SuperMUC-NG

Setting up GitHub on SuperMuc-NG

see Accessing github behind a firewall.

Building SeisSol

Clone SeisSol including the submodules using

git clone --recursive https://github.com/SeisSol/SeisSol.git

Load module. Add these lines to .bashrc:

##### module load for SeisSol
module load gcc
module load cmake/3.21.4
module load python/3.8.11-extended
module load numactl/2.0.14-intel21
#To use dependencies preinstalled with spack
module use /hppfs/work/pn49ha/ru76tuj2/modules/linux-sles15-skylake_avx512/
# you need to have access to project pn49ha
module load seissol-env/develop-intel21-impi-x2b
export CC=mpicc
export CXX=mpiCC
export FC=mpif90

Alternatively (and for reference), to compile seissol-env on SuperMUC-NG, follow the procedure below:

# load spack
module load user_spack
# clone seissol-spack-aid and add the repository
# we use a supermuc specific branch as supermuc spack is too old (0.17.1) for the main branch
git clone --branch supermuc_NG https://github.com/SeisSol/seissol-spack-aid.git
cd seissol-spack-aid
spack repo add ./spack
# locate externally build pkg-config
spack external find pkg-config

# install all dependencies of seissol.
# We specify the intel and intel-mpi version matching preinstalled version on supermuc-ng
# These can be found with:
# >spack find intel-mpi
# >spack compiler list
spack install seissol-env %intel@21.4.0 ^intel-mpi@2019.12.320
# or
spack install seissol-env %gcc@11.2.0 ^intel-mpi@2019.12.320

# now create a module:
spack module tcl refresh seissol-env@develop%intel@21.4.0

#to access the module at start up, add to your ~/.bashrc
module use $HOME/spack/modules/x86_avx512/linux-sles15-skylake_avx512/
# change this path to your_custom_path_2_modules if you update ~/.spack/modules.yaml

Custom install directory for packages and modules can be set with, by changing ~/.spack/config.yaml:

config:
  install_tree: path_2_packages

and ~/.spack/modules.yaml:

modules:
  default:
    roots:
     tcl: your_custom_path_2_modules

This can be useful to share packages with other user of a SuperMUC project.

The seissol-env compilation can also be reduced by adding the python module to ~/.spack/packages.yaml:

packages:
  python:
    externals:
    - spec: python@3.8.11
      buildable: False
      modules:
       - python/3.8.11-extended

Install SeisSol with cmake, e.g. with (more options with ccmake)

mkdir build-release && cd build-release
cmake -DCOMMTHREAD=ON -DNUMA_AWARE_PINNING=ON -DASAGI=ON -DCMAKE_BUILD_TYPE=Release -DHOST_ARCH=skx -DPRECISION=double -DORDER=4 -DGEMM_TOOLS_LIST=LIBXSMM,PSpaMM ..
make -j 48

Note that to use sanitizer (https://en.wikipedia.org/wiki/AddressSanitizer), SeisSol needs to be compiled with gcc. For that modules and compiler need to be switched:

module switch seissol-env seissol-env/develop-gcc11

export CC=mpigcc
export CXX=mpigxx
export FC=mpifc

Then cmake on a new build folder. To enable sanitizer, add -DADDRESS_SANITIZER_DEBUG=ON to the argument list of cmake, and change the CMAKE_BUILD_TYPE to RelWithDebInfo or Debug.

Running SeisSol

This is an example job submission script for SeisSol on SuperMUC-NG. For your applications, change #SBATCH –nodes= to the amount of nodes you want to run on. A rule of thumb for optimal performance is to distribute your jobs to 1 node per 100k elements. This rule of thumb does not account for potentially shorter queue times, for example when using the test queue or when asking for a large amount of nodes.

#!/bin/bash
# Job Name and Files (also --job-name)

#SBATCH -J <job name>
#Output and error (also --output, --error):
#SBATCH -o ./%j.%x.out
#SBATCH -e ./%j.%x.err

#Initial working directory:
#SBATCH --chdir=<work directory>

#Notification and type
#SBATCH --mail-type=END
#SBATCH --mail-user=<your email address>

# Wall clock limit:
#SBATCH --time=03:00:00
#SBATCH --no-requeue

#Setup of execution environment
#SBATCH --export=ALL
#SBATCH --account=<project id>
#constraints are optional
#--constraint="scratch&work"
#SBATCH --partition=general

#Number of nodes and MPI tasks per node:
#SBATCH --nodes=40
#SBATCH --ntasks-per-node=1
#EAR may impact code performance
#SBATCH --ear=off

module load slurm_setup

#Run the program:
export MP_SINGLE_THREAD=no
unset KMP_AFFINITY
export OMP_NUM_THREADS=94
export OMP_PLACES="cores(47)"
#Prevents errors such as experience in Issue #691
export I_MPI_SHM_HEAP_VSIZE=8192

export XDMFWRITER_ALIGNMENT=8388608
export XDMFWRITER_BLOCK_SIZE=8388608
export SC_CHECKPOINT_ALIGNMENT=8388608

export SEISSOL_CHECKPOINT_ALIGNMENT=8388608
export SEISSOL_CHECKPOINT_DIRECT=1
export ASYNC_MODE=THREAD
export ASYNC_BUFFER_ALIGNMENT=8388608
source /etc/profile.d/modules.sh

echo 'num_nodes:' $SLURM_JOB_NUM_NODES 'ntasks:' $SLURM_NTASKS 'cpus_per_task:' $SLURM_CPUS_PER_TASK
ulimit -Ss 2097152
mpiexec -n $SLURM_NTASKS SeisSol_Release_sskx_4_elastic parameters.par

Accessing PyPI

Many post-processing scripts of SeisSol require Python dependencies. We describe how to use pip on SuperMUC at see Accessing PyPI behind a firewall.