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JUSUF Deployment
Jorge Blanco Alonso edited this page Sep 28, 2020
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11 revisions
- neurodamus-hippocampus/0.4
- neurodamus-neocortex/0.3
- neurodamus-mousify/0.3
- neuron/7.8.0c
- py-neurodamus/1.3.1
- py-bluepy/0.14.14
- py-bluepyopt/1.9.37
- py-sonata-network-reduction/0.0.10
- 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=vsk25
module purge
module load Intel/2019.5.281-GCC-8.3.0 IntelMPI/2019.6.154 HDF5
module use /p/project/cvsk25/software-deployment/HBP/jusuf/10-08-2020/modules/tcl/linux-centos7-zen
# load only relevant modules needed for your job
module load neurodamus-hippocampus/0.4
time srun special -NFRAME 1000 $HOC_LIBRARY_PATH/init.hoc -mpi
# Run the simulation with neurodamus py instead
module load py-bluepy # h5py
module load py-neurodamus
srun neurodamus BlueConfig
- Using py-bluepy or BluePyOpt
module load Python/3.6.8
module load SciPy-Stack/2019a-Python-3.6.8
module use /p/project/cvsk25/software-deployment/HBP/jusuf/10-08-2020/modules/tcl/linux-centos7-zen
# always load neuron module
module load neuron/7.8.0c
# 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