working scripts for Tursa
This commit is contained in:
24
Grid/systems/tursa/bootstrap-env.sh
Executable file
24
Grid/systems/tursa/bootstrap-env.sh
Executable file
@@ -0,0 +1,24 @@
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#!/usr/bin/env bash
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set -euo pipefail
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if (( $# != 1 )); then
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echo "usage: $(basename "$0") <environment directory>" 1>&2
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exit 1
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fi
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dir=$1
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call_dir=$(pwd -P)
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script_dir="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")"
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if [ -d "${dir}" ]; then
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echo "error: directory '${dir}' exists"
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exit 1
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fi
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mkdir -p "${dir}"
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cd "${dir}"
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git clone https://github.com/spack/spack.git
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cd "${call_dir}"
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cp "${script_dir}"/files/* "${dir}"
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cp "${script_dir}/env.sh" "${script_dir}/grid-config.json" "${dir}"
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source "${dir}"/spack/share/spack/setup-env.sh
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"${script_dir}"/spack-bootstrap.sh "${dir}"
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@@ -1,5 +0,0 @@
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#!/usr/bin/env bash
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# shellcheck disable=SC2046
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script_dir="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")"
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spack load $(cat "${script_dir}"/grid-cpu.spack)
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@@ -1,5 +0,0 @@
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#!/usr/bin/env bash
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# shellcheck disable=SC2046
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script_dir="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")"
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spack load $(cat "${script_dir}"/grid-gpu.spack)
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8
Grid/systems/tursa/env.sh
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8
Grid/systems/tursa/env.sh
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@@ -0,0 +1,8 @@
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#!/usr/bin/env bash
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# shellcheck disable=SC1091
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GRIDENVDIR="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")"
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export GRIDENVDIR
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export PATH="${GRIDENVDIR}/prefix/base/bin:${PATH}"
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export ACLOCAL_PATH="${GRIDENVDIR}/prefix/base/share/aclocal:${ACLOCAL_PATH}"
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source "${GRIDENVDIR}"/spack/share/spack/setup-env.sh
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4
Grid/systems/tursa/files/env-cpu.sh
Normal file
4
Grid/systems/tursa/files/env-cpu.sh
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@@ -0,0 +1,4 @@
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#!/usr/bin/env bash
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spack env activate grid-cpu
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spack env status
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4
Grid/systems/tursa/files/env-gpu.sh
Normal file
4
Grid/systems/tursa/files/env-gpu.sh
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@@ -0,0 +1,4 @@
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#!/usr/bin/env bash
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spack env activate grid-gpu
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spack env status
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25
Grid/systems/tursa/grid-config.json
Normal file
25
Grid/systems/tursa/grid-config.json
Normal file
@@ -0,0 +1,25 @@
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{
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"configs": [
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{
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"name": "gpu",
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"env-script": "env-gpu.sh",
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"commit": "796abfad80625d81bb16af7ff6ec612a836f17d8",
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"config-options": "--enable-comms=mpi --enable-simd=GPU --enable-alloc-align=4k --enable-accelerator-cshift --enable-shm=nvlink --enable-gen-simd-width=64 --enable-accelerator=cuda --disable-unified --enable-gparity=no --enable-fermion-reps=no",
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"env" : {
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"CXX": "nvcc",
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"LDFLAGS": "-cudart shared",
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"CXXFLAGS": "-ccbin mpicxx -gencode arch=compute_80,code=sm_80 -std=c++14 -cudart shared"
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}
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},
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{
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"name": "cpu",
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"env-script": "env-cpu.sh",
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"commit": "796abfad80625d81bb16af7ff6ec612a836f17d8",
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"config-options": "--enable-comms=mpi-auto --enable-simd=AVX2 --enable-alloc-align=4k --enable-shm=shmget --enable-gparity=no --enable-fermion-reps=no",
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"env" : {
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"CXX": "clang++",
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"MPICXX": "mpicxx"
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}
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}
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]
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}
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@@ -1,10 +0,0 @@
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gcc@9.4.0
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llvm@12.0.1
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ucx@1.12.0.CPU%gcc@9.4.0
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openmpi@4.1.1.CPU%gcc@9.4.0
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hdf5^openmpi@4.1.1.CPU%gcc@9.4.0
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fftw^openmpi@4.1.1.CPU%gcc@9.4.0
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openssl
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gmp%gcc@9.4.0
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mpfr%gcc@9.4.0
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c-lime
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@@ -1,10 +0,0 @@
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gcc@9.4.0
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cuda@11.4.0
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ucx@1.12.0.GPU%gcc@9.4.0
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openmpi@4.1.1.GPU%gcc@9.4.0
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hdf5^openmpi@4.1.1.GPU%gcc@9.4.0
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fftw^openmpi@4.1.1.GPU%gcc@9.4.0
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openssl
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gmp%gcc@9.4.0
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mpfr%gcc@9.4.0
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c-lime
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169
Grid/systems/tursa/spack-bootstrap.sh
Normal file → Executable file
169
