Proper runscript example for Tursa

This commit is contained in:
Antonin Portelli 2023-01-30 16:58:54 +00:00
parent 51eae5723e
commit 43e264d29b
6 changed files with 139 additions and 170 deletions

View File

@ -2,5 +2,7 @@
# shellcheck disable=SC1091 # shellcheck disable=SC1091
env_dir="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")" env_dir="$(dirname "$(readlink -f "${BASH_SOURCE:-$0}")")"
mkdir -p ~/.config/lattice-benchmarks
echo "${env_dir}" > ~/.config/lattice-benchmarks/grid-env
source "${env_dir}/spack/share/spack/setup-env.sh" source "${env_dir}/spack/share/spack/setup-env.sh"
spack load jq git spack load jq git

View File

@ -0,0 +1,17 @@
#!/usr/bin/env bash
# OpenMP/OpenMPI/UCX environment ###############################################
export OMP_NUM_THREADS=8
export OMPI_MCA_btl=^uct,openib
export OMPI_MCA_pml=ucx
export UCX_TLS=gdr_copy,rc,rc_x,sm,cuda_copy,cuda_ipc
export UCX_RNDV_SCHEME=put_zcopy
export UCX_RNDV_THRESH=16384
export UCX_IB_GPU_DIRECT_RDMA=yes
export UCX_MEMTYPE_CACHE=n
# IO environment ###############################################################
export OMPI_MCA_io=romio321
export OMPI_MCA_btl_openib_allow_ib=true
export OMPI_MCA_btl_openib_device_type=infiniband
export OMPI_MCA_btl_openib_if_exclude=mlx5_1,mlx5_2,mlx5_3

View File

@ -1,86 +0,0 @@
#!/usr/bin/env bash
# shellcheck disable=SC1091,SC2050,SC2170
## This set of slurm settings assumes that the AMD chips are using bios setting NPS4 (4 mpi taks per socket).
#SBATCH -J @job-name@
#SBATCH -A @budget@
#SBATCH -t 48:00:00
#SBATCH --nodes=@nnodes@
#SBATCH --ntasks=@ntasks@
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=32
#SBATCH --partition=@partition@
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
#SBATCH --qos=standard
#SBATCH --no-requeue
set -e
# OpenMP/OpenMPI/UCX environment ###############################################
export OMP_NUM_THREADS=16
export OMP_DISPLAY_AFFINITY=true
export OMPI_MCA_btl=^uct,openib
export OMPI_MCA_pml=ucx
export UCX_TLS=rc,sm,self
export UCX_RNDV_THRESH=16384
export UCX_MEMTYPE_CACHE=n
export UCX_NET_DEVICES=mlx5_0:1
export OMPI_MCA_BTL_SM_USE_KNEM=1
export OMPI_MCA_coll_hcoll_enable=1
export OMPI_MCA_coll_hcoll_np=0
# IO environment ###############################################################
if [ @nnodes@ -eq 1 ]; then
export OMPI_MCA_io=ompio
else
export OMPI_MCA_io=romio321
fi
export OMPI_MCA_btl_openib_allow_ib=true
export OMPI_MCA_btl_openib_device_type=infiniband
export OMPI_MCA_btl_openib_if_exclude=mlx5_1,mlx5_2,mlx5_3 # are these needed here?
# load environment #############################################################
env_dir="$(readlink -f @env-dir@)"
source "${env_dir}/env-base.sh"
if [ "${SLURM_JOB_PARTITION}" = 'cpu' ]; then
source "${env_dir}/env-cpu.sh"
else
echo "error: partition ${SLURM_JOB_PARTITION} not supported for this template" 1>&2
exit 1
fi
# application and parameters ###################################################
app='@application@'
opt='--comms-overlap --comms-concurrent'
par='@par@'
# collect job information ######################################################
job_info_dir=job/${SLURM_JOB_NAME}.${SLURM_JOB_ID}
mkdir -p "${job_info_dir}"
date > "${job_info_dir}/start-date"
set > "${job_info_dir}/env"
ldd ${app} > "${job_info_dir}/ldd"
md5sum ${app} > "${job_info_dir}/app-hash"
readelf -a ${app} > "${job_info_dir}/elf"
echo "${SLURM_JOB_NODELIST}" > "${job_info_dir}/nodes"
cp "${BASH_SOURCE[0]}" "${job_info_dir}/script"
if [ -n "${par}" ]; then cp "${par}" "${job_info_dir}/par"; fi
# run! #########################################################################
mpirun -np "${SLURM_NTASKS}" -x LD_LIBRARY_PATH --bind-to none \
./cpu-mpi-wrapper.sh \
${app} "${par}" "${opt[@]}" \
--mpi @mpi-geom@ \
--grid @grid-geom@ \
--shm 2048 &> "${job_info_dir}/log"
# if we reach that point the application exited successfully ###################
touch "${job_info_dir}/success"
date > "${job_info_dir}/end-date"
################################################################################

