rewrote hibench-on-physix.sh in python
this work is preliminary work to add options to make it more generic (eg run something else than hibridon) work related to [https://bugzilla.ipr.univ-rennes.fr/show_bug.cgi?id=3372]
This commit is contained in:
parent
46d7fd1fa7
commit
4e0e3b60bc
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@ -1,259 +0,0 @@
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#!/usr/bin/env bash
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# this script launches jobs to run hibridon benchmarks on physix cluster for the given version of hibridon (commit number)
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function show_usage()
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{
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echo "launches hibridon benchmark jobs on IPR's physix cluster"
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echo
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echo "syntax :"
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echo " $0 <hibridon_version>"
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echo
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echo "example:"
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echo " $0 a3bed1c3ccfbca572003020d3e3d3b1ff3934fad"
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}
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if [ "$#" != "1" ]
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then
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show_usage
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exit 1
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fi
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HIBRIDON_VERSION="$1" # the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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# '53894da48505892bfa05693a52312bacb12c70c9' # latest from branch master as of 10/06/2022 00:30
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# code_version='dd0f413b85cf0f727a5a4e88b2b02d75a28b377f' # latest from branch graffy-issue51 as of 10/06/2022 00:30
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SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}"; )" &> /dev/null && pwd 2> /dev/null; )";
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function substitute_TAG_with_FILEcontents {
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local TAG="${1}"
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local FILE="${2}"
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sed -e "/${TAG}/r ${FILE}" -e "/${TAG}/d"
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}
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function launch_job_for_host_group()
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{
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local hibridon_version="$1" # the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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local host_group_id="$2" # eg 'xeon_gold_6140'
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local compiler_id="$3" # eg 'gfortran' 'ifort'
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local hosts=''
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local num_cores=''
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case "${host_group_id}" in
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'intel_xeon_x5550')
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hosts="${hosts}physix48.ipr.univ-rennes1.fr"
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num_cores='8'
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;;
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'intel_xeon_x5650')
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hosts="${hosts}physix49.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix50.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix51.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix52.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix53.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix54.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix55.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix56.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix57.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix58.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix59.ipr.univ-rennes1.fr"
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num_cores='12'
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;;
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'intel_xeon_e5-2660')
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hosts="${hosts}physix60.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix61.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix62.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix63.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix64.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix65.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix66.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix67.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix68.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix69.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix70.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix71.ipr.univ-rennes1.fr"
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num_cores='16'
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;;
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'intel_xeon_e5-2660v2')
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hosts="${hosts}physix72.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix73.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix74.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix75.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix76.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix77.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix78.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix79.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix80.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix81.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix82.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix84.ipr.univ-rennes1.fr"
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num_cores='20'
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;;
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'intel_xeon_e5-2660v4')
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hosts="${hosts}physix84.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix85.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix86.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix87.ipr.univ-rennes1.fr"
