Cori (NERSC)
The Cori cluster is located at NERSC.
Introduction
If you are new to this system, please see the following resources:
Batch system: Slurm
-
$SCRATCH
: per-user production directory, purged every 30 days (20TB)/global/cscratch1/sd/m3239
: shared production directory for users in the projectm3239
, purged every 30 days (50TB)/global/cfs/cdirs/m3239/
: community file system for users in the projectm3239
(100TB)
Installation
Use the following commands to download the WarpX source code and switch to the correct branch:
git clone https://github.com/ECP-WarpX/WarpX.git $HOME/src/warpx
KNL
We use the following modules and environments on the system ($HOME/knl_warpx.profile
).
module swap craype-haswell craype-mic-knl
module swap PrgEnv-intel PrgEnv-gnu
module load cmake/3.22.1
module switch cray-libsci cray-libsci/20.09.1
module load cray-hdf5-parallel/1.10.5.2
module load cray-fftw/3.3.8.10
module load cray-python/3.9.7.1
export PKG_CONFIG_PATH=$FFTW_DIR/pkgconfig:$PKG_CONFIG_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/knl/c-blosc-1.12.1-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/knl/adios2-2.7.1-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/knl/blaspp-master-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/knl/lapackpp-master-install:$CMAKE_PREFIX_PATH
if [ -d "$HOME/sw/knl/venvs/knl_warpx" ]
then
source $HOME/sw/knl/venvs/knl_warpx/bin/activate
fi
export CXXFLAGS="-march=knl"
export CFLAGS="-march=knl"
And install ADIOS2, BLAS++ and LAPACK++:
source $HOME/knl_warpx.profile
# c-blosc (I/O compression)
git clone -b v1.21.1 https://github.com/Blosc/c-blosc.git src/c-blosc
rm -rf src/c-blosc-knl-build
cmake -S src/c-blosc -B src/c-blosc-knl-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/knl/c-blosc-1.12.1-install
cmake --build src/c-blosc-knl-build --target install --parallel 16
# ADIOS2
git clone -b v2.7.1 https://github.com/ornladios/ADIOS2.git src/adios2
rm -rf src/adios2-knl-build
cmake -S src/adios2 -B src/adios2-knl-build -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/knl/adios2-2.7.1-install
cmake --build src/adios2-knl-build --target install --parallel 16
# BLAS++ (for PSATD+RZ)
git clone https://github.com/icl-utk-edu/blaspp.git src/blaspp
rm -rf src/blaspp-knl-build
cmake -S src/blaspp -B src/blaspp-knl-build -Duse_openmp=ON -Duse_cmake_find_blas=ON -DBLAS_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=$HOME/sw/knl/blaspp-master-install
cmake --build src/blaspp-knl-build --target install --parallel 16
# LAPACK++ (for PSATD+RZ)
git clone https://github.com/icl-utk-edu/lapackpp.git src/lapackpp
rm -rf src/lapackpp-knl-build
CXXFLAGS="-DLAPACK_FORTRAN_ADD_" cmake -S src/lapackpp -B src/lapackpp-knl-build -Duse_cmake_find_lapack=ON -DBLAS_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DLAPACK_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=$HOME/sw/knl/lapackpp-master-install
cmake --build src/lapackpp-knl-build --target install --parallel 16
For PICMI and Python workflows, also install a virtual environment:
# establish Python dependencies
python3 -m pip install --user --upgrade pip
python3 -m pip install --user virtualenv
python3 -m venv $HOME/sw/knl/venvs/knl_warpx
source $HOME/sw/knl/venvs/knl_warpx/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install --upgrade wheel
python3 -m pip install --upgrade cython
python3 -m pip install --upgrade numpy
python3 -m pip install --upgrade pandas
python3 -m pip install --upgrade scipy
MPICC="cc -shared" python3 -m pip install -U --no-cache-dir -v mpi4py
python3 -m pip install --upgrade openpmd-api
python3 -m pip install --upgrade matplotlib
python3 -m pip install --upgrade yt
# optional: for libEnsemble
#python3 -m pip install -r $HOME/src/warpx/Tools/LibEnsemble/requirements.txt
Haswell
We use the following modules and environments on the system ($HOME/haswell_warpx.profile
).
