README.md

EEE_network

Prepare for simulations

1. Clone the repo (git clone https://github.com/Neurosim-lab/EEE_network.git)
2. Compile the mod files (cd EEE_network/mod ; nrnivmodl)
3. Symlink the mod dir (cd ../eee_net ; ln -s "../mod/x86_64" x86_64)

Single line command:

git clone https://github.com/Neurosim-lab/EEE_network.git ; cd EEE_network/mod ; nrnivmodl ; cd ../eee_net ; ln -s "../mod/x86_64" x86_64

Running simulations using MPI

To run a single sim using MPI

1. Change to the eee_net directory (cd EEE_network/eee_net)
2. Modify the file cfg.py
   1. Update sim label
   2. Set desired parameter values
3. Run the simulation (two options):
   1. Execute runsim #processes (e.g. ./runsim 4)
   2. Execute mpiexec -np #processes nrniv -python -mpi init.py (e.g. mpiexec -np 4 nrniv -python -mpi init.py)

To run a batch of sims using MPI

1. Change to the eee_net directory (cd EEE_network/eee_net)
2. Open the file batch.py
   1. Ensure runType = mpi_bulletin
   2. Update the batchLabel
3. Run the batch of sims (two options):
   1. Execute runbatch #processes (e.g. ./runbatch 4)
   2. Execute mpiexec -np #processes nrniv -python -mpi batch.py (e.g. mpiexec -np 4 nrniv -python -mpi batch.py)

Running simulations on Comet

To run a single sim on Comet

1. Change to the eee_net directory (cd EEE_network/eee_net)
2. Modify the file cfg.py
   1. Update sim label
   2. Set desired parameter values
3. Modify the file runsim_comet
   1. Update names for job, output file, error file
   2. Set desired HPC settings
4. Execute sbatch runsim_comet

To run a batch of simulations on Comet

1. Change to the eee_net directory (cd EEE_network/eee_net)
2. Open batch.py
   1. Ensure runType = hpc_slurm
   2. Update the batchLabel
   3. Set desired HPC settings in runCfg
3. Execute python batch.py