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num_cores='28'
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;;
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'intel_xeon_gold_6140')
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hosts="${hosts}physix88.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix89.ipr.univ-rennes1.fr"
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num_cores='36'
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;;
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'intel_xeon_gold_6154')
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hosts="${hosts}physix90.ipr.univ-rennes1.fr"
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num_cores='72'
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;;
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'intel_xeon_gold_5222')
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hosts="${hosts}physix92.ipr.univ-rennes1.fr"
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num_cores='4'
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;;
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'intel_xeon_gold_6226r')
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hosts="${hosts}physix93.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix94.ipr.univ-rennes1.fr"
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num_cores='32'
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;;
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'intel_xeon_gold_6240r')
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hosts="${hosts}physix99.ipr.univ-rennes1.fr"
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num_cores='48'
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;;
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'intel_xeon_gold_6248r')
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hosts="${hosts}physix95.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix96.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix97.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix98.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix99.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix100.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix101.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix102.ipr.univ-rennes1.fr"
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num_cores='48'
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;;
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'amd_epyc_7282')
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hosts="${hosts}physix12.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix13.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix14.ipr.univ-rennes1.fr"
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hosts="${hosts}|physix15.ipr.univ-rennes1.fr"
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num_cores='32'
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;;
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*)
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error "unhandled host_group_id : ${host_group_id}"
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exit 1
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;;
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esac
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quick_test='arch4_quick' # about 2s on a core i5 8th generation
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representative_test='nh3h2_qma_long' # about 10min on a core i5 8th generation
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benchmark_test="${representative_test}"
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case "${benchmark_test}" in
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'arch4_quick')
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ram_per_core='1G'
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;;
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'nh3h2_qma_long')
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ram_per_core='2.8G' # this was enough on physix48, but maybe we can reduce more
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;;
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*)
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error "unhandled benchmark_test : ${benchmark_test}"
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exit 1
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;;
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esac
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git_repos_url="https://github.com/hibridon/hibridon"
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git_user='g-raffy' # os.environ['HIBRIDON_REPOS_USER']
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git_pass_file="$HOME/.github/personal_access_tokens/bench.hibridon.cluster.ipr.univ-rennes1.fr.pat"
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cmake_options=''
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cmake_options="${cmake_options} -DCMAKE_BUILD_TYPE=Release" # build in release mode for highest performance
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cmake_options="${cmake_options} -DBUILD_TESTING=ON" # enable hibridon tests
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benchmark_command="ctest --output-on-failure -L ^${benchmark_test}\$"
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local env_vars_bash_commands=''
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case "${compiler_id}" in
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'ifort')
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env_vars_bash_commands='module load compilers/ifort/latest'
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cmake_options="${cmake_options} -DCMAKE_Fortran_COMPILER=ifort" # use intel fortran compiler
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cmake_options="${cmake_options} -DBLA_VENDOR=Intel10_64lp" # use 64 bits intel mkl with multithreading
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;;
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'gfortran')
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env_vars_bash_commands=''
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cmake_options="${cmake_options} -DCMAKE_Fortran_COMPILER=gfortran" # use gfortran compiler
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;;
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*)
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error "unhandled compiler_id : ${compiler_id}"
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exit 1
