#!/bin/bash WGET_OPTIONS="--no-check-certificate" MRO_VERSION="3.2.4" CHECKPOINT_DATE="2016-04-01" R_SAMPLE_BENCHMARK="Rscript sample-benchmark.R" DIR_BLAP="/opt/blap-lib" function mro_install { echo "Started installing Microsoft R Open and dependencies." # update debian repos & upgrade packages apt-get update DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" upgrade # install new packages for R apt-get -y install build-essential gfortran ed htop libxml2-dev ca-certificates curl libcurl4-openssl-dev gdebi-core sshpass git cpufrequtils # 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)" sample-benchmark.R # make directory for BLAS and LAPACK libraries mkdir -p ${DIR_BLAP} # clean archives apt-get clean echo "Finished installing Microsoft R Open and dependencies." } ############################################################## ############################################################## ## CPU ## ############################################################## ############################################################## ############################################################## # netlib # # - http://www.netlib.org/ # # - BLAS + LAPACK # # - single-threaded (reference) # ############################################################## DIR_NETLIB="${DIR_BLAP}/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 clean echo "Installed files:" find ${DIR_NETLIB} -type f echo "Finished installing netlib." } function netlib_check { echo "Started checking netlib." LD_PRELOAD="${DIR_NETLIB}/libblas.so.3.0 ${DIR_NETLIB}/liblapack.so.3.0" ${R_SAMPLE_BENCHMARK} echo "Finished checking netlib." } ############################################################## # ATLAS (st) # # - http://math-atlas.sourceforge.net/ # # - BLAS + LAPACK # # - single-threaded # ############################################################## DIR_ATLAS_ST="${DIR_BLAP}/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 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" ${R_SAMPLE_BENCHMARK} echo "Finished checking ATLAS (single-threaded)." } ############################################################## # OpenBLAS # # - http://www.openblas.net/ # # - BLAS + LAPACK # # - multi-threaded # ############################################################## DIR_OPENBLAS="${DIR_BLAP}/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 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" ${R_SAMPLE_BENCHMARK} echo "Finished checking OpenBLAS." } ############################################################## # ATLAS (mt) # # - http://math-atlas.sourceforge.net/ # # - BLAS + netlib LAPACK # # - multi-threaded # ############################################################## DIR_ATLAS_MT="${DIR_BLAP}/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 ../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" ${R_SAMPLE_BENCHMARK} echo "Finished checking ATLAS (multi-threaded)." } ############################################################## # GotoBLAS2 # # - https://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/ # # - BLAS + LAPACK # # - multi-threaded # ############################################################## DIR_GOTOBLAS2="${DIR_BLAP}/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 ${DIR_GOTOBLAS2} cd .. rm -r survivegotoblas2-3.141 echo "${DIR_GOTOBLAS2}" > /etc/ld.so.conf.d/gotoblas2.conf ldconfig Rscript -e "library(checkpoint); checkpoint('${CHECKPOINT_DATE}', scanForPackages=FALSE, verbose=FALSE); install.packages('RhpcBLASctl')" echo "Installed files:" find ${DIR_GOTOBLAS2} -type f echo "Finished installing GotoBLAS2." } function gotoblas2_check { echo "Started checking GotoBLAS2." sed "2i\library(RhpcBLASctl); blas_set_num_threads(`nproc`)" sample-benchmark.R > sample-benchmark-gotoblas2.R LD_PRELOAD="${DIR_GOTOBLAS2}/libgoto2blas.so ${DIR_GOTOBLAS2}/libgoto2lapack.so" GOTO_NUM_THREADS=`nproc` Rscript sample-benchmark-gotoblas2.R rm sample-benchmark-gotoblas2.R echo "Finished checking GotoBLAS2." } ############################################################## # MKL # # - https://mran.microsoft.com/documents/rro/multithread/ # # - BLAS + LAPACK # # - multi-threaded # ############################################################## DIR_MKL="${DIR_BLAP}/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" ${R_SAMPLE_BENCHMARK} echo "Finished checking MKL." } ############################################################## # BLIS # # - https://github.com/flame/blis # # - BLAS # # - multi-threaded # ############################################################## DIR_BLIS="${DIR_BLAP}/blis" function blis_install { echo "Started installing BLIS." mkdir ${DIR_BLIS} git clone https://github.com/flame/blis.git cd blis git checkout 0b01d355ae861754ae2da6c9a545474af010f02e ./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 ${DIR_BLIS} -type f echo "Finished installing BLIS." } function blis_check { echo "Started checking BLIS." # TODO: auto set variables according to https://github.com/flame/blis/wiki/Multithreading LD_PRELOAD="${DIR_BLIS}/libblis.so" BLIS_JC_NT=2 BLIS_IC_NT=1 BLIS_JR_NT=1 BLIS_IR_NT=1 ${R_SAMPLE_BENCHMARK} echo "Finished checking BLIS." } ############################################################## ############################################################## ## GPU ## ############################################################## ############################################################## ############################################################## # clBLAS # # - https://github.com/clMathLibraries/clBLAS # # - BLAS # # - OpenCL # ############################################################## function clblas_install { echo "Started installing clBLAS." wget ${WGET_OPTIONS} https://github.com/clMathLibraries/clBLAS/archive/v2.10.tar.gz -O clBLAS-2.10.tar.gz tar -xvzf clBLAS-2.10.tar.gz rm clBLAS-2.10.tar.gz #cd clBLAS-2.10 # #cd .. echo "TODO!" echo "Finished installing clBLAS." } ############################################################## # cuBLAS (NVBLAS) # # - https://developer.nvidia.com/cublas # # - BLAS # # - CUDA # ############################################################## function cublas_install { echo "Started installing cuBLAS." # TODO: cuSOLVE (dense, LAPACK)? mkdir /opt/blap-lib/cublas # 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 gdebi -n cuda-repo-ubuntu1504_7.5-18_amd64.deb rm cuda-repo-ubuntu1504_7.5-18_amd64.deb apt-get update apt-get install cuda echo "NVBLAS_LOGFILE nvblas.log NVBLAS_CPU_BLAS_LIB /opt/blap-lib/netlib/libblas.so.3.0 NVBLAS_GPU_LIST ALL0 NVBLAS_TILE_DIM 2048 NVBLAS_AUTOPIN_MEM_ENABLED" > /opt/blap-lib/cublas/nvblas.conf apt-get clean # run R: # 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 echo "Finished installing cuBLAS." } ############################################################## # MAGMA # # - http://icl.cs.utk.edu/magma/software/ # # - LAPACK # # - OpenCL, CUDA # ############################################################## function magma_install { echo "Started installing MAGMA." echo "TODO!" echo "Finished installing MAGMA." } ############################################################## # CULA # # - http://www.culatools.com/ # # - LAPACK # # - CUDA # ############################################################## function cula_install { echo "Started installing CULA." echo "TODO!" echo "Finished installing CULA." } ############################################################## ############################################################## if [ $# -eq 0 ]; then echo "No arguments supplied" else for i in "$@" do $i done fi