Taurus (ZIH)
The Taurus cluster is located at ZIH (TU Dresden).
The cluster has multiple partitions, this section describes how to use the AMD Rome CPUs + NVIDIA A100¶.
Introduction
If you are new to this system, please see the following resources:
Batch system: Slurm
Jupyter service: Missing?
-
$PSCRATCH: per-user production directory, purged every 30 days (<TBD>TB)/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/BLAST-WarpX/warpx.git $HOME/src/warpx
We use the following modules and environments on the system ($HOME/taurus_warpx.profile).
# please set your project account
#export proj="<yourProject>" # change me
# required dependencies
module load modenv/hiera
module load foss/2021b
module load CUDA/11.8.0
module load CMake/3.27.6
# optional: for QED support with detailed tables
#module load Boost # TODO
# optional: for openPMD and PSATD+RZ support
module load HDF5/1.13.1
# optional: for Python bindings or libEnsemble
#module load python # TODO
#
#if [ -d "$HOME/sw/taurus/venvs/warpx" ]
#then
# source $HOME/sw/taurus/venvs/warpx/bin/activate
#fi
# an alias to request an interactive batch node for one hour
# for parallel execution, start on the batch node: srun <command>
alias getNode="salloc --time=2:00:00 -N1 -n1 --cpus-per-task=6 --mem-per-cpu=2048 --gres=gpu:1 --gpu-bind=single:1 -p alpha-interactive --pty bash"
# an alias to run a command on a batch node for up to 30min
# usage: runNode <command>
alias runNode="srun --time=2:00:00 -N1 -n1 --cpus-per-task=6 --mem-per-cpu=2048 --gres=gpu:1 --gpu-bind=single:1 -p alpha-interactive --pty bash"
# optimize CUDA compilation for A100
export AMREX_CUDA_ARCH=8.0
# compiler environment hints
#export CC=$(which gcc)
#export CXX=$(which g++)
#export FC=$(which gfortran)
#export CUDACXX=$(which nvcc)
#export CUDAHOSTCXX=${CXX}
We recommend to store the above lines in a file, such as $HOME/taurus_warpx.profile, and load it into your shell after a login:
source $HOME/taurus_warpx.profile
Then, cd into the directory $HOME/src/warpx and use the following commands to compile:
cd $HOME/src/warpx
rm -rf build
cmake -S . -B build -DWarpX_DIMS="1;2;3" -DWarpX_COMPUTE=CUDA
cmake --build build -j 16
The general cmake compile-time options apply as usual.
Running
A100 GPUs (40 GB)
The alpha partition has 34 nodes with 8 x NVIDIA A100-SXM4 Tensor Core-GPUs and 2 x AMD EPYC CPU 7352 (24 cores) @ 2.3 GHz (multithreading disabled) per node.
The batch script below can be used to run a WarpX simulation on multiple nodes (change -N accordingly).
Replace descriptions between chevrons <> by relevant values, for instance <input file> could be plasma_mirror_inputs.
Note that we run one MPI rank per GPU.
#!/bin/bash -l
# Copyright 2023 Axel Huebl, Thomas Miethlinger
#
# This file is part of WarpX.
#
# License: BSD-3-Clause-LBNL
#SBATCH -t 00:10:00
#SBATCH -N 1
#SBATCH -J WarpX
#SBATCH -p alpha
#SBATCH --exclusive
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=2048
#SBATCH --gres=gpu:1
#SBATCH --gpu-bind=single:1
#SBATCH -o WarpX.o%j
#SBATCH -e WarpX.e%j
# executable & inputs file or python interpreter & PICMI script here
EXE=./warpx
INPUTS=inputs_small
# run
srun ${EXE} ${INPUTS} \
> output.txt
To run a simulation, copy the lines above to a file taurus.sbatch and run
sbatch taurus.sbatch
to submit the job.