| # For install via Yale packaged version: see http://www.neuron.yale.edu/ftp/neuron/nrn_mac_install.pdf | |
| # For install via Brew prackage manager: see https://bbp.epfl.ch/nmc-portal/tools | |
| # Set environment variables automatically: | |
| /Applications/NEURON-7.5/nrn/x86_64/bin/nrnpyenv.sh | |
| # Or do it manually by adding following to ~/.bash_profile | |
| nrn_installdir=/path/to/NEURON/installdir # for example /Applications/NEURON-7.5 | |
| my_anaconda_path=/path/to/anaconda/dir # for example /Users/me/anaconda |
| wine start installer.msi # install the program | |
| cd '~/.wine/drive_c/Program Files (x86)/Neuronland/NLMorphologyConverter' | |
| wine NLMorphologyConverter.exe --help | |
| # you can pass file paths in UNIX format to windows executables run via 'wine' command: they will be converted automatically | |
| wine NLMorphologyConverter.exe /home/me/mymorph.p /home/me/mymorph.swc SWC |
| ### NEURON Installation from source ### | |
| # Based on documentation at: | |
| # https://www.neuron.yale.edu/neuron/download/compile_linux | |
| # http://www.davison.webfactional.com/notes/installation-neuron-python/ | |
| # http://pub.ist.ac.at/~jguzman/doc/neuron/index.html | |
| # Install C/C++ Development tools (compiler etc.) | |
| sudo apt install build-essential | |
| # Install InterView dependencies |
| # -*- coding: utf-8 -*- | |
| r""" | |
| Run a parallel ring network of ball-and-stick cells and write the spike times | |
| to a file. | |
| To execute with MPI across 2 processors:: | |
| $ mpiexec -n 2 python ringnet_mpi.py | |
| To modify any simulation parameters, specify individual variables encased in |
Download the FSL installer (python script) from https://fsl.fmrib.ox.ac.uk/fsldownloads_registration.
Type following commands in a Python interpreter:
from fslinstaller import *
manifest = get_web_manifest(Settings.mirror)
import json
with open('~/manifest.json', 'w') as fp:
json.dump(manifest, fp)
Installation instructions are based on the RPM spec file at https://github.com/neurord/fedora-genesis-simulator/blob/master/genesis-simulator.spec
by making the relevant macro substitutions usign rpm --eval.
git clone https://github.com/genesis-sim/genesis-2.4.git
cd genesis-2.4/genesis
rm -rf ./src/diskio/interface/netcdf/netcdf-3.4
| #!/bin/bash | |
| # Based on 'scripts and utilities' in Duplicacy user guide: https://forum.duplicacy.com/t/duplicacy-user-guide/1197 | |
| ################################################################################ | |
| # HOWTO | |
| # - Follow steps 1-3 in https://forum.duplicacy.com/t/how-to-run-duplicacy-as-a-cron-job-on-linux/1611 | |
| # 1. initialize backup repositories | |
| # 2. save password in preferences |
| # Load modules required for NEURON Python install | |
| module purge | |
| module load gcc intel-mpi anaconda | |
| # Create local Python environment | |
| conda create -n localpy27 python=2 anaconda | |
| source activate localpy27 | |
| # Install Python MPI support | |
| # (must install using pip/setup.py when linking to system libraries rather than conda packaged libraries) |
| # Load modules required for NEURON Python install | |
| module purge | |
| module load anaconda | |
| # For GCC toolchain load following modules: | |
| module load gcc openmpi/3.1.6 | |
| # For Intel toolchain load following instead of gcc and openmpi: | |
| # export FI_PROVIDER=verbs | |
| # module load intel/intel-cc | |
| # module load intel/intel-mkl |
| # Based on following sources: | |
| # - https://arbor.readthedocs.io/en/latest/install.html | |
| # - https://github.com/arbor-sim/arbor/blob/master/scripts/travis/build.sh | |
| # Create python 3 environment with MPI support | |
| conda create -n py3arbor python=3 | |
| conda activate py3arbor | |
| # Install an mpi distribution and compile python module mpi4py with it | |
| sudo apt install openmpi-bin openmpi-common libopenmpi2 libopenmpi-dev | |
| pip install mpi4py |