module swap PrgEnv-intel PrgEnv-gnu
module load cmake/3.22.1
module switch cray-libsci cray-libsci/20.09.1
module load cray-hdf5-parallel/1.10.5.2
module load cray-fftw/3.3.8.10
module load cray-python/3.9.7.1
export PKG_CONFIG_PATH=$FFTW_DIR/pkgconfig:$PKG_CONFIG_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/haswell/c-blosc-1.12.1-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/haswell/adios2-2.7.1-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/haswell/blaspp-master-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/haswell/lapackpp-master-install:$CMAKE_PREFIX_PATH
if [ -d "$HOME/sw/haswell/venvs/haswell_warpx" ]
then
source $HOME/sw/haswell/venvs/haswell_warpx/bin/activate
fi
And install ADIOS2, BLAS++ and LAPACK++:
source $HOME/haswell_warpx.profile
# c-blosc (I/O compression)
git clone -b v1.21.1 https://github.com/Blosc/c-blosc.git src/c-blosc
rm -rf src/c-blosc-haswell-build
cmake -S src/c-blosc -B src/c-blosc-haswell-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/haswell/c-blosc-1.12.1-install
cmake --build src/c-blosc-haswell-build --target install --parallel 16
# ADIOS2
git clone -b v2.7.1 https://github.com/ornladios/ADIOS2.git src/adios2
rm -rf src/adios2-haswell-build
cmake -S src/adios2 -B src/adios2-haswell-build -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/haswell/adios2-2.7.1-install
cmake --build src/adios2-haswell-build --target install --parallel 16
# BLAS++ (for PSATD+RZ)
git clone https://github.com/icl-utk-edu/blaspp.git src/blaspp
rm -rf src/blaspp-haswell-build
cmake -S src/blaspp -B src/blaspp-haswell-build -Duse_openmp=ON -Duse_cmake_find_blas=ON -DBLAS_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=$HOME/sw/blaspp-master-haswell-install
cmake --build src/blaspp-haswell-build --target install --parallel 16
# LAPACK++ (for PSATD+RZ)
git clone https://github.com/icl-utk-edu/lapackpp.git src/lapackpp
rm -rf src/lapackpp-haswell-build
CXXFLAGS="-DLAPACK_FORTRAN_ADD_" cmake -S src/lapackpp -B src/lapackpp-haswell-build -Duse_cmake_find_lapack=ON -DBLAS_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DLAPACK_LIBRARIES=${CRAY_LIBSCI_PREFIX_DIR}/lib/libsci_gnu.a -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=$HOME/sw/haswell/lapackpp-master-install
cmake --build src/lapackpp-haswell-build --target install --parallel 16
For PICMI and Python workflows, also install a virtual environment:
# establish Python dependencies
python3 -m pip install --user --upgrade pip
python3 -m pip install --user virtualenv
python3 -m venv $HOME/sw/haswell/venvs/haswell_warpx
source $HOME/sw/haswell/venvs/haswell_warpx/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install --upgrade wheel
python3 -m pip install --upgrade cython
python3 -m pip install --upgrade numpy
python3 -m pip install --upgrade pandas
python3 -m pip install --upgrade scipy
MPICC="cc -shared" python3 -m pip install -U --no-cache-dir -v mpi4py
python3 -m pip install --upgrade openpmd-api
python3 -m pip install --upgrade matplotlib
python3 -m pip install --upgrade yt
# optional: for libEnsemble
#python3 -m pip install -r $HOME/src/warpx/Tools/LibEnsemble/requirements.txt
GPU (V100)
Cori provides a partition with 18 nodes that include V100 (16 GB) GPUs.
We use the following modules and environments on the system ($HOME/gpu_warpx.profile
).
