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eb01728fb6
blas-benchmarks/slave-cmds.sh
Andrzej Wójtowicz eb01728fb6 added saving host info; 
added saving results in rds files;
renamed benchmark scripts
2016-05-19 19:11:33 +02:00

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#!/bin/bash
WGET_OPTIONS="--no-check-certificate"
MRO_VERSION="3.2.4"
CHECKPOINT_DATE="2016-04-01"
R_BENCHMARK_SCRIPT="benchmark-sample.R"
DIR_BLAS="/opt/blas-libs"
if [ ! -f ./cpuinfo ]; then
echo "Intel processor family information utility not found, aborting..."
exit 1
fi
PROCESSOR_CORES=`./cpuinfo -g | grep -oP 'Cores( +):( +)\K(\d+)'`
PROCESSOR_CPUS=`./cpuinfo -g | grep -oP 'Processors\(CPUs\)( +):( +)\K(\d+)'`
NPROC=${PROCESSOR_CORES}
function mro_install {
echo "Started installing Microsoft R Open and dependencies"
# save host info
./cpuinfo -g | grep -oP 'Processor name( +):( +)\K(.+)' > host-info.log
cat /proc/meminfo | grep -oP 'MemTotal:( +)\K(\d+)' >> host-info.log
lspci -nn | grep -oP "VGA.*\KNVIDIA.*?]" >> host-info.log
# update debian repos & upgrade packages
echo "deb http://snapshot.debian.org/archive/debian/20160411T102554Z/ jessie-backports main" >> /etc/apt/sources.list
apt-get -o Acquire::Check-Valid-Until=false update
DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" upgrade
# install core packages
apt-get -y install build-essential gfortran ed htop libxml2-dev ca-certificates curl libcurl4-openssl-dev gdebi-core sshpass git cpufrequtils cmake initramfs-tools linux-headers-$(uname -r) nvidia-detect bc
# disable CPU throttling for ATLAS multi-threading
echo performance | tee /sys/devices/system/cpu/cpu**/cpufreq/scaling_governor
# hack with Microsoft R Open deps
wget ${WGET_OPTIONS} http://ftp.pl.debian.org/debian/pool/main/libj/libjpeg8/libjpeg8_8d1-2_amd64.deb
gdebi -n libjpeg8_8d1-2_amd64.deb
rm libjpeg8_8d1-2_amd64.deb
# install Microsoft R Open
wget ${WGET_OPTIONS} https://mran.microsoft.com/install/mro/${MRO_VERSION}/MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
gdebi -n MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
rm MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
# make symbolic link to R libraries dir
ln -s /usr/lib64/MRO-${MRO_VERSION}/R-${MRO_VERSION}/lib/R/lib/ /opt/MRO-lib
# prepare R checkpoint
mkdir ~/.checkpoint
Rscript -e "library(checkpoint); checkpoint('${CHECKPOINT_DATE}')"
sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-sample.R
sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-urbanek.R
sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" benchmark-revolution.R
# make directory for BLAS and LAPACK libraries
mkdir -p ${DIR_BLAS}
# clean archives
apt-get clean
echo "Finished installing Microsoft R Open and dependencies"
}
##############################################################
##############################################################
## CPU ##
##############################################################
##############################################################
##############################################################
# netlib #
# - http://www.netlib.org/ #
# - BLAS + LAPACK #
# - single-threaded (reference) #
##############################################################
DIR_NETLIB="${DIR_BLAS}/netlib"
function netlib_install {
echo "Started installing netlib"
mkdir ${DIR_NETLIB}
apt-get -y install libblas3 liblapack3
cp /usr/lib/libblas/libblas.so.3.0 ${DIR_NETLIB}
cp /usr/lib/lapack/liblapack.so.3.0 ${DIR_NETLIB}
apt-get -y purge libblas3 liblapack3
apt-get -y autoremove
apt-get clean
echo "Installed files:"
find ${DIR_NETLIB} -type f
echo "Finished installing netlib."
}
function netlib_remove {
echo "Started removing netlib"
rm ${DIR_NETLIB} -r
echo "Finished removing netlib."
