mirror of
https://github.com/andre-wojtowicz/blas-benchmarks
synced 2024-11-03 20:50:27 +01:00
Andrzej Wójtowicz
fd5e9d734f
externalized checkpoint to bash script; added functions for each library; added info about current process
468 lines
15 KiB
Bash
468 lines
15 KiB
Bash
#!/bin/bash
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WGET_OPTIONS="--no-check-certificate"
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MRO_VERSION="3.2.4"
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CHECKPOINT_DATE="2016-04-01"
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R_SAMPLE_BENCHMARK="Rscript sample-benchmark.R"
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DIR_BLAP="/opt/blap-lib"
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function mro_install {
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echo "Started installing Microsoft R Open and dependencies."
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# update debian repos & upgrade packages
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apt-get update
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DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" upgrade
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# install new packages for R
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apt-get -y install build-essential gfortran ed htop libxml2-dev ca-certificates curl libcurl4-openssl-dev gdebi-core sshpass git cpufrequtils
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# disable CPU throttling for ATLAS multi-threading
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echo performance | tee /sys/devices/system/cpu/cpu**/cpufreq/scaling_governor
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# hack with Microsoft R Open deps
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wget ${WGET_OPTIONS} http://ftp.pl.debian.org/debian/pool/main/libj/libjpeg8/libjpeg8_8d1-2_amd64.deb
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gdebi -n libjpeg8_8d1-2_amd64.deb
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rm libjpeg8_8d1-2_amd64.deb
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# install Microsoft R Open
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wget ${WGET_OPTIONS} https://mran.microsoft.com/install/mro/${MRO_VERSION}/MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
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gdebi -n MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
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rm MRO-${MRO_VERSION}-Ubuntu-15.4.x86_64.deb
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# make symbolic link to R libraries dir
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ln -s /usr/lib64/MRO-${MRO_VERSION}/R-${MRO_VERSION}/lib/R/lib/ /opt/MRO-lib
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# prepare R checkpoint
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mkdir ~/.checkpoint
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Rscript -e "library(checkpoint); checkpoint('${CHECKPOINT_DATE}')"
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sed -i "1i\library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE)" sample-benchmark.R
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# make directory for BLAS and LAPACK libraries
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mkdir -p ${DIR_BLAP}
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# clean archives
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apt-get clean
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echo "Finished installing Microsoft R Open and dependencies."
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}
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##############################################################
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##############################################################
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## CPU ##
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##############################################################
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##############################################################
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##############################################################
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# netlib #
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# - http://www.netlib.org/ #
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# - BLAS + LAPACK #
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# - single-threaded (reference) #
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##############################################################
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DIR_NETLIB="${DIR_BLAP}/netlib"
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function netlib_install {
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echo "Started installing netlib."
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mkdir ${DIR_NETLIB}
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apt-get -y install libblas3 liblapack3
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cp /usr/lib/libblas/libblas.so.3.0 ${DIR_NETLIB}
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cp /usr/lib/lapack/liblapack.so.3.0 ${DIR_NETLIB}
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apt-get -y purge libblas3 liblapack3
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apt-get clean
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echo "Installed files:"
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find ${DIR_NETLIB} -type f
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echo "Finished installing netlib."
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}
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function netlib_check {
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echo "Started checking netlib."
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LD_PRELOAD="${DIR_NETLIB}/libblas.so.3.0 ${DIR_NETLIB}/liblapack.so.3.0" ${R_SAMPLE_BENCHMARK}
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echo "Finished checking netlib."
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}
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##############################################################
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# ATLAS (st) #
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# - http://math-atlas.sourceforge.net/ #
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# - BLAS + LAPACK #
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# - single-threaded #
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##############################################################
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DIR_ATLAS_ST="${DIR_BLAP}/atlas-st"
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function atlas_st_install {
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echo "Started installing ATLAS (single-threaded)."
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mkdir ${DIR_ATLAS_ST}
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apt-get -y install libatlas3-base
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cp /usr/lib/atlas-base/libatlas.so.3 ${DIR_ATLAS_ST}
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cp /usr/lib/atlas-base/atlas/libblas.so.3 ${DIR_ATLAS_ST}
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cp /usr/lib/atlas-base/atlas/liblapack.so.3 ${DIR_ATLAS_ST}
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apt-get -y purge libatlas3-base
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apt-get clean
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echo "Installed files:"
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find ${DIR_ATLAS_ST} -type f
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echo "Finished installing ATLAS (single-threaded)."
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}
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function atlas_st_check {
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echo "Started checking ATLAS (single-threaded)."
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LD_PRELOAD="${DIR_ATLAS_ST}/libatlas.so.3 ${DIR_ATLAS_ST}/libblas.so.3 ${DIR_ATLAS_ST}/liblapack.so.3" ${R_SAMPLE_BENCHMARK}
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echo "Finished checking ATLAS (single-threaded)."
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}
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##############################################################
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# OpenBLAS #
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# - http://www.openblas.net/ #
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# - BLAS + LAPACK #
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# - multi-threaded #
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##############################################################
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DIR_OPENBLAS="${DIR_BLAP}/openblas"
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function openblas_install {
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echo "Started installing OpenBLAS."
