made changes needed to get hibridon benchmark running on physix (ipr's cluster):
- added in `starbench` the option to choose which cmake executable to use - fixed typos in sge environment variables - added job submit mechanism With these changes, hibridon's benchmark succeeded on physix48
This commit is contained in:
parent
6715cd1714
commit
936dfa793a
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@ -8,16 +8,22 @@ code_version="$4" # git branch id or commit id eg : 'a3bed1c3ccfbca572003020d3e
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cmake_options="$5" # eg '-DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON'
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benchmark_command="$6" # eg 'ctest -L ^arch4_quick$'
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if [ "${JOBID}" = '' ]
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cmake_path='/opt/cmake/cmake-3.23.0/bin/cmake'
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if [ "${JOB_ID}" = '' ]
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then
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# this script is not executed by sge... set dummy values for test
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TMP_DIR=/tmp
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JOBID=666666
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TMPDIR=/tmp
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JOB_ID=666666
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NSLOTS=2
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fi
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echo "Executing on $(hostname)"
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temp_dir=${TMP_DIR}/$(whoami)/${JOBID}
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echo "Executing job ${JOB_ID} on $(hostname)"
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temp_dir=${TMPDIR}/$(whoami)/${JOB_ID}
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if [ -d "${temp_dir}" ]
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then
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rm -Rf "${temp_dir}"
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fi
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mkdir -p "${temp_dir}"
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starbench_path="${temp_dir}/starbench.py"
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@ -38,6 +44,7 @@ command="${command} --git-pass-file ${git_pass_file}"
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command="${command} --num-cores ${num_cores}"
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command="${command} --output-dir ${output_dir}"
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command="${command} --code-version ${code_version}"
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command="${command} --cmake-path ${cmake_path}"
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# echo "cmake_options: @$cmake_options@"
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for cmake_option in ${cmake_options}
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do
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@ -1,6 +1,23 @@
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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="$1" # the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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# 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad' # latest from branch master as of 01/06/2022 12:52
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# code_version='775048db02dfb317d5eaddb6d6db520be71a2fdf' # latest from branch graffy-issue51 as of 01/06/
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@ -21,36 +38,59 @@ function launch_job_for_host_group()
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local hosts=''
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local num_cores=''
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case "${host_group_id}" in
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'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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'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_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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*)
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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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benchmark_test='^nh3h2_qma_long$' # about 10min on a core i5 8th generation
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quick_test='arch4_quick' # about 2s on a core i5 8th generation
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representative_test='nh3h2_qma_long' # about 10min on a core i5 8th generation
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benchmark_test="${quick_test}"
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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='-DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON'
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benchmark_command="ctest --output-on-failure -L ${quick_test}"
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benchmark_command="ctest --output-on-failure -L ^${benchmark_test}\$"
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# cat $SCRIPT_DIR/hibench.job | sed "s~<include:starbench.py>~$(cat $SCRIPT_DIR/starbench.py)~" > /tmp/hibench.job
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cat $SCRIPT_DIR/hibench.job | substitute_TAG_with_FILEcontents '<include:starbench.py>' "$SCRIPT_DIR/starbench.py" > /tmp/hibench.job
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chmod a+x /tmp/hibench.job
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command="/tmp/hibench.job \"${git_repos_url}\" \"${git_user}\" \"${git_pass_file}\" \"${HIBRIDON_VERSION}\" \"${cmake_options}\" \"${benchmark_command}\""
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echo "command = $command"
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eval $command
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local hibench_root_dir="$GLOBAL_WORK_DIR/graffy/hibridon/benchmarks/starbench"
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mkdir -p "${hibench_root_dir}"
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# qsub -pe smp "$num_cores" -l "hostname=${hosts}"
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local this_bench_dir="${hibench_root_dir}/${hibridon_version}/${benchmark_test}/${host_group_id}"
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mkdir -p "${this_bench_dir}"
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command="/tmp/hibench.job \"${git_repos_url}\" \"${git_user}\" \"${git_pass_file}\" \"${hibridon_version}\" \"${cmake_options}\" \"${benchmark_command}\""
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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=1G"
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qsub_command="${qsub_command} -N ${benchmark_test}_${host_group_id}"
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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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@ -58,7 +98,8 @@ function launch_perf_jobs()
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{
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local hibridon_version="$1" # the version of hibridon to test, in the form of a valid commit number eg 'a3bed1c3ccfbca572003020d3e3d3b1ff3934fad'
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launch_job_for_host_group "${hibridon_version}" 'xeon_gold_6140'
