JURECA Deployment

Instructions for Using Software Stack

• Sample job script for cpu/cluster partition

#!/bin/bash
#SBATCH --nodes=100
#SBATCH --ntasks-per-node=24
#SBATCH --job-name=test-hippo-cluster
#SBATCH --time=6:00:00
#SBATCH --partition=batch
#SBATCH --mail-user=email
#SBATCH --mail-type=ALL
#SBATCH --account=vsk25

module --force purge all
module load Architecture/Haswell
module load Intel/2019.5.281-GCC-8.3.0 IntelMPI/2019.6.154
module load Python/3.6.8 SciPy-Stack/2019a-Python-3.6.8
module load HDF5/1.10.5

module use /p/project/cvsk25/software-deployment/HBP/jureca-cluster/25-03-2020/modules/tcl/linux-centos7-haswell

module load neurodamus-hippocampus/0.4
module load neuron/7.8.0b
module load py-bluepyopt/1.9.12

export I_MPI_DEBUG=5
srun --cpus-per-task=1 special -NFRAME 1024 $HOC_LIBRARY_PATH/init.hoc -mpi

• Sample job script for knl/booster partition

#!/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
#SBATCH --account=vsk25

module --force purge all
module load Architecture/KNL
module load Intel/2019.5.281-GCC-8.3.0 IntelMPI/2019.6.154
module load Python/3.6.8 SciPy-Stack/2019a-Python-3.6.8
module load HDF5/1.10.5

module use /p/project/cvsk25/software-deployment/HBP/jureca-booster/25-03-2020/modules/tcl/linux-centos7-haswell

module load neurodamus-hippocampus/0.4-knl
module load neuron/7.8.0b
module load py-bluepyopt/1.9.12

export I_MPI_DEBUG=5
srun --cpus-per-task=1 special -NFRAME 1024 $HOC_LIBRARY_PATH/init.hoc -mpi