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mkdir ${DIR_OPENBLAS}
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apt-get -y install libopenblas-base
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cp /usr/lib/libopenblas.so.0 ${DIR_OPENBLAS}
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cp /usr/lib/openblas-base/libblas.so.3 ${DIR_OPENBLAS}
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cp /usr/lib/openblas-base/liblapack.so.3 ${DIR_OPENBLAS}
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apt-get -y purge libopenblas-base
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apt-get clean
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echo "Installed files:"
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find ${DIR_OPENBLAS} -type f
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echo "Finished installing OpenBLAS."
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}
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function openblas_check {
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echo "Started checking OpenBLAS."
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LD_PRELOAD="${DIR_OPENBLAS}/libopenblas.so.0 ${DIR_OPENBLAS}/libblas.so.3 ${DIR_OPENBLAS}/liblapack.so.3" ${R_SAMPLE_BENCHMARK}
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echo "Finished checking OpenBLAS."
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}
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##############################################################
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# ATLAS (mt) #
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# - http://math-atlas.sourceforge.net/ #
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# - BLAS + netlib LAPACK #
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# - multi-threaded #
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##############################################################
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DIR_ATLAS_MT="${DIR_BLAP}/atlas-mt"
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function atlas_mt_install {
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echo "Started installing ATLAS (multi-threaded)."
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mkdir ${DIR_ATLAS_MT}
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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
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tar -xvf atlas3.11.38.tar.bz2
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rm atlas3.11.38.tar.bz2
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cd ATLAS
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mkdir build
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cd build
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wget ${WGET_OPTIONS} http://www.netlib.org/lapack/lapack-3.6.0.tgz
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../configure --shared --with-netlib-lapack-tarfile=`pwd`/lapack-3.6.0.tgz
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make
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cp lib/libtatlas.so ${DIR_ATLAS_MT}
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cd ../../
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rm -r ATLAS
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echo "Installed files:"
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find ${DIR_ATLAS_MT} -type f
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echo "Finished installing ATLAS (multi-threaded)."
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}
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function atlas_mt_check {
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echo "Started checking ATLAS (multi-threaded)."
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LD_PRELOAD="${DIR_ATLAS_MT}/libtatlas.so" ${R_SAMPLE_BENCHMARK}
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echo "Finished checking ATLAS (multi-threaded)."
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}
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##############################################################
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# GotoBLAS2 #
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# - https://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/ #
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# - BLAS + LAPACK #
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# - multi-threaded #
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##############################################################
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DIR_GOTOBLAS2="${DIR_BLAP}/gotoblas2"
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function gotoblas2_install {
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echo "Started installing GotoBLAS2."
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mkdir ${DIR_GOTOBLAS2}
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wget ${WGET_OPTIONS} https://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/SurviveGotoBLAS2_3.141.tar.gz
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tar -xvf SurviveGotoBLAS2_3.141.tar.gz
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rm SurviveGotoBLAS2_3.141.tar.gz
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cd survivegotoblas2-3.141
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make REFBLAS_ANTILOGY=1 NO_CBLAS=1 GOTOBLASLIBSONAME=libgoto2blas.so GOTOLAPACKLIBSONAME=libgoto2lapack.so -j `nproc`
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cp exports/libgoto2blas.so ${DIR_GOTOBLAS2}
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cp exports/libgoto2lapack.so ${DIR_GOTOBLAS2}
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cd ..
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rm -r survivegotoblas2-3.141
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echo "${DIR_GOTOBLAS2}" > /etc/ld.so.conf.d/gotoblas2.conf
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ldconfig
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Rscript -e "library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE); install.packages('RhpcBLASctl')"
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echo "Installed files:"
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find ${DIR_GOTOBLAS2} -type f
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echo "Finished installing GotoBLAS2."
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}
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function gotoblas2_check {
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echo "Started checking GotoBLAS2."
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sed "2i\library(RhpcBLASctl); blas_set_num_threads(`nproc`)" sample-benchmark.R > sample-benchmark-gotoblas2.R
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LD_PRELOAD="${DIR_GOTOBLAS2}/libgoto2blas.so ${DIR_GOTOBLAS2}/libgoto2lapack.so" GOTO_NUM_THREADS=`nproc` Rscript sample-benchmark-gotoblas2.R
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rm sample-benchmark-gotoblas2.R
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echo "Finished checking GotoBLAS2."
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}
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##############################################################
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# MKL #
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# - https://mran.microsoft.com/documents/rro/multithread/ #
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# - BLAS + LAPACK #
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# - multi-threaded #
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##############################################################
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DIR_MKL="${DIR_BLAP}/mkl"
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function mkl_install {
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echo "Started installing MKL."
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mkdir ${DIR_MKL}
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wget ${WGET_OPTIONS} https://mran.microsoft.com/install/mro/${MRO_VERSION}/RevoMath-${MRO_VERSION}.tar.gz
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tar -xvzf RevoMath-${MRO_VERSION}.tar.gz
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rm RevoMath-${MRO_VERSION}.tar.gz
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cp RevoMath/mkl/libs/*.so ${DIR_MKL}
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rm RevoMath -r
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echo "Installed files:"
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find ${DIR_MKL} -type f
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echo "Finished installing MKL."