}
function netlib_check {
echo "Started checking netlib"
LD_PRELOAD="${DIR_NETLIB}/libblas.so.3.0 ${DIR_NETLIB}/liblapack.so.3.0" Rscript -e "blasLibName='netlib'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking netlib"
}
##############################################################
# ATLAS (st) #
# - http://math-atlas.sourceforge.net/ #
# - BLAS + LAPACK #
# - single-threaded #
##############################################################
DIR_ATLAS_ST="${DIR_BLAS}/atlas-st"
function atlas_st_install {
echo "Started installing ATLAS (single-threaded)"
mkdir ${DIR_ATLAS_ST}
apt-get -y install libatlas3-base
cp /usr/lib/atlas-base/libatlas.so.3 ${DIR_ATLAS_ST}
cp /usr/lib/atlas-base/atlas/libblas.so.3 ${DIR_ATLAS_ST}
cp /usr/lib/atlas-base/atlas/liblapack.so.3 ${DIR_ATLAS_ST}
apt-get -y purge libatlas3-base
apt-get -y autoremove
apt-get clean
echo "Installed files:"
find ${DIR_ATLAS_ST} -type f
echo "Finished installing ATLAS (single-threaded)"
}
function atlas_st_check {
echo "Started checking ATLAS (single-threaded)"
LD_PRELOAD="${DIR_ATLAS_ST}/libatlas.so.3 ${DIR_ATLAS_ST}/libblas.so.3 ${DIR_ATLAS_ST}/liblapack.so.3" Rscript -e "blasLibName='atlas_st'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking ATLAS (single-threaded)"
}
function atlas_st_remove {
echo "Started removing ATLAS (single-threaded)"
rm ${DIR_ATLAS_ST} -r
echo "Finished removing ATLAS (single-threaded)"
}
##############################################################
# OpenBLAS #
# - http://www.openblas.net/ #
# - BLAS + LAPACK #
# - multi-threaded #
##############################################################
DIR_OPENBLAS="${DIR_BLAS}/openblas"
function openblas_install {
echo "Started installing OpenBLAS"
mkdir ${DIR_OPENBLAS}
apt-get -y install libopenblas-base
cp /usr/lib/libopenblas.so.0 ${DIR_OPENBLAS}
cp /usr/lib/openblas-base/libblas.so.3 ${DIR_OPENBLAS}
cp /usr/lib/openblas-base/liblapack.so.3 ${DIR_OPENBLAS}
apt-get -y purge libopenblas-base
apt-get -y autoremove
apt-get clean
echo "Installed files:"
find ${DIR_OPENBLAS} -type f
echo "Finished installing OpenBLAS"
}
function openblas_check {
echo "Started checking OpenBLAS"
LD_PRELOAD="${DIR_OPENBLAS}/libopenblas.so.0 ${DIR_OPENBLAS}/libblas.so.3 ${DIR_OPENBLAS}/liblapack.so.3" Rscript -e "blasLibName='openblas'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking OpenBLAS"
}
function openblas_remove {
echo "Started removing OpenBLAS"
rm ${DIR_OPENBLAS} -r
echo "Finished removing OpenBLAS"
}
##############################################################
# ATLAS (mt) #
# - http://math-atlas.sourceforge.net/ #
# - BLAS + netlib LAPACK #
# - multi-threaded #
##############################################################
DIR_ATLAS_MT="${DIR_BLAS}/atlas-mt"
function atlas_mt_install {
echo "Started installing ATLAS (multi-threaded)"
mkdir ${DIR_ATLAS_MT}
curl -L https://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.38/atlas3.11.38.tar.bz2/download > atlas3.11.38.tar.bz2
tar -xvf atlas3.11.38.tar.bz2
rm atlas3.11.38.tar.bz2
cd ATLAS
mkdir build
cd build
wget ${WGET_OPTIONS} http://www.netlib.org/lapack/lapack-3.6.0.tgz
sed -i "1423i\thrchk=0;" ../CONFIG/src/config.c
../configure --shared --with-netlib-lapack-tarfile=`pwd`/lapack-3.6.0.tgz
make
cp lib/libtatlas.so ${DIR_ATLAS_MT}
cd ../../
rm -r ATLAS
echo "Installed files:"
find ${DIR_ATLAS_MT} -type f
echo "Finished installing ATLAS (multi-threaded)"
}
function atlas_mt_check {
echo "Started checking ATLAS (multi-threaded)"
LD_PRELOAD="${DIR_ATLAS_MT}/libtatlas.so" Rscript -e "blasLibName='atlas_mt'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking ATLAS (multi-threaded)"
}
function atlas_mt_remove {
echo "Started removing ATLAS (multi-threaded)"
rm ${DIR_ATLAS_MT} -r
echo "Finished removing ATLAS (multi-threaded)"
}
##############################################################
# GotoBLAS2 #
# - https://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/ #
# - BLAS + LAPACK #
# - multi-threaded #
##############################################################
DIR_GOTOBLAS2="${DIR_BLAS}/gotoblas2"
function gotoblas2_install {
echo "Started installing GotoBLAS2"
mkdir ${DIR_GOTOBLAS2}
wget ${WGET_OPTIONS} https://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/SurviveGotoBLAS2_3.141.tar.gz
tar -xvf SurviveGotoBLAS2_3.141.tar.gz
rm SurviveGotoBLAS2_3.141.tar.gz
cd survivegotoblas2-3.141
make REFBLAS_ANTILOGY=1 NO_CBLAS=1 GOTOBLASLIBSONAME=libgoto2blas.so GOTOLAPACKLIBSONAME=libgoto2lapack.so -j ${NPROC}
cp exports/libgoto2blas.so ${DIR_GOTOBLAS2}
cp exports/libgoto2lapack.so ${DIR_GOTOBLAS2}
cd ..