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launch_job_for_host_group "${hibridon_version}" 'intel_xeon_x5550'
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#launch_job_for_host_group "${hibridon_version}" 'intel_xeon_gold_6140'
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}
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@ -186,13 +186,15 @@ class StarBencher():
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self._runs[run.id] = run
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def run(self):
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print("executing the following command in parallel (%d parallel runs) : '%s'" % (self.num_parallel_runs, str(self.run_command)))
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for worker_id in range(self.num_parallel_runs):
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self._start_run(worker_id)
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# wait until all runs have finished
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self._finished_event.wait()
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with self._runs_lock:
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if not all([run.return_code == 0 for run in self._runs.values()]):
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raise Exception('at least one run failed')
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workers_success = [run.return_code == 0 for run in self._runs.values()]
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if not all(workers_success):
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raise Exception('at least one run failed (workers_success = %s)' % workers_success)
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mean_duration, num_runs = self._get_run_mean_duration()
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print('mean duration : %.3f s (%d runs)' % (mean_duration, num_runs))
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return mean_duration
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@ -214,7 +216,7 @@ def test_starbencher():
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# end of starbencher
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def starbench_cmake_app(git_repos_url: str, code_version: str, tmp_dir: Path, num_cores: int, git_user: str, git_password: str, benchmark_command: List[str], cmake_options: List[str] = None):
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def starbench_cmake_app(git_repos_url: str, code_version: str, tmp_dir: Path, num_cores: int, git_user: str, git_password: str, benchmark_command: List[str], cmake_options: List[str] = None, cmake_exe_location: Path = None):
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"""
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tests_to_run : regular expression as understood by ctest's -L option. eg '^arch4_quick$'
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"""
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@ -247,8 +249,11 @@ def starbench_cmake_app(git_repos_url: str, code_version: str, tmp_dir: Path, nu
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# build_dir.mkdir(exist_ok=True)
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print('configuring %s into %s ...' % (src_dir, build_dir))
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cmake_prog = 'cmake'
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if cmake_exe_location:
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cmake_prog = str(cmake_exe_location)
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configure = StarBencher(
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run_command=['cmake'] + cmake_options + [src_dir],
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run_command=[cmake_prog] + cmake_options + [src_dir],
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num_cores_per_run=1,
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num_parallel_runs=num_cores,
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max_num_cores=num_cores,
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@ -289,7 +294,7 @@ if __name__ == '__main__':
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example_text = '''example:
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%(prog)s --git-repos-url https://github.com/hibridon/hibridon --code-version a3bed1c3ccfbca572003020d3e3d3b1ff3934fad --git-user g-raffy --git-pass-file "$HOME/.github/personal_access_tokens/bench.hibridon.cluster.ipr.univ-rennes1.fr.pat" --num-cores 2 --output-dir=/tmp/hibench --cmake-option=-DCMAKE_BUILD_TYPE=Release --cmake-option=-DBUILD_TESTING=ON --benchmark-command='ctest --output-on-failure -L ^arch4_quick$'
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%(prog)s --git-repos-url https://github.com/hibridon/hibridon --code-version a3bed1c3ccfbca572003020d3e3d3b1ff3934fad --git-user g-raffy --git-pass-file "$HOME/.github/personal_access_tokens/bench.hibridon.cluster.ipr.univ-rennes1.fr.pat" --num-cores 2 --output-dir=/tmp/hibench --cmake-path=/opt/cmake/cmake-3.23.0/bin/cmake --cmake-option=-DCMAKE_BUILD_TYPE=Release --cmake-option=-DBUILD_TESTING=ON --benchmark-command='ctest --output-on-failure -L ^arch4_quick$'
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'''
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@ -302,6 +307,7 @@ if __name__ == '__main__':
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password_group.add_argument('--git-pass', type=str, help='the password (or personal access token) to use (not recommended for security reasons)')
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parser.add_argument('--num-cores', type=int, required=True, help='the number of cores that the benchmark will use')
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parser.add_argument('--output-dir', type=Path, required=True, help='where the output files will be placed')
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parser.add_argument('--cmake-path', type=Path, help='the path to the cmake executable to use in case a specific cmake is wanted')
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parser.add_argument('--cmake-option', type=str, action='append', help='additional option passed to cmake in the configure step (use this flag multiple times if you need more than one cmake option)')
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parser.add_argument('--benchmark-command', required=True, type=str, help='the command to benchmark')
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args = parser.parse_args()
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@ -316,4 +322,4 @@ if __name__ == '__main__':
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with open(args.git_pass_file, 'r') as f:
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git_password = f.readline().replace('\n', '') # os.environ['HIBRIDON_REPOS_PAT']
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starbench_cmake_app(git_repos_url=git_repos_url, code_version=args.code_version, tmp_dir=args.output_dir, num_cores=args.num_cores, git_user=git_user, git_password=git_password, cmake_options=args.cmake_option, benchmark_command=args.benchmark_command.split(' '))
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starbench_cmake_app(git_repos_url=git_repos_url, code_version=args.code_version, tmp_dir=args.output_dir, num_cores=args.num_cores, git_user=git_user, git_password=git_password, cmake_options=args.cmake_option, benchmark_command=args.benchmark_command.split(' '), cmake_exe_location=args.cmake_path)
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