
in tracking of performance. It is interesting because 0.96 is a single
core Eigenlib version and 0.97 went multi-core with
openblas. Unfortunately I linked in lapack and an older BLAS which
slowed things down. In 0.98 openblas is mostly used and is faster.
* GEMMA 0.98-pre
#+BEGIN_SRC bash
/gnu/store/icz3hd36aqpjz5slyp4hhr8wsfbgiml1-bash-minimal-4.4.12/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_GB.UTF-8)
linux-vdso.so.1 (0x00007ffe2abe1000)
libgsl.so.23 => /home/wrk/opt/gemma-dev-env/lib/libgsl.so.23 (0x00007f685a9c0000)
libopenblas.so.0 => /home/wrk/opt/gemma-dev-env/lib/libopenblas.so.0 (0x00007f6858422000)
libz.so.1 => /home/wrk/opt/gemma-dev-env/lib/libz.so.1 (0x00007f6858207000)
libgfortran.so.3 => /home/wrk/opt/gemma-dev-env/lib/libgfortran.so.3 (0x00007f6857ee6000)
libquadmath.so.0 => /home/wrk/opt/gemma-dev-env/lib/libquadmath.so.0 (0x00007f6857ca5000)
libstdc++.so.6 => /home/wrk/opt/gemma-dev-env/lib/libstdc++.so.6 (0x00007f685792a000)
libm.so.6 => /home/wrk/opt/gemma-dev-env/lib/libm.so.6 (0x00007f68575de000)
libgcc_s.so.1 => /home/wrk/opt/gemma-dev-env/lib/libgcc_s.so.1 (0x00007f68573c7000)
libpthread.so.0 => /home/wrk/opt/gemma-dev-env/lib/libpthread.so.0 (0x00007f68571a9000)
libc.so.6 => /home/wrk/opt/gemma-dev-env/lib/libc.so.6 (0x00007f6856df7000)
/gnu/store/n6acaivs0jwiwpidjr551dhdni5kgpcr-glibc-2.26.105-g0890d5379c/lib/ld-linux-x86-64.so.2 => /gnu/store/gf30mz7cfx4fyj4cckgxfxwlsc3c7a8r-glibc-2.26.105-g0890d5379c/lib/ld-linux-x86-64.so.2 (0x000055ae91968000)
#+END_SRC
#+BEGIN_SRC bash
lario:~/izip/git/opensource/genenetwork/gemma$ time ./bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -gk
GEMMA 0.98-pre1 (2018/02/10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Calculating Relatedness Matrix ...
================================================== 100%
real 0m15.995s
user 0m31.884s
sys 0m4.680s
#+END_SRC
#+BEGIN_SRC bash
lario:~/izip/git/opensource/genenetwork/gemma$ time bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -n 1 -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm
GEMMA 0.98-pre1 (2018/02/10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
================================================== 100%
real 0m13.440s
user 0m20.528s
sys 0m4.324s
#+END_SRC
* GEMMA 0.97
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.97$ ldd gemma-gn2-0.97-c760aa0-xqhsidq7h5/bin/gemma
linux-vdso.so.1 (0x00007ffc237a8000)
libgsl.so.23 => /home/wrk/tmp/gemma-release-0.97/gsl-2.4-as8vm64028/lib/libgsl.so.23 (0x00007f8b415f5000)
libopenblas.so.0 => /home/wrk/tmp/gemma-release-0.97/openblas-0.2.19-f7j1vq0ncc/lib/libopenblas.so.0 (0x00007f8b3fbc3000)
libz.so.1 => /home/wrk/tmp/gemma-release-0.97/zlib-1.2.11-sfx1wh27i6/lib/libz.so.1 (0x00007f8b3f9a8000)
libgfortran.so.3 => /home/wrk/tmp/gemma-release-0.97/gfortran-5.4.0-lib-15plffwjdv/lib/libgfortran.so.3 (0x00007f8b3f687000)
libquadmath.so.0 => /home/wrk/tmp/gemma-release-0.97/gcc-5.4.0-lib-3x53yv4v14/lib/libquadmath.so.0 (0x00007f8b3f448000)
liblapack.so.3 => /home/wrk/tmp/gemma-release-0.97/lapack-3.7.1-nyd19c9ccy/lib/liblapack.so.3 (0x00007f8b3eb83000)
libstdc++.so.6 => /home/wrk/tmp/gemma-release-0.97/gcc-5.4.0-lib-3x53yv4v14/lib/libstdc++.so.6 (0x00007f8b3e809000)
libm.so.6 => /home/wrk/tmp/gemma-release-0.97/glibc-2.25-n6nvxlk2j8/lib/libm.so.6 (0x00007f8b3e4f7000)
libgcc_s.so.1 => /home/wrk/tmp/gemma-release-0.97/gcc-5.4.0-lib-3x53yv4v14/lib/libgcc_s.so.1 (0x00007f8b3e2e0000)
libpthread.so.0 => /home/wrk/tmp/gemma-release-0.97/glibc-2.25-n6nvxlk2j8/lib/libpthread.so.0 (0x00007f8b3e0c2000)
libc.so.6 => /home/wrk/tmp/gemma-release-0.97/glibc-2.25-n6nvxlk2j8/lib/libc.so.6 (0x00007f8b3dd23000)
libblas.so.3 => /home/wrk/tmp/gemma-release-0.97/lapack-3.7.1-nyd19c9ccy/lib/libblas.so.3 (0x00007f8b3dacb000)
/home/wrk/tmp/gemma-release-0.97/glibc-2.25-n6nvxlk2j8/lib/ld-linux-x86-64.so.2 (0x00007f8b41a5c000)
#+END_SRC
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.97$ time ./gemma-gn2-0.97-c760aa0-xqhsidq7h5/bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -gk
GEMMA 0.97 (2017/12/27) by Xiang Zhou and team (C) 2012-2017
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Calculating Relatedness Matrix ...
================================================== 100%
real 0m21.389s
user 0m34.980s
sys 0m4.560s
#+END_SRC
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.97$ time ./gemma-gn2-0.97-c760aa0-xqhsidq7h5/bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -n 1 -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm
GEMMA 0.97 (2017/12/27) by Xiang Zhou and team (C) 2012-2017
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
================================================== 100%
real 0m13.296s
user 0m18.332s
sys 0m5.020s
#+END_SRC
* GEMMA 0.96
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.96$ ldd gemma.linux
linux-vdso.so.1 (0x00007ffd9ee8f000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc2a94a1000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fc2a9183000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fc2a8e01000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc2a8afd000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc2a88e6000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc2a86c9000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc2a832b000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fc2a80ec000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc2a96bb000)
#+END_SRC
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.96$ time ./gemma.linux -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -gk
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs = 12226
## number of analyzed SNPs = 10768
Calculating Relatedness Matrix ...
Reading SNPs ==================================================100.00%
real 0m16.347s
user 0m16.204s
sys 0m0.116s
#+END_SRC
#+BEGIN_SRC bash
lario:~/tmp/gemma-release-0.96$ time ./gemma.linux -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -n 1 -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs = 12226
## number of analyzed SNPs = 10768
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
Reading SNPs ==================================================100.00%
real 0m20.377s
user 0m20.240s
sys 0m0.132s
#+END_SRC
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