rm -r survivegotoblas2-3.141
Rscript -e "library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE); install.packages('RhpcBLASctl')"
echo "Installed files:"
find ${DIR_GOTOBLAS2} -type f
echo "Finished installing GotoBLAS2"
}
function gotoblas2_check {
echo "Started checking GotoBLAS2"
echo "${DIR_GOTOBLAS2}" > /etc/ld.so.conf.d/gotoblas2.conf
ldconfig
LD_PRELOAD="${DIR_GOTOBLAS2}/libgoto2blas.so ${DIR_GOTOBLAS2}/libgoto2lapack.so" GOTO_NUM_THREADS=${NPROC} Rscript -e "blasLibName='gotoblas2'; library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE); library(RhpcBLASctl); blas_set_num_threads(${NPROC}); source('${R_BENCHMARK_SCRIPT}')"
rm /etc/ld.so.conf.d/gotoblas2.conf
ldconfig
echo "Finished checking GotoBLAS2"
}
function gotoblas2_remove {
echo "Started removing GotoBLAS2"
rm ${DIR_GOTOBLAS2} -r
echo "Finished removing GotoBLAS2"
}
##############################################################
# MKL #
# - https://mran.microsoft.com/documents/rro/multithread/ #
# - BLAS + LAPACK #
# - multi-threaded #
##############################################################
DIR_MKL="${DIR_BLAS}/mkl"
function mkl_install {
echo "Started installing MKL"
mkdir ${DIR_MKL}
wget ${WGET_OPTIONS} https://mran.microsoft.com/install/mro/${MRO_VERSION}/RevoMath-${MRO_VERSION}.tar.gz
tar -xvzf RevoMath-${MRO_VERSION}.tar.gz
rm RevoMath-${MRO_VERSION}.tar.gz
cp RevoMath/mkl/libs/*.so ${DIR_MKL}
rm RevoMath -r
echo "Installed files:"
find ${DIR_MKL} -type f
echo "Finished installing MKL"
}
function mkl_check {
echo "Started checking MKL"
LD_PRELOAD="${DIR_MKL}/libRblas.so ${DIR_MKL}/libRlapack.so ${DIR_MKL}/libmkl_vml_mc3.so ${DIR_MKL}/libmkl_vml_def.so ${DIR_MKL}/libmkl_gnu_thread.so ${DIR_MKL}/libmkl_core.so ${DIR_MKL}/libmkl_gf_lp64.so ${DIR_MKL}/libiomp5.so ${DIR_MKL}/libmkl_gf_ilp64.so" MKL_INTERFACE_LAYER="GNU,LP64" MKL_THREADING_LAYER="GNU" Rscript -e "blasLibName='mkl'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking MKL"
}
function mkl_remove {
echo "Started removing MKL"
rm ${DIR_MKL} -r
echo "Finished removing MKL"
}
##############################################################
# BLIS #
# - https://github.com/flame/blis #
# - BLAS #
# - multi-threaded #
##############################################################
DIR_BLIS="${DIR_BLAS}/blis"
function blis_install {
echo "Started installing BLIS"
mkdir ${DIR_BLIS}
git clone https://github.com/flame/blis.git
cd blis
git checkout 32db0adc218ea4ae370164dbe8d23b41cd3526d3 # 17.05.2016
./configure -t pthreads --enable-shared auto
make -j ${NPROC}
cd ..