Grid/systems/tursa/spack-bootstrap.sh
Normal file → Executable file
@@ -2,16 +2,19 @@
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# shellcheck disable=SC2016
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set -euo pipefail
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GCC='gcc@9.4.0'
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CUDA='cuda@11.4.0'
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HDF5='hdf5@1.10.7'
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gcc_spec='gcc@9.4.0'
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cuda_spec='cuda@11.4.0'
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hdf5_spec='hdf5@1.10.7'
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if (( $# != 1 )); then
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echo "usage: $(basename "$0") <env dir>" 1>&2
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exit 1
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fi
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ENVDIR=$1
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CWD=$(pwd -P)
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dir=$1
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cwd=$(pwd -P)
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cd "${dir}"
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dir=$(pwd -P)
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cd "${cwd}"
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# General configuration ########################################################
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# build with 128 tasks
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@@ -33,107 +36,92 @@ echo 'packages:
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spack config --scope site add -f external.yaml
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rm external.yaml
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# Base compilers ###############################################################
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# configure system base
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spack compiler find --scope site
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# Base packages ################################################################
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# install GCC
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spack install ${GCC}
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spack load ${GCC}
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# install GCC, CUDA & LLVM
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spack install ${gcc_spec} ${cuda_spec} llvm
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spack load llvm
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spack compiler find --scope site
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spack unload ${GCC}
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spack unload llvm
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# clean
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spack clean
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spack gc -y
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# install CUDA
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spack install ${CUDA}
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# install development tools
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dev_tools=("autoconf" "automake" "libtool" "git")
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spack install "${dev_tools[@]}"
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# create view for CLI & dev tools
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spack view symlink -i "${ENVDIR}/prefix/base" "${dev_tools[@]}"
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# install clang
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spack install llvm@12.0.1
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# locate new compilers
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spack load llvm@12.0.1
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spack load ${gcc_spec}
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spack compiler find --scope site
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spack unload llvm@12.0.1
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spack unload ${gcc_spec}
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# Manual compilation of OpenMPI & UCX ##########################################
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# set build directories
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mkdir -p "${ENVDIR}"/build
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cd "${ENVDIR}"/build
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mkdir -p "${dir}"/build
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cd "${dir}"/build
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spack load ${GCC} ${CUDA}
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spack load ${gcc_spec} ${cuda_spec}
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CUDA_PATH=$(which nvcc | sed "s/bin/@/g" | cut -d "@" -f1)
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GDRCOPY_PATH=/mnt/lustre/tursafs1/apps/gdrcopy/2.3.1
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cuda_path=$(spack find --format "{prefix}" cuda)
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gdrcopy_path=/mnt/lustre/tursafs1/apps/gdrcopy/2.3.1
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# Install ucx 1.12.0
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UCX_URL=https://github.com/openucx/ucx/releases/download/v1.12.0/ucx-1.12.0.tar.gz
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ucx_url=https://github.com/openucx/ucx/releases/download/v1.12.0/ucx-1.12.0.tar.gz
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echo "-- building UCX from source"
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wget ${UCX_URL}
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UCX_AR=$(basename ${UCX_URL})
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tar -xvf "${UCX_AR}"
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cd "${UCX_AR%.tar.gz}"
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wget ${ucx_url}
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ucx_ar=$(basename ${ucx_url})
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tar -xvf "${ucx_ar}"
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cd "${ucx_ar%.tar.gz}"
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# ucx gpu build
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mkdir build_gpu; cd build_gpu
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mkdir -p build_gpu; cd build_gpu
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../configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu \
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--disable-dependency-tracking --prefix="${ENVDIR}"/prefix/ucx_gpu \
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--disable-dependency-tracking --prefix="${dir}"/prefix/ucx_gpu \
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--enable-devel-headers --enable-examples --enable-optimizations \
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--with-gdrcopy=${GDRCOPY_PATH} --with-verbs --disable-logging \
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--with-gdrcopy=${gdrcopy_path} --with-verbs --disable-logging \
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--disable-debug --disable-assertions --enable-cma \
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--with-knem=/opt/knem-1.1.4.90mlnx1/ --with-rdmacm \
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--without-rocm --without-ugni --without-java \
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--enable-compiler-opt=3 --with-cuda="${CUDA_PATH}" --without-cm \
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--enable-compiler-opt=3 --with-cuda="${cuda_path}" --without-cm \
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--with-rc --with-ud --with-dc --with-mlx5-dv --with-dm \
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--enable-mt LDFLAGS=-L${GDRCOPY_PATH}/lib
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--enable-mt --without-go LDFLAGS=-L${gdrcopy_path}/lib
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make -j 128
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make install
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cd ..