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;;
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esac
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local hibench_root_dir="$GLOBAL_WORK_DIR/graffy/hibridon/benchmarks/starbench"
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mkdir -p "${hibench_root_dir}"
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local this_bench_dir="${hibench_root_dir}/${hibridon_version}/${benchmark_test}/${host_group_id}/${compiler_id}"
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mkdir -p "${this_bench_dir}"
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local starbench_job_path="${this_bench_dir}/starbench.job"
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cat $SCRIPT_DIR/starbench-template.job | substitute_TAG_with_FILEcontents '<include:starbench.py>' "$SCRIPT_DIR/starbench.py" > "${starbench_job_path}"
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chmod a+x "${starbench_job_path}"
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command="${starbench_job_path} \"${git_repos_url}\" \"${git_user}\" \"${git_pass_file}\" \"${hibridon_version}\" \"${cmake_options}\" \"${benchmark_command}\" \"${env_vars_bash_commands}\""
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echo "command = $command"
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# eval $command
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pushd "${this_bench_dir}"
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qsub_command="qsub"
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qsub_command="${qsub_command} -pe smp ${num_cores}"
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qsub_command="${qsub_command} -l \"hostname=${hosts}\""
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qsub_command="${qsub_command} -cwd"
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qsub_command="${qsub_command} -m ae"
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qsub_command="${qsub_command} -l mem_available=${ram_per_core}"
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qsub_command="${qsub_command} -j y" # medge stderr file into stdout file for easier reading of history of events
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qsub_command="${qsub_command} -N hibench_${host_group_id}_${compiler_id}_${hibridon_version}"
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qsub_command="${qsub_command} ${command}"
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# qsub -pe smp "$num_cores" -l "hostname=${hosts}"
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echo "qsub_command = $qsub_command"
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eval $qsub_command
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popd
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}
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function launch_perf_jobs()
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{
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local hibridon_version="$1" # the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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local compilers=''
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compilers="${compilers} gfortran"
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compilers="${compilers} ifort"
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local host_groups=''
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host_groups="${host_groups} intel_xeon_x5550"
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host_groups="${host_groups} intel_xeon_x5650"
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host_groups="${host_groups} intel_xeon_e5-2660"
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host_groups="${host_groups} intel_xeon_e5-2660v2"
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host_groups="${host_groups} intel_xeon_e5-2660v4"
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host_groups="${host_groups} intel_xeon_gold_6140"
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host_groups="${host_groups} intel_xeon_gold_6154"
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host_groups="${host_groups} intel_xeon_gold_5222"
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host_groups="${host_groups} intel_xeon_gold_6226r"
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host_groups="${host_groups} intel_xeon_gold_6240r"
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host_groups="${host_groups} intel_xeon_gold_6248r"
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host_groups="${host_groups} amd_epyc_7282"
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local compiler=''
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local host_group=''
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for compiler in ${compilers}
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do
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for host_group in ${host_groups}
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do
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launch_job_for_host_group "${hibridon_version}" "${host_group}" "${compiler}"
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done
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done
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#launch_job_for_host_group "${hibridon_version}" 'intel_xeon_gold_6140'
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}
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launch_perf_jobs "${HIBRIDON_VERSION}"
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@ -0,0 +1,237 @@
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#!/usr/bin/env python3
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# this script launches jobs to run hibridon benchmarks on physix cluster for the given version of hibridon (commit number)
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from typing import List, Tuple
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from argparse import ArgumentParser
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import os
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from os import getenv, makedirs
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from pathlib import Path
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import subprocess
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HostFqdn = str # eg 'physix90.ipr.univ-rennes1.fr'
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GitCommitTag = str # commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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HostGroupId = str # eg 'xeon_gold_6140'