cp `find ./blis/ -name "libblis.so"` ${DIR_BLIS}
rm -r blis
echo "Installed files:"
find ${DIR_BLIS} -type f
echo "Finished installing BLIS"
}
function blis_check {
echo "Started checking BLIS"
# auto set threading variables (more or less) according to https://github.com/flame/blis/wiki/Multithreading
CPU_L3_PRESENT=`./cpuinfo -c | grep -coP "^L3"`
CPU_L3_PRIVATE=`./cpuinfo -c | grep -coP "^L3(.*)no sharing"`
CPU_L2_PRIVATE=`./cpuinfo -c | grep -coP "^L2(.*)no sharing"`
CPU_L1_PRIVATE=`./cpuinfo -c | grep -coP "^L1(.*)no sharing"`
COUNT_JC=1
COUNT_IC=1
COUNT_JR=1
COUNT_IR=1
PARALLEL_STEPS=`echo "l(${NPROC})/l(2)" | bc -l | grep -oP "^\d+"`
PARALLEL_I_LOOP=0
PARALLEL_J_LOOP=0
while [ $PARALLEL_STEPS -gt 0 ]
do
if [ $PARALLEL_I_LOOP -lt $PARALLEL_J_LOOP ]; then
if [ ${CPU_L2_PRIVATE} -eq 1 ]; then
COUNT_IC=$((${COUNT_IC} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
elif [ ${CPU_L3_PRESENT} -eq 1 -a ${CPU_L3_PRIVATE} -eq 1 ]; then
COUNT_JC=$((${COUNT_JC} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
elif [ ${CPU_L1_PRIVATE} -eq 1 ]; then
COUNT_JR=$((${COUNT_JR} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
else
COUNT_IR=$((${COUNT_IR} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
fi
elif [ $PARALLEL_J_LOOP -lt $PARALLEL_I_LOOP ]; then
if [ ${CPU_L3_PRESENT} -eq 1 -a ${CPU_L3_PRIVATE} -eq 1 ]; then
COUNT_JC=$((${COUNT_JC} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
elif [ ${CPU_L1_PRIVATE} -eq 1 ]; then
COUNT_JR=$((${COUNT_JR} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
elif [ ${CPU_L2_PRIVATE} -eq 1 ]; then
COUNT_IC=$((${COUNT_IC} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
else
COUNT_IR=$((${COUNT_IR} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
fi
else
if [ ${CPU_L3_PRESENT} -eq 1 -a ${CPU_L3_PRIVATE} -eq 1 ]; then
COUNT_JC=$((${COUNT_JC} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
elif [ ${CPU_L2_PRIVATE} -eq 1 ]; then
COUNT_IC=$((${COUNT_IC} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
elif [ ${CPU_L1_PRIVATE} -eq 1 ]; then
COUNT_JR=$((${COUNT_JR} * 2))
PARALLEL_J_LOOP=$((${PARALLEL_J_LOOP} + 1))
else
COUNT_IR=$((${COUNT_IR} * 2))
PARALLEL_I_LOOP=$((${PARALLEL_I_LOOP} + 1))
fi
fi
((PARALLEL_STEPS--))
done
LD_PRELOAD="${DIR_BLIS}/libblis.so" BLIS_JC_NT=${COUNT_JC} BLIS_IC_NT=${COUNT_IC} BLIS_JR_NT=${COUNT_JR} BLIS_IR_NT=${COUNT_IR} Rscript -e "blasLibName='blis'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking BLIS"
}
function blis_remove {
echo "Started removing BLIS"
rm ${DIR_BLIS} -r
echo "Finished removing BLIS"
}
##############################################################
##############################################################
## GPU ##
##############################################################
##############################################################
##############################################################
# cuBLAS (NVBLAS) #
# - https://developer.nvidia.com/cublas #
# - BLAS #
# - CUDA #
##############################################################
DIR_CUBLAS="${DIR_BLAS}/cublas"
function cublas_install {
if [ $(nvidia-detect | grep -c "No NVIDIA GPU detected.") -eq 1 ]; then
echo "No NVIDIA GPU detected, cuBLAS installation aborted"
return 1
fi
echo "Started installing cuBLAS"
mkdir ${DIR_CUBLAS}