You can copy this file from Tools/machines/cori-nersc/gpu_warpx.profile.example
:
export proj="m1759"
module purge
module load modules
module load cgpu
module load esslurm
module load gcc/8.3.0 cuda/11.4.0 cmake/3.22.1
module load openmpi
export CMAKE_PREFIX_PATH=$HOME/sw/cori_gpu/c-blosc-1.12.1-install:$CMAKE_PREFIX_PATH
export CMAKE_PREFIX_PATH=$HOME/sw/cori_gpu/adios2-2.7.1-install:$CMAKE_PREFIX_PATH
if [ -d "$HOME/sw/cori_gpu/venvs/cori_gpu_warpx" ]
then
source $HOME/sw/cori_gpu/venvs/cori_gpu_warpx/bin/activate
fi
# compiler environment hints
export CC=$(which gcc)
export CXX=$(which g++)
export FC=$(which gfortran)
export CUDACXX=$(which nvcc)
export CUDAHOSTCXX=$(which g++)
# optimize CUDA compilation for V100
export AMREX_CUDA_ARCH=7.0
# allocate a GPU, e.g. to compile on
# 10 logical cores (5 physical), 1 GPU
function getNode() {
salloc -C gpu -N 1 -t 30 -c 10 --gres=gpu:1 -A $proj
}
And install ADIOS2:
source $HOME/gpu_warpx.profile
# c-blosc (I/O compression)
git clone -b v1.21.1 https://github.com/Blosc/c-blosc.git src/c-blosc
rm -rf src/c-blosc-gpu-build
cmake -S src/c-blosc -B src/c-blosc-gpu-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/cori_gpu/c-blosc-1.12.1-install
cmake --build src/c-blosc-gpu-build --target install --parallel 16
git clone -b v2.7.1 https://github.com/ornladios/ADIOS2.git src/adios2
rm -rf src/adios2-gpu-build
cmake -S src/adios2 -B src/adios2-gpu-build -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/cori_gpu/adios2-2.7.1-install
cmake --build src/adios2-gpu-build --target install --parallel 16
For PICMI and Python workflows, also install a virtual environment:
# establish Python dependencies
python3 -m pip install --user --upgrade pip
python3 -m pip install --user virtualenv
python3 -m venv $HOME/sw/cori_gpu/venvs/gpu_warpx
source $HOME/sw/cori_gpu/venvs/gpu_warpx/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install --upgrade wheel
python3 -m pip install --upgrade cython
python3 -m pip install --upgrade numpy
python3 -m pip install --upgrade pandas
python3 -m pip install --upgrade scipy
python3 -m pip install -U --no-cache-dir -v mpi4py
python3 -m pip install --upgrade openpmd-api
python3 -m pip install --upgrade matplotlib
python3 -m pip install --upgrade yt
# optional: for libEnsemble
#python3 -m pip install -r $HOME/src/warpx/Tools/LibEnsemble/requirements.txt
Building WarpX
We recommend to store the above lines in individual warpx.profile
files, as suggested above.
If you want to run on either of the three partitions of Cori, open a new terminal, log into Cori and source the environment you want to work with:
# KNL:
source $HOME/knl_warpx.profile
# Haswell:
#source $HOME/haswell_warpx.profile
# GPU:
#source $HOME/gpu_warpx.profile
Warning
Consider that all three Cori partitions are incompatible.
Do not source multiple ...warpx.profile
files in the same terminal session.
Open a new terminal and log into Cori again, if you want to switch the targeted Cori partition.
If you re-submit an already compiled simulation that you ran on another day or in another session, make sure to source the corresponding ...warpx.profile
again after login!
Then, cd
into the directory $HOME/src/warpx
and use the following commands to compile:
cd $HOME/src/warpx
rm -rf build
# append if you target GPUs: -DWarpX_COMPUTE=CUDA
cmake -S . -B build -DWarpX_DIMS=3
cmake --build build -j 16
The general cmake compile-time options apply as usual.
That’s it!
A 3D WarpX executable is now in build/bin/
and can be run with a 3D example inputs file.
Most people execute the binary directly or copy it out to a location in $SCRATCH
.
The general cmake compile-time options and instructions for Python (PICMI) bindings apply as usual:
# PICMI build
cd $HOME/src/warpx
# install or update dependencies
python3 -m pip install -r requirements.txt
# compile parallel PICMI interfaces with openPMD support and 3D, 2D and RZ
WARPX_MPI=ON BUILD_PARALLEL=16 python3 -m pip install --force-reinstall --no-deps -v .
Testing
To run all tests (here on KNL), do:
change in
Regressions/WarpX-tests.ini
frommpiexec
tosrun
:MPIcommand = srun -n @nprocs@ @command@
# set test directory to a shared directory available on all nodes
# note: the tests will create the directory automatically
export WARPX_CI_TMP="$HOME/warpx-regression-tests"
# compile with more cores
export WARPX_CI_NUM_MAKE_JOBS=16
# run all integration tests
# note: we set MPICC as a build-setting for mpi4py on KNL/Haswell
MPICC="cc -shared" ./run_test.sh
Running
Navigate (i.e. cd
) into one of the production directories (e.g. $SCRATCH
) before executing the instructions below.
KNL
The batch script below can be used to run a WarpX simulation on 2 KNL nodes on
the supercomputer Cori at NERSC. Replace descriptions between chevrons <>
by relevant values, for instance <job name>
could be laserWakefield
.
Do not forget to first source $HOME/knl_warpx.profile
if you have not done so already for this terminal session.