View File

@ -0,0 +1,60 @@
#!/usr/bin/env bash
# shellcheck disable=SC1091,SC2050,SC2170
#SBATCH -J benchmark-grid-16
#SBATCH -t 1:00:00
#SBATCH --nodes=16
#SBATCH --ntasks=64
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=8
#SBATCH --partition=gpu
#SBATCH --gres=gpu:4
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
#SBATCH --qos=standard
#SBATCH --no-requeue
#SBATCH --gpu-freq=1410
set -euo pipefail
# load environment #############################################################
env_cfg="${HOME}/.config/lattice-benchmarks/grid-env"
if [ ! -f "${env_cfg}" ]; then
echo "error: ${env_cfg} does not exists, did you execute 'source env.sh' with your user account?"
exit 1
fi
env_dir="$(readlink -f "$(cat "${env_cfg}")")"
source "${env_dir}/env.sh" # load base Spack environment
source "${env_dir}/env-gpu.sh" # load GPU-sepcific packages
source "${env_dir}/ompi-gpu.sh" # set GPU-specific OpenMPI variables
# application and parameters ###################################################
app="${env_dir}/prefix/gridbench_gpu/bin/Benchmark_Grid"
# collect job information ######################################################
job_info_dir=job/${SLURM_JOB_NAME}.${SLURM_JOB_ID}
mkdir -p "${job_info_dir}"
date > "${job_info_dir}/start-date"
set > "${job_info_dir}/env"
ldd "${app}" > "${job_info_dir}/ldd"
md5sum "${app}" > "${job_info_dir}/app-hash"
readelf -a "${app}" > "${job_info_dir}/elf"
echo "${SLURM_JOB_NODELIST}" > "${job_info_dir}/nodes"
cp "${BASH_SOURCE[0]}" "${job_info_dir}/script"
# run! #########################################################################
mpirun -np "${SLURM_NTASKS}" -x LD_LIBRARY_PATH --bind-to none \
"${env_dir}/gpu-mpi-wrapper.sh" \
"${app}" \
--json-out "${job_info_dir}/result.json" \
--mpi 1.4.4.4 \
--accelerator-threads 8 \
--threads 8 \
--shm 2048 &> "${job_info_dir}/log"
# if we reach that point the application exited successfully ###################
touch "${job_info_dir}/success"
date > "${job_info_dir}/end-date"
################################################################################

View File

@ -0,0 +1,60 @@
#!/usr/bin/env bash
# shellcheck disable=SC1091,SC2050,SC2170
#SBATCH -J benchmark-grid-1
#SBATCH -t 1:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=8
#SBATCH --partition=gpu
#SBATCH --gres=gpu:4
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
#SBATCH --qos=standard
#SBATCH --no-requeue
#SBATCH --gpu-freq=1410
set -euo pipefail
# load environment #############################################################
env_cfg="${HOME}/.config/lattice-benchmarks/grid-env"
if [ ! -f "${env_cfg}" ]; then
echo "error: ${env_cfg} does not exists, did you execute 'source env.sh' with your user account?"
exit 1
fi
env_dir="$(readlink -f "$(cat "${env_cfg}")")"
source "${env_dir}/env.sh" # load base Spack environment
source "${env_dir}/env-gpu.sh" # load GPU-sepcific packages
source "${env_dir}/ompi-gpu.sh" # set GPU-specific OpenMPI variables
# application and parameters ###################################################
app="${env_dir}/prefix/gridbench_gpu/bin/Benchmark_Grid"
# collect job information ######################################################
job_info_dir=job/${SLURM_JOB_NAME}.${SLURM_JOB_ID}
mkdir -p "${job_info_dir}"
date > "${job_info_dir}/start-date"
set > "${job_info_dir}/env"
ldd "${app}" > "${job_info_dir}/ldd"
md5sum "${app}" > "${job_info_dir}/app-hash"
readelf -a "${app}" > "${job_info_dir}/elf"
echo "${SLURM_JOB_NODELIST}" > "${job_info_dir}/nodes"
cp "${BASH_SOURCE[0]}" "${job_info_dir}/script"
# run! #########################################################################
mpirun -np "${SLURM_NTASKS}" -x LD_LIBRARY_PATH --bind-to none \
"${env_dir}/gpu-mpi-wrapper.sh" \
"${app}" \
--json-out "${job_info_dir}/result.json" \
--mpi 1.1.1.4 \
--accelerator-threads 8 \
--threads 8 \
--shm 2048 &> "${job_info_dir}/log"
# if we reach that point the application exited successfully ###################
touch "${job_info_dir}/success"
date > "${job_info_dir}/end-date"
################################################################################

