| # Install Development tools | |
| # - ripgrep | |
| # - fzf: improved fuzzy finder (better ctrl+r + fuzy autocompletion with ** trigger) | |
| # - bat: cat with syntax higlighting: https://github.com/sharkdp/bat/ | |
| # - eza: better ls: https://github.com/eza-community/eza?tab=readme-ov-file | |
| # - tealdeer (tldr) | |
| # - zoxide: `z`, a smarter cd and jump command: https://github.com/ajeetdsouza/zoxide | |
| # With sudo/apt | |
| sudo apt install build-essential \ |
| # Remove previous cuda and driver installs | |
| # https://stackoverflow.com/questions/56431461/how-to-remove-cuda-completely-from-ubuntu | |
| sudo apt-get --purge remove "*nvidia-driver*" | |
| sudo apt-get --purge remove "cuda*" "*cublas*" "*cufft*" "*curand*" \ | |
| "*cusolver*" "*cusparse*" "*npp*" "*nvjpeg*" "cuda*" "nsight*" | |
| sudo apt-get autoremove | |
| sudo rm -rf /usr/local/cuda* | |
| # Remove (comment out) old nvidia repos in file: | |
| sudo nano /etc/apt/sources.list |
| { | |
| "<Ctrl-x><0>": "Unsplit", | |
| "<Ctrl-x><2>": "HSplit", | |
| "<Ctrl-x><3>": "VSplit", | |
| "<Ctrl-x><Ctrl-c>": "QuitAll", | |
| "<Ctrl-x><k>": "Quit", | |
| "<Ctrl-x><Ctrl-f>": "OpenFile", | |
| "<Ctrl-x><Ctrl-s>": "Save", | |
| "<Ctrl-x><Ctrl-w>": "SaveAs", | |
| "<Ctrl-x><b>": "NextTab", |
| # 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 |
| # 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 |
| # 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) |
| #!/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 |
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
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)
| # -*- 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 |