For PICMI Python runs, the <path/to/executable>
has to read python3
and the <input file>
is the path to your PICMI input script.
#!/bin/bash -l
# Copyright 2019 Maxence Thevenet
#
# This file is part of WarpX.
#
# License: BSD-3-Clause-LBNL
#SBATCH -N 2
#SBATCH -t 01:00:00
#SBATCH -q regular
#SBATCH -C knl
#SBATCH -S 4
#SBATCH -J <job name>
#SBATCH -A <allocation ID>
#SBATCH -e WarpX.e%j
#SBATCH -o WarpX.o%j
export OMP_PLACES=threads
export OMP_PROC_BIND=spread
# KNLs have 4 hyperthreads max
export CORI_MAX_HYPETHREAD_LEVEL=4
# We use 64 cores out of the 68 available on Cori KNL,
# and leave 4 to the system (see "#SBATCH -S 4" above).
export CORI_NCORES_PER_NODE=64
# Typically use 8 MPI ranks per node without hyperthreading,
# i.e., OMP_NUM_THREADS=8
export WARPX_NMPI_PER_NODE=8
export WARPX_HYPERTHREAD_LEVEL=1
# Compute OMP_NUM_THREADS and the thread count (-c option)
export CORI_NHYPERTHREADS_MAX=$(( ${CORI_MAX_HYPETHREAD_LEVEL} * ${CORI_NCORES_PER_NODE} ))
export WARPX_NTHREADS_PER_NODE=$(( ${WARPX_HYPERTHREAD_LEVEL} * ${CORI_NCORES_PER_NODE} ))
export OMP_NUM_THREADS=$(( ${WARPX_NTHREADS_PER_NODE} / ${WARPX_NMPI_PER_NODE} ))
export WARPX_THREAD_COUNT=$(( ${CORI_NHYPERTHREADS_MAX} / ${WARPX_NMPI_PER_NODE} ))
# for async_io support: (optional)
export MPICH_MAX_THREAD_SAFETY=multiple
srun --cpu_bind=cores -n $(( ${SLURM_JOB_NUM_NODES} * ${WARPX_NMPI_PER_NODE} )) -c ${WARPX_THREAD_COUNT} \
<path/to/executable> <input file> \
> output.txt
To run a simulation, copy the lines above to a file cori_knl.sbatch
and run
sbatch cori_knl.sbatch
to submit the job.
For a 3D simulation with a few (1-4) particles per cell using FDTD Maxwell solver on Cori KNL for a well load-balanced problem (in our case laser wakefield acceleration simulation in a boosted frame in the quasi-linear regime), the following set of parameters provided good performance:
amr.max_grid_size=64
andamr.blocking_factor=64
so that the size of each grid is fixed to64**3
(we are not using load-balancing here).8 MPI ranks per KNL node, with
OMP_NUM_THREADS=8
(that is 64 threads per KNL node, i.e. 1 thread per physical core, and 4 cores left to the system).2 grids per MPI, i.e., 16 grids per KNL node.
Haswell
The batch script below can be used to run a WarpX simulation on 1 Haswell node on the supercomputer Cori at NERSC.
Do not forget to first source $HOME/haswell_warpx.profile
if you have not done so already for this terminal session.
#!/bin/bash -l
# Just increase this number of you need more nodes.
#SBATCH -N 1
#SBATCH -t 03:00:00
#SBATCH -q regular
#SBATCH -C haswell
#SBATCH -J <job name>
#SBATCH -A <allocation ID>
#SBATCH -e error.txt
#SBATCH -o output.txt
# one MPI rank per half-socket (see below)
#SBATCH --tasks-per-node=4
# request all logical (virtual) cores per half-socket
#SBATCH --cpus-per-task=16
# each Cori Haswell node has 2 sockets of Intel Xeon E5-2698 v3
# each Xeon CPU is divided into 2 bus rings that each have direct L3 access
export WARPX_NMPI_PER_NODE=4
# each MPI rank per half-socket has 8 physical cores
# or 16 logical (virtual) cores
# over-subscribing each physical core with 2x
# hyperthreading leads to a slight (3.5%) speedup
# the settings below make sure threads are close to the
# controlling MPI rank (process) per half socket and
# distribute equally over close-by physical cores and,
# for N>8, also equally over close-by logical cores
export OMP_PROC_BIND=spread
export OMP_PLACES=threads
export OMP_NUM_THREADS=16
# for async_io support: (optional)
export MPICH_MAX_THREAD_SAFETY=multiple
EXE="<path/to/executable>"
srun --cpu_bind=cores -n $(( ${SLURM_JOB_NUM_NODES} * ${WARPX_NMPI_PER_NODE} )) \
${EXE} <input file> \
> output.txt
To run a simulation, copy the lines above to a file cori_haswell.sbatch
and
run
sbatch cori_haswell.sbatch
to submit the job.