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CompilerId = str # eg 'gfortran'
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def substitute_tag_with_filecontents(input_file_path: Path, tag: str, contents_file: Path, output_file_path: Path):
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contents = open(contents_file, 'rt', encoding='utf8').read()
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with open(input_file_path, 'rt', encoding='utf8') as template_file, open(output_file_path, 'wt', encoding='utf8') as out_file:
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for template_line in template_file.readlines():
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line = template_line.replace(tag, contents)
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out_file.write(line)
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def get_host_group_info(host_group_id: HostGroupId) -> Tuple[List[HostFqdn], int]:
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if host_group_id == 'intel_xeon_x5550':
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hosts = ['physix48.ipr.univ-rennes1.fr']
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num_cores = '8'
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elif host_group_id == 'intel_xeon_x5650':
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hosts = [
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'physix49.ipr.univ-rennes1.fr',
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'physix50.ipr.univ-rennes1.fr',
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'physix51.ipr.univ-rennes1.fr',
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'physix52.ipr.univ-rennes1.fr',
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'physix53.ipr.univ-rennes1.fr',
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'physix54.ipr.univ-rennes1.fr',
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'physix55.ipr.univ-rennes1.fr',
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'physix56.ipr.univ-rennes1.fr',
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'physix57.ipr.univ-rennes1.fr',
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'physix58.ipr.univ-rennes1.fr',
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'physix59.ipr.univ-rennes1.fr',]
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num_cores = '12'
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elif host_group_id == 'intel_xeon_e5-2660':
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hosts = [
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'physix60.ipr.univ-rennes1.fr',
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'physix61.ipr.univ-rennes1.fr',
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'physix62.ipr.univ-rennes1.fr',
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'physix63.ipr.univ-rennes1.fr',
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'physix64.ipr.univ-rennes1.fr',
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'physix65.ipr.univ-rennes1.fr',
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'physix66.ipr.univ-rennes1.fr',
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'physix67.ipr.univ-rennes1.fr',
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'physix68.ipr.univ-rennes1.fr',
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'physix69.ipr.univ-rennes1.fr',
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'physix70.ipr.univ-rennes1.fr',
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'physix71.ipr.univ-rennes1.fr']
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num_cores = '16'
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elif host_group_id == 'intel_xeon_e5-2660v2':
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hosts = [
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'physix72.ipr.univ-rennes1.fr',
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'physix73.ipr.univ-rennes1.fr',
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'physix74.ipr.univ-rennes1.fr',
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'physix75.ipr.univ-rennes1.fr',
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'physix76.ipr.univ-rennes1.fr',
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'physix77.ipr.univ-rennes1.fr',
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'physix78.ipr.univ-rennes1.fr',
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'physix79.ipr.univ-rennes1.fr',
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'physix80.ipr.univ-rennes1.fr',
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'physix81.ipr.univ-rennes1.fr',
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'physix82.ipr.univ-rennes1.fr',
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'physix84.ipr.univ-rennes1.fr']
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num_cores = '20'
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elif host_group_id == 'intel_xeon_e5-2660v4':
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hosts = [
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'physix84.ipr.univ-rennes1.fr',
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'physix85.ipr.univ-rennes1.fr',
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'physix86.ipr.univ-rennes1.fr',
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'physix87.ipr.univ-rennes1.fr']
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num_cores = '28'
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elif host_group_id == 'intel_xeon_gold_6140':
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hosts = [
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'physix88.ipr.univ-rennes1.fr',
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'physix89.ipr.univ-rennes1.fr']
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num_cores = '36'
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elif host_group_id == 'intel_xeon_gold_6154':
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hosts = [
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'physix90.ipr.univ-rennes1.fr']
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num_cores = '72'
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elif host_group_id == 'intel_xeon_gold_5222':
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hosts = [
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'physix92.ipr.univ-rennes1.fr']
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num_cores = '4'
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elif host_group_id == 'intel_xeon_gold_6226r':
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hosts = [
