JURECA Deployment

• Make sure SSH key from JURECA account is added to bbpcode and SSH config is in place:

$ cat ~/.ssh/config

Host bbpcode.epfl.ch
    HostName bbpcode.epfl.ch
    User GASPER_USERNAME

• Install simulation stack as

#!/bin/bash
set -x
set -e

# Deployment directory
DEPLOYMENT_HOME=$HOME/HBP/jureca
mkdir -p $DEPLOYMENT_HOME
mkdir -p $DEPLOYMENT_HOME/sources
mkdir -p $DEPLOYMENT_HOME/install

# Clone spack repository
cd $DEPLOYMENT_HOME/sources
git clone https://github.com/BlueBrain/spack.git

# Setup environment
export SPACK_ROOT=`pwd`/spack
export PATH=$SPACK_ROOT/bin:$PATH
source $SPACK_ROOT/share/spack/setup-env.sh

# Copy configurations
mkdir -p $SPACK_ROOT/etc/spack/defaults/linux/
cp $SPACK_ROOT/sysconfig/jureca/* $SPACK_ROOT/etc/spack/defaults/linux/

# Setup directory for deployment
export SOFTS_DIR_PATH=$DEPLOYMENT_HOME/install/$(date '+%d-%m-%Y')
mkdir -p $SOFTS_DIR_PATH

# Install neurodamus
spack install neurodamus@hippocampus~coreneuron

# Link module path to latest installation
cd $DEPLOYMENT_HOME/install
ln -s $(date '+%d-%m-%Y')/modules/tcl/linux-centos7-x86_64 latest

• Notify user for new deployment

 export MODULEPATH=$MODULEPATH:$HOME/HBP/jureca/install/latest

• Sample job script is

#!/bin/bash
#SBATCH --nodes=100
#SBATCH --ntasks-per-node=68
#SBATCH --job-name=test-full
#SBATCH --time=12:00:00
#SBATCH --partition=largebooster
#SBATCH --mail-user=email
#SBATCH --mail-type=ALL

module purge all
module load Architecture/KNL
module load Intel
module load IntelMPI/2018.1.163
module load HDF5/1.8.19

export MODULEPATH=$MODULEPATH:$HOME/HBP/jureca/install/latest
module load neurodamus/hippocampus