JUSUF Deployment

List of latest packages deployed

• neurodamus-hippocampus/1.5-3.3.0
• neurodamus-neocortex/1.4-3.3.0
• neurodamus-mousify/1.4-3.3.0
• neuron/8.0.0
• py-neurodamus/2.6.0
• py-bluepy/2.3.0
• py-bluepyopt/1.9.37
• py-sonata-network-reduction/0.1.0

Instructions for Using Software Stack

• Make sure SSH key from JUDOR 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	

• 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 Intel/2020.2.254-GCC-9.3.0 ParaStationMPI/5.4.7-1 HDF5
module load Python/3.8.5 SciPy-Stack/2020-Python-3.8.5
module use /p/project/icei-hbp-2020-0013/software-deployment/HBP/jusuf/03-06-2021/modules/tcl/linux-centos7-zen2/

# load only relevant modules needed for your job
module load neurodamus-hippocampus/1.5-3.3.0

time srun special -NFRAME 1000 $HOC_LIBRARY_PATH/init.hoc -mpi

# Run the simulation with neurodamus py instead
module load py-neurodamus

srun neurodamus BlueConfig

• Using py-bluepy or BluePyOpt

module load Python/3.8.5 SciPy-Stack/2020-Python-3.8.5
module use /p/project/icei-hbp-2020-0013/software-deployment/HBP/jusuf/03-06-2021/modules/tcl/linux-centos7-zen2/

# always load neuron module
module load neuron/8.0.0

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

$ python
>>> import bluepy
>>> import pandas
>>> import bluepyopt