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'physix93.ipr.univ-rennes1.fr',
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'physix94.ipr.univ-rennes1.fr']
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num_cores = '32'
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elif host_group_id == 'intel_xeon_gold_6240r':
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hosts = [
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'physix99.ipr.univ-rennes1.fr']
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num_cores = '48'
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elif host_group_id == 'intel_xeon_gold_6248r':
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hosts = [
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'physix95.ipr.univ-rennes1.fr',
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'physix96.ipr.univ-rennes1.fr',
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'physix97.ipr.univ-rennes1.fr',
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'physix98.ipr.univ-rennes1.fr',
|
||||
'physix99.ipr.univ-rennes1.fr',
|
||||
'physix100.ipr.univ-rennes1.fr',
|
||||
'physix101.ipr.univ-rennes1.fr',
|
||||
'physix102.ipr.univ-rennes1.fr']
|
||||
num_cores = '48'
|
||||
elif host_group_id == 'amd_epyc_7282':
|
||||
hosts = [
|
||||
'physix12.ipr.univ-rennes1.fr',
|
||||
'physix13.ipr.univ-rennes1.fr',
|
||||
'physix14.ipr.univ-rennes1.fr',
|
||||
'physix15.ipr.univ-rennes1.fr']
|
||||
num_cores = '32'
|
||||
else:
|
||||
assert f"unhandled host_group_id : {host_group_id}"
|
||||
return (hosts, num_cores)
|
||||
|
||||
|
||||
def launch_job_for_host_group(hibridon_version: GitCommitTag, host_group_id: HostGroupId, compiler_id: CompilerId):
|
||||
|
||||
(hosts, num_cores) = get_host_group_info(host_group_id)
|
||||
|
||||
# quick_test = 'arch4_quick' # about 2s on a core i5 8th generation
|
||||
representative_test = 'nh3h2_qma_long' # about 10min on a core i5 8th generation
|
||||
benchmark_test = representative_test
|
||||
if benchmark_test == 'arch4_quick':
|
||||
ram_per_core = '1G'
|
||||
elif benchmark_test == 'nh3h2_qma_long':
|
||||
ram_per_core = '2.8G' # this was enough on physix48, but maybe we can reduce more
|
||||
else:
|
||||
assert f'unhandled benchmark_test : {benchmark_test}'
|
||||
|
||||
git_repos_url = 'https://github.com/hibridon/hibridon'
|
||||
git_user = 'g-raffy' # os.environ['HIBRIDON_REPOS_USER']
|
||||
git_pass_file = f'{getenv("HOME")}/.github/personal_access_tokens/bench.hibridon.cluster.ipr.univ-rennes1.fr.pat'
|
||||
cmake_options = [
|
||||
'-DCMAKE_BUILD_TYPE=Release', # build in release mode for highest performance
|
||||
'-DBUILD_TESTING=ON' # enable hibridon tests
|
||||
]
|
||||
|
||||
benchmark_command = f'ctest --output-on-failure -L ^{benchmark_test}$'
|
||||
|
||||
env_vars_bash_commands = ''
|
||||
if compiler_id == 'ifort':
|
||||
env_vars_bash_commands = 'module load compilers/ifort/latest'
|
||||
cmake_options.append('-DCMAKE_Fortran_COMPILER=ifort') # use intel fortran compiler
|
||||
cmake_options.append('-DBLA_VENDOR=Intel10_64lp') # use 64 bits intel mkl with multithreading
|
||||
elif compiler_id == 'gfortran':
|
||||
env_vars_bash_commands = ''
|
||||
cmake_options.append('-DCMAKE_Fortran_COMPILER=gfortran') # use gfortran compiler
|
||||
else:
|
||||
assert f'unhandled compiler_id : {compiler_id}'
|
||||
|
||||
hibench_root_dir = Path(f'{getenv("GLOBAL_WORK_DIR")}/graffy/hibridon/benchmarks/starbench')
|
||||
makedirs(hibench_root_dir, exist_ok=True)
|
||||
|
||||
this_bench_dir = Path(f'{hibench_root_dir}/{hibridon_version}/{benchmark_test}/{host_group_id}/{compiler_id}')
|
||||
makedirs(this_bench_dir, exist_ok=True)
|
||||
|
||||
starbench_job_path = this_bench_dir / 'starbench.job'
|
||||
this_file_path = os.path.realpath(__file__)
|
||||
scripts_dir = this_file_path.parent
|
||||
|
||||
# create the job file (which embeds starbench.py)
|
||||
substitute_tag_with_filecontents(input_file_path=scripts_dir / 'starbench-template.job', tag='<include:starbench.py>', contents_file=scripts_dir / 'starbench.py', output_file_path=starbench_job_path)
|
||||
subprocess.run(f'chmod a+x {starbench_job_path}', check=True)
|
||||
|
||||
command = f'{starbench_job_path} "{git_repos_url}" "{git_user}" "{git_pass_file}" "{hibridon_version}" "{cmake_options}" "{benchmark_command}" "{env_vars_bash_commands}"'
|
||||
print(f'command = {command}')
|
||||
|
||||
qsub_command = 'qsub'
|
||||
qsub_command += f' -pe smp {num_cores}'
|
||||
qsub_command += f' -l "hostname={hosts}"'
|
||||
qsub_command += ' -cwd'
|
||||
qsub_command += ' -m ae'
|
||||
qsub_command += f' -l mem_available={ram_per_core}'
|
||||
qsub_command += ' -j y' # merge stderr file into stdout file for easier reading of history of events
|
||||
qsub_command += f' -N hibench_{host_group_id}_{compiler_id}_{hibridon_version}'
|
||||
qsub_command += f' {command}'
|
||||
print(f'qsub_command = {qsub_command}')
|
||||
|
||||
subprocess.run(qsub_command, cwd=this_bench_dir, check=True)
|
||||
|
||||
|
||||
def launch_perf_jobs(hibridon_version: GitCommitTag):
|
||||
"""
|
||||
hibridon_version: the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
|
||||
"""
|
||||
|
||||
compilers = [
|
||||
'gfortran'
|
||||
'ifort'
|
||||
]
|
||||
|
||||
host_groups = [
|
||||
'intel_xeon_x5550',
|
||||
'intel_xeon_x5650',
|
||||
'intel_xeon_e5-2660',
|
||||
'intel_xeon_e5-2660v2',
|
||||
'intel_xeon_e5-2660v4',
|
||||
'intel_xeon_gold_6140',
|
||||
'intel_xeon_gold_6154',
|
||||
'intel_xeon_gold_5222',
|
||||
'intel_xeon_gold_6226r',
|
||||
'intel_xeon_gold_6240r',
|
||||
'intel_xeon_gold_6248r',
|
||||
'amd_epyc_7282',
|
||||
]
|
||||
|
||||
for compiler in compilers:
|
||||
for host_group in host_groups:
|
||||
launch_job_for_host_group(hibridon_version, host_group, compiler)
|
||||
|
||||
|
||||
def main():
|
||||
arg_parser = ArgumentParser(description='launches hibridon benchmark jobs on IPR\'s physix cluster', epilog='example:\n --commit-id a3bed1c3ccfbca572003020d3e3d3b1ff3934fad')
|
||||
arg_parser.add_argument('--commit-id', type=str, required=True, help='the commit id of the version of code to benchmark')
|
||||
|
||||
args = arg_parser.parse_args()
|
||||
hibridon_version = args.commit_id
|
||||
# the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
|
||||
# '53894da48505892bfa05693a52312bacb12c70c9' # latest from branch master as of 10/06/2022 00:30
|
||||
# code_version='dd0f413b85cf0f727a5a4e88b2b02d75a28b377f' # latest from branch graffy-issue51 as of 10/06/2022 00:30
|
||||
|
||||
launch_perf_jobs(hibridon_version)
|
||||
|
||||
|
||||
main()
|
||||
Loading…
Reference in New Issue