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# ucx cpu build
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mkdir build_cpu; cd build_cpu
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mkdir -p build_cpu; cd build_cpu
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../configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu \
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--disable-dependency-tracking --prefix="${ENVDIR}"/prefix/ucx_cpu \
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--disable-dependency-tracking --prefix="${dir}"/prefix/ucx_cpu \
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--enable-devel-headers --enable-examples --enable-optimizations \
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--with-verbs --disable-logging --disable-debug \
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--disable-assertions --enable-mt --enable-cma \
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--with-knem=/opt/knem-1.1.4.90mlnx1/ --with-rdmacm \
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--without-rocm --without-ugni --without-java \
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--enable-compiler-opt=3 --without-cm --without-ugni --with-rc \
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--with-ud --with-dc --with-mlx5-dv --with-dm --enable-mt
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--with-ud --with-dc --with-mlx5-dv --with-dm --enable-mt --without-go
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make -j 128
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make install
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cd "${ENVDIR}"/build
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cd "${dir}"/build
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# Install openmpi 4.1.1 (needs to be done on a gpu node)
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OMPI_URL=https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
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# Install openmpi 4.1.1
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ompi_url=https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
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echo "-- building OpenMPI from source"
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wget ${OMPI_URL}
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OMPI_AR=$(basename ${OMPI_URL})
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tar -xvf "${OMPI_AR}"
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cd "${OMPI_AR%.tar.gz}"
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wget ${ompi_url}
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ompi_ar=$(basename ${ompi_url})
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tar -xvf "${ompi_ar}"
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cd "${ompi_ar%.tar.gz}"
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export AUTOMAKE_JOBS=128
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./autogen.pl -f
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# openmpi gpu build
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mkdir build_gpu; cd build_gpu
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../configure --prefix="${ENVDIR}"/prefix/ompi_gpu --without-xpmem \
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--with-ucx="${ENVDIR}"/prefix/ucx_gpu \
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--with-ucx-libdir="${ENVDIR}"/prefix/ucx_gpu/lib \
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../configure --prefix="${dir}"/prefix/ompi_gpu --without-xpmem \
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--with-ucx="${dir}"/prefix/ucx_gpu \
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--with-ucx-libdir="${dir}"/prefix/ucx_gpu/lib \
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--with-knem=/opt/knem-1.1.4.90mlnx1/ \
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--enable-mca-no-build=btl-uct \
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--with-cuda="${CUDA_PATH}" --disable-getpwuid \
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--with-cuda="${cuda_path}" --disable-getpwuid \
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--with-verbs --with-slurm --enable-mpi-fortran=all \
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--with-pmix=internal --with-libevent=internal
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make -j 128
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@@ -142,61 +130,76 @@ cd ..