For a 3D simulation with a few (1-4) particles per cell using FDTD Maxwell solver on Cori Haswell for a well load-balanced problem (in our case laser wakefield acceleration simulation in a boosted frame in the quasi-linear regime), the following set of parameters provided good performance:
4 MPI ranks per Haswell node (2 MPI ranks per Intel Xeon E5-2698 v3), with
OMP_NUM_THREADS=16
(which uses 2x hyperthreading)
GPU (V100)
Do not forget to first source $HOME/gpu_warpx.profile
if you have not done so already for this terminal session.
Due to the limited amount of GPU development nodes, just request a single node with the above defined getNode
function.
For single-node runs, try to run one grid per GPU.
A multi-node batch script template can be found below:
#!/bin/bash -l
# Copyright 2021 Axel Huebl
# This file is part of WarpX.
# License: BSD-3-Clause-LBNL
#
# Ref:
# - https://docs-dev.nersc.gov/cgpu/hardware/
# - https://docs-dev.nersc.gov/cgpu/access/
# - https://docs-dev.nersc.gov/cgpu/usage/#controlling-task-and-gpu-binding
# Just increase this number of you need more nodes.
#SBATCH -N 2
#SBATCH -t 03:00:00
#SBATCH -J <job name>
#SBATCH -A m1759
#SBATCH -q regular
#SBATCH -C gpu
# 8 V100 GPUs (16 GB) per node
#SBATCH --gres=gpu:8
#SBATCH --exclusive
# one MPI rank per GPU (a quarter-socket)
#SBATCH --tasks-per-node=8
# request all logical (virtual) cores per quarter-socket
#SBATCH --cpus-per-task=10
#SBATCH -e WarpX.e%j
#SBATCH -o WarpX.o%j
# each Cori GPU node has 2 sockets of Intel Xeon Gold 6148 ('Skylake') @ 2.40 GHz
export WARPX_NMPI_PER_NODE=8
# each MPI rank per half-socket has 10 physical cores
# or 20 logical (virtual) cores
# we split half-sockets again by 2 to have one MPI rank per GPU
# over-subscribing each physical core with 2x
# hyperthreading leads to often to slight speedup on Intel
# the settings below make sure threads are close to the
# controlling MPI rank (process) per half socket and
# distribute equally over close-by physical cores and,
# for N>20, also equally over close-by logical cores
export OMP_PROC_BIND=spread
export OMP_PLACES=threads
export OMP_NUM_THREADS=10
# for async_io support: (optional)
export MPICH_MAX_THREAD_SAFETY=multiple
EXE="<path/to/executable>"
srun --cpu_bind=cores --gpus-per-task=1 --gpu-bind=map_gpu:0,1,2,3,4,5,6,7 \
-n $(( ${SLURM_JOB_NUM_NODES} * ${WARPX_NMPI_PER_NODE} )) \
${EXE} <input file> \
> output.txt
Post-Processing
For post-processing, most users use Python via NERSC’s Jupyter service (Docs).
As a one-time preparatory setup, create your own Conda environment as described in NERSC docs.
In this manual, we often use this conda create
line over the officially documented one:
conda create -n myenv -c conda-forge python mamba ipykernel ipympl==0.8.6 matplotlib numpy pandas yt openpmd-viewer openpmd-api h5py fast-histogram dask dask-jobqueue pyarrow
We then follow the Customizing Kernels with a Helper Shell Script section to finalize the setup of using this conda-environment as a custom Jupyter kernel.
kernel_helper.sh
should read:
#!/bin/bash
module load python
source activate myenv
exec "$@"
When opening a Jupyter notebook, just select the name you picked for your custom kernel on the top right of the notebook.
Additional software can be installed later on, e.g., in a Jupyter cell using !mamba install -c conda-forge ...
.
Software that is not available via conda can be installed via !python -m pip install ...
.
Warning
Jan 6th, 2022 (NERSC-INC0179165 and ipympl #416):
Above, we fixated the ipympl
version to not take the latest release of Matplotlib Jupyter Widgets.
This is an intentional work-around; the ipympl
version needs to exactly fit the version pre-installed on the Jupyter base system.