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}
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function mkl_check {
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echo "Started checking MKL."
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LD_PRELOAD="${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" ${R_SAMPLE_BENCHMARK}
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echo "Finished checking MKL."
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}
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##############################################################
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# BLIS #
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# - https://github.com/flame/blis #
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# - BLAS #
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# - multi-threaded #
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##############################################################
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DIR_BLIS="${DIR_BLAP}/blis"
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function blis_install {
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echo "Started installing BLIS."
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mkdir ${DIR_BLIS}
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git clone https://github.com/flame/blis.git
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cd blis
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git checkout 0b01d355ae861754ae2da6c9a545474af010f02e
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./configure -t pthreads --enable-shared auto
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make -j `nproc`
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cd ..
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cp `find ./blis/ -name "libblis.so"` ${DIR_BLIS}
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rm -r blis
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echo "Installed files:"
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find ${DIR_BLIS} -type f
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echo "Finished installing BLIS."
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}
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function blis_check {
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echo "Started checking BLIS."
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# TODO: auto set variables according to https://github.com/flame/blis/wiki/Multithreading
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LD_PRELOAD="${DIR_BLIS}/libblis.so" BLIS_JC_NT=2 BLIS_IC_NT=1 BLIS_JR_NT=1 BLIS_IR_NT=1 ${R_SAMPLE_BENCHMARK}
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echo "Finished checking BLIS."
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}
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##############################################################
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##############################################################
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## GPU ##
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##############################################################
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##############################################################
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##############################################################
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# clBLAS #
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# - https://github.com/clMathLibraries/clBLAS #
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# - BLAS #
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# - OpenCL #
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##############################################################
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function clblas_install {
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echo "Started installing clBLAS."
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wget ${WGET_OPTIONS} https://github.com/clMathLibraries/clBLAS/archive/v2.10.tar.gz -O clBLAS-2.10.tar.gz
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tar -xvzf clBLAS-2.10.tar.gz
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rm clBLAS-2.10.tar.gz
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#cd clBLAS-2.10
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#
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#cd ..
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echo "TODO!"
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echo "Finished installing clBLAS."
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}
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##############################################################
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# cuBLAS (NVBLAS) #
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# - https://developer.nvidia.com/cublas #
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# - BLAS #
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# - CUDA #
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##############################################################
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function cublas_install {
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echo "Started installing cuBLAS."
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# TODO: cuSOLVE (dense, LAPACK)?
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mkdir /opt/blap-lib/cublas
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# Ubuntu dependencies
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wget ${WGET_OPTIONS} http://de.archive.ubuntu.com/ubuntu/pool/main/x/x-kit/python3-xkit_0.5.0ubuntu2_all.deb
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wget ${WGET_OPTIONS} http://de.archive.ubuntu.com/ubuntu/pool/main/s/screen-resolution-extra/screen-resolution-extra_0.17.1_all.deb
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gdebi -n python3-xkit_0.5.0ubuntu2_all.deb
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gdebi -n screen-resolution-extra_0.17.1_all.deb
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wget ${WGET_OPTIONS} http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1504/x86_64/cuda-repo-ubuntu1504_7.5-18_amd64.deb
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gdebi -n cuda-repo-ubuntu1504_7.5-18_amd64.deb
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rm cuda-repo-ubuntu1504_7.5-18_amd64.deb
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apt-get update
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apt-get install cuda
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echo "NVBLAS_LOGFILE nvblas.log
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NVBLAS_CPU_BLAS_LIB /opt/blap-lib/netlib/libblas.so.3.0
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NVBLAS_GPU_LIST ALL0
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NVBLAS_TILE_DIM 2048
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NVBLAS_AUTOPIN_MEM_ENABLED" > /opt/blap-lib/cublas/nvblas.conf
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apt-get clean
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# run R:
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# NVBLAS_CONFIG_FILE=/opt/blap-lib/cublas/nvblas.conf LD_PRELOAD="/usr/local/cuda-7.5/targets/x86_64-linux/lib/libnvblas.so.7.5 /usr/local/cuda-7.5/targets/x86_64-linux/lib/libcublas.so.7.5" R
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echo "Finished installing cuBLAS."
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}
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##############################################################
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# MAGMA #
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# - http://icl.cs.utk.edu/magma/software/ #
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# - LAPACK #
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# - OpenCL, CUDA #
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##############################################################
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function magma_install {
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echo "Started installing MAGMA."
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echo "TODO!"
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echo "Finished installing MAGMA."
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}
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##############################################################
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# CULA #
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# - http://www.culatools.com/ #
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# - LAPACK #
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# - CUDA #
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##############################################################
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function cula_install {
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echo "Started installing CULA."
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echo "TODO!"
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echo "Finished installing CULA."
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}
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##############################################################
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##############################################################
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if [ $# -eq 0 ]; then
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echo "No arguments supplied"
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else
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for i in "$@"
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do
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$i
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done
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fi
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