View File

@ -1,84 +0,0 @@
#!/usr/bin/env bash
# shellcheck disable=SC1091,SC2050,SC2170
# using options from https://github.com/paboyle/Grid/tree/develop/systems/Tursa
#SBATCH -J @job-name@
#SBATCH -A @budget@
#SBATCH -t 48:00:00
#SBATCH --nodes=@nnodes@
#SBATCH --ntasks=@ntasks@
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=8
#SBATCH --partition=@partition@
#SBATCH --gres=gpu:4
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
#SBATCH --qos=standard
#SBATCH --no-requeue
set -e
# OpenMP/OpenMPI/UCX environment ###############################################
export OMP_NUM_THREADS=8
export OMPI_MCA_btl=^uct,openib
export OMPI_MCA_pml=ucx
export UCX_TLS=gdr_copy,rc,rc_x,sm,cuda_copy,cuda_ipc
export UCX_RNDV_SCHEME=put_zcopy
export UCX_RNDV_THRESH=16384
export UCX_IB_GPU_DIRECT_RDMA=yes
export UCX_MEMTYPE_CACHE=n
# IO environment ###############################################################
if [ @nnodes@ -eq 1 ]; then
export OMPI_MCA_io=ompio
else
export OMPI_MCA_io=romio321
fi
export OMPI_MCA_btl_openib_allow_ib=true
export OMPI_MCA_btl_openib_device_type=infiniband
export OMPI_MCA_btl_openib_if_exclude=mlx5_1,mlx5_2,mlx5_3
# load environment #############################################################
env_dir="$(readlink -f @env-dir@)"
source "${env_dir}/env-base.sh"
if [ "${SLURM_JOB_PARTITION}" = 'gpu' ]; then
source "${env_dir}/env-gpu.sh"
else
echo "error: partition ${SLURM_JOB_PARTITION} not supported for this template" 1>&2
exit 1
fi
# application and parameters ###################################################
app='@application@'
opt=('--comms-overlap' '--comms-concurrent')
par='@par@'
# collect job information ######################################################
job_info_dir=job/${SLURM_JOB_NAME}.${SLURM_JOB_ID}
mkdir -p "${job_info_dir}"
date > "${job_info_dir}/start-date"
set > "${job_info_dir}/env"
ldd ${app} > "${job_info_dir}/ldd"
md5sum ${app} > "${job_info_dir}/app-hash"
readelf -a ${app} > "${job_info_dir}/elf"
echo "${SLURM_JOB_NODELIST}" > "${job_info_dir}/nodes"
cp "${BASH_SOURCE[0]}" "${job_info_dir}/script"
if [ -n "${par}" ]; then cp "${par}" "${job_info_dir}/par"; fi
# run! #########################################################################
mpirun -np "${SLURM_NTASKS}" -x LD_LIBRARY_PATH --bind-to none \
./gpu-mpi-wrapper.sh \
${app} "${par}" "${opt[@]}" \
--mpi @mpi-geom@ \
--accelerator-threads 8 \
--grid @grid-geom@ \
--shm 2048 &> "${job_info_dir}/log"
# if we reach that point the application exited successfully ###################
touch "${job_info_dir}/success"
date > "${job_info_dir}/end-date"
################################################################################