# see: https://nouveau.freedesktop.org/wiki/KernelModeSetting/ and https://askubuntu.com/questions/16998/switch-between-nvidia-current-and-nouveau-without-a-reboot
echo 0 > /sys/class/vtconsole/vtcon1/bind
modprobe -r nouveau
DEBIAN_FRONTEND=noninteractive apt-get install nvidia-driver nvidia-modprobe libcuda1 libnvblas6.5 -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
nvidia-modprobe
echo "
NVBLAS_LOGFILE /dev/null
NVBLAS_CPU_BLAS_LIB ${DIR_MKL}/libRblas.so
NVBLAS_GPU_LIST ALL0
NVBLAS_TILE_DIM 2048
#NVBLAS_AUTOPIN_MEM_ENABLED" > ${DIR_CUBLAS}/nvblas.conf
apt-get clean
echo "Finished installing cuBLAS"
}
# CUDA 7.5 currently supports linux kernel 3.x
#
#function cublas_online_install {
#
# if [ $(nvidia-detect | grep -c "No NVIDIA GPU detected.") -eq 1 ]; then
# echo "No NVIDIA GPU detected, cuBLAS online installation aborted"
# return 1
# fi
#
# echo "Started installing online cuBLAS"
#
# mkdir ${DIR_CUBLAS}
#
# # see: https://nouveau.freedesktop.org/wiki/KernelModeSetting/ and https://askubuntu.com/questions/16998/switch-between-nvidia-current-and-nouveau-without-a-reboot
# echo 0 > /sys/class/vtconsole/vtcon1/bind
# modprobe -r nouveau
#
# # Ubuntu dependencies
# wget ${WGET_OPTIONS} http://de.archive.ubuntu.com/ubuntu/pool/main/x/x-kit/python3-xkit_0.5.0ubuntu2_all.deb
# wget ${WGET_OPTIONS} http://de.archive.ubuntu.com/ubuntu/pool/main/s/screen-resolution-extra/screen-resolution-extra_0.17.1_all.deb
# gdebi -n python3-xkit_0.5.0ubuntu2_all.deb
# gdebi -n screen-resolution-extra_0.17.1_all.deb
#
# wget ${WGET_OPTIONS} http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1504/x86_64/cuda-repo-ubuntu1504_7.5-18_amd64.deb
# dpkg -i cuda-repo-ubuntu1504_7.5-18_amd64.deb
# apt-get -o Acquire::Check-Valid-Until=false update
#
# DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" install cuda-drivers cuda-cublas-7-5 nvidia-modprobe libcuda1-352
#
# nvidia-modprobe
#
# echo "
# NVBLAS_LOGFILE /dev/null
# NVBLAS_CPU_BLAS_LIB ${DIR_MKL}/libRblas.so
# NVBLAS_GPU_LIST ALL0
# NVBLAS_TILE_DIM 2048
# #NVBLAS_AUTOPIN_MEM_ENABLED" > ${DIR_CUBLAS}/nvblas.conf
#
# rm python3-xkit_0.5.0ubuntu2_all.deb
# rm screen-resolution-extra_0.17.1_all.deb
# rm cuda-repo-ubuntu1504_7.5-18_amd64.deb
#
# apt-get clean
#
# echo "Finished installing online cuBLAS"
#}
function cublas_check {
if [ $(nvidia-detect | grep -c "No NVIDIA GPU detected.") -eq 1 ]; then
echo "No NVIDIA GPU detected, cuBLAS check aborted"
return 1
fi
echo "Started checking cuBLAS"
NVBLAS_CONFIG_FILE="${DIR_CUBLAS}/nvblas.conf" LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libnvblas.so.6.5 /usr/lib/x86_64-linux-gnu/libcublas.so.6.5" Rscript -e "blasLibName='cublas'; source('${R_BENCHMARK_SCRIPT}')"
echo "Finished checking cuBLAS"
}
##############################################################
##############################################################
if [ $# -eq 0 ]; then
echo "No arguments supplied"
else
for i in "$@"
do
case "$i" in
nproc_cores)
NPROC=${PROCESSOR_CORES}
;;
nproc_cpus)
NPROC=${PROCESSOR_CPUS}
;;
test_sample)
R_BENCHMARK_SCRIPT="benchmark-sample.R"
;;
test_urbanek)
R_BENCHMARK_SCRIPT="benchmark-urbanek.R"
;;
test_revolution)
R_BENCHMARK_SCRIPT="benchmark-revolution.R"
;;
*)
$i
esac
done
fi
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