JUSUF Deployment

List of latest packages deployed

• neurodamus-hippocampus/1.6-2.10.1
• neurodamus-neocortex/1.6-2.10.1
• neurodamus-mousify/1.6-2.10.1
• neuron/8.0.2
• py-neurodamus/2.10.1
• py-bluepy/2.4.3
• py-bluepyopt/1.10.38
• py-sonata-network-reduction/0.1.8
• psp-validation/0.4.0
• py-netpyne/1.0.2

Instructions for Using Software Stack

• Run a simulation with small circuit target

#!/bin/bash -l
#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=icei-hbp-2020-0013

module purge
module load Stages/2022
module load Intel/2021.4.0 ParaStationMPI/5.5.0-1
module load HDF5/1.12.1

module load Python/3.9.6
module load SciPy-Stack/2021b
module unload XZ/.5.2.5

module use /p/project/icei-hbp-2020-0013/software-deployment/HBP/jusuf/23-02-2022/modules/lmod/linux-rocky8-x86_64/Core/

# load only relevant modules needed for your job
module load neurodamus-hippocampus/1.6-2.10.1
module load py-neurodamus/2.10.1

time srun special -mpi -python $NEURODAMUS_PYTHON/init.py 

• Using py-bluepy or BluePyOpt

module purge
module load Stages/2022
module load Intel/2021.4.0 ParaStationMPI/5.5.0-1
module load HDF5/1.12.1

module load Python/3.9.6
module load SciPy-Stack/2021b
module unload XZ/.5.2.5

module use /p/project/icei-hbp-2020-0013/software-deployment/HBP/jusuf/23-02-2022/modules/lmod/linux-rocky8-x86_64/Core/

# always load neuron module
module load neuron/8.0.2

# load only relevant modules needed for your job
module load py-bluepyopt
module load py-sonata-network-reduction
module load py-bluepy
module load py-netpyne

$ python
>>> import bluepy
>>> import pandas
>>> import bluepyopt
>>> import netpyne
...