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# openmpi cpu build
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mkdir build_cpu; cd build_cpu
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../configure --prefix="${ENVDIR}"/prefix/ompi_cpu --without-xpmem \
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--with-ucx="${ENVDIR}"/prefix/ucx_cpu \
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--with-ucx-libdir="${ENVDIR}"/prefix/ucx_cpu/lib \
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../configure --prefix="${dir}"/prefix/ompi_cpu --without-xpmem \
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--with-ucx="${dir}"/prefix/ucx_cpu \
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--with-ucx-libdir="${dir}"/prefix/ucx_cpu/lib \
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--with-knem=/opt/knem-1.1.4.90mlnx1/ \
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--enable-mca-no-build=btl-uct --disable-getpwuid \
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--with-verbs --with-slurm --enable-mpi-fortran=all \
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--with-pmix=internal --with-libevent=internal
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make -j 128
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make install
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cd "${ENVDIR}"
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cd "${dir}"
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# Add externals to spack
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echo "packages:
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ucx:
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externals:
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- spec: \"ucx@1.12.0.GPU%gcc@9.4.0\"
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prefix: ${ENVDIR}/prefix/ucx_gpu
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prefix: ${dir}/prefix/ucx_gpu
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- spec: \"ucx@1.12.0.CPU%gcc@9.4.0\"
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prefix: ${ENVDIR}/prefix/ucx_cpu
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prefix: ${dir}/prefix/ucx_cpu
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buildable: False
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openmpi:
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externals:
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- spec: \"openmpi@4.1.1.GPU%gcc@9.4.0\"
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prefix: ${ENVDIR}/prefix/ompi_gpu
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prefix: ${dir}/prefix/ompi_gpu
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- spec: \"openmpi@4.1.1.CPU%gcc@9.4.0\"
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prefix: ${ENVDIR}/prefix/ompi_cpu
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prefix: ${dir}/prefix/ompi_cpu
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buildable: False" > spack.yaml
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spack config --scope site add -f spack.yaml
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rm spack.yaml
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spack install ucx@1.12.0.GPU%gcc@9.4.0
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spack install ucx@1.12.0.CPU%gcc@9.4.0
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spack install openmpi@4.1.1.GPU%gcc@9.4.0
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spack install openmpi@4.1.1.CPU%gcc@9.4.0
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spack install ucx@1.12.0.GPU%gcc@9.4.0 openmpi@4.1.1.GPU%gcc@9.4.0
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spack install ucx@1.12.0.CPU%gcc@9.4.0 openmpi@4.1.1.CPU%gcc@9.4.0
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# Install Grid dependencies ####################################################
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cd "${CWD}"
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cd "${cwd}"
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OPENMPIGPUHASH=$(spack find --format "{hash}" openmpi@4.1.1.GPU)
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OPENMPICPUHASH=$(spack find --format "{hash}" openmpi@4.1.1.CPU)
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# environments #################################################################
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dev_tools=("autoconf" "automake" "libtool" "jq")
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ompi_gpu_hash=$(spack find --format "{hash}" openmpi@4.1.1.GPU)
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ompi_cpu_hash=$(spack find --format "{hash}" openmpi@4.1.1.CPU)
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spack install ${HDF5}+cxx+threadsafe ^/"${OPENMPIGPUHASH}"
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spack install ${HDF5}+cxx+threadsafe ^/"${OPENMPICPUHASH}"
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spack install fftw ^/"${OPENMPIGPUHASH}"
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spack install fftw ^/"${OPENMPICPUHASH}"
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spack install openssl gmp mpfr c-lime
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spack env create grid-gpu
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spack env activate grid-gpu
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spack add ${gcc_spec} ${cuda_spec} "${dev_tools[@]}"
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spack add ucx@1.12.0.GPU%gcc@9.4.0 openmpi@4.1.1.GPU%gcc@9.4.0
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spack add ${hdf5_spec}+cxx+threadsafe ^/"${ompi_gpu_hash}"
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spack add fftw ^/"${ompi_gpu_hash}"
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spack add openssl gmp mpfr c-lime
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spack install
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spack env deactivate
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spack env create grid-cpu
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spack env activate grid-cpu
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spack add llvm "${dev_tools[@]}"
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spack add ucx@1.12.0.CPU%gcc@9.4.0 openmpi@4.1.1.CPU%gcc@9.4.0
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spack add ${hdf5_spec}+cxx+threadsafe ^/"${ompi_cpu_hash}"
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spack add fftw ^/"${ompi_cpu_hash}"
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spack add openssl gmp mpfr c-lime
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spack install
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spack env deactivate
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# Final setup ##################################################################
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spack clean
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spack gc -y
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# add more environment variables in module loading
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spack config --scope site add 'modules:prefix_inspections:lib:[LIBRARY_PATH]'
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spack config --scope site add 'modules:prefix_inspections:lib:[LD_LIBRARY_PATH,LIBRARY_PATH]'
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spack config --scope site add 'modules:prefix_inspections:lib64:[LD_LIBRARY_PATH,LIBRARY_PATH]'
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spack config --scope site add 'modules:prefix_inspections:include:[C_INCLUDE_PATH,CPLUS_INCLUDE_PATH,INCLUDE]'
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spack module tcl refresh -y
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# permission change for group access
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chmod -R g+rw "${ENVDIR}/spack/var/spack/cache"
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setfacl -d -R -m g::rwX "${ENVDIR}/spack/var/spack/cache"
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chmod -R g+rw "${dir}/spack/var/spack/cache"
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setfacl -d -R -m g::rwX "${dir}/spack/var/spack/cache"
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||||
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Reference in New Issue
Block a user