From Source#

The installation consist two part: python-dependencies and external libraries.

Core Software/Libraries#

Before the installation, following software/libraries should be installed on the system.

  • Python 3.8+

  • GCC 7.8+, cmake 3.18+

  • HDF5 (parallel build)

  • MPICH

  • OpenMPI (for cluster)

Python Dependencies#

The python-dependencies are managed through [poetry][link-poetry-website]. We provide important alias in makefile.

make poetry-downloads  # Install poetry on the system
make install           # Install MiV-Simulator

Note: If any issues are encoutered, please make a report to GitHub-Issue.

The installation using pip is not yet supported due to the dependency compilation.

External Libraries#

  1. Building and installing NEURON

pip install neuron
How to install from the source ```sh git clone https://github.com/neuronsimulator/nrn.git cd nrn mkdir build cd build cmake .. -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx make install ```

  1. Building and installing NeuroH5

The NeuroH5 build system requires cmake.

git clone https://github.com/soltesz-lab/neuroh5.git
cd neuroh5
CMAKE_BUILD_PARALLEL_LEVEL=8 pip install .

Cluster Usage#

For architecture-level optimization, some of the core libraries should be built within the worker node.

Note

Make sure to run on a worker node, not the login-node!

Necessary Modules#

Following modules (or equivalent modules) are necessary before starting the installation.

module load python/3
module load cmake
module load gcc
module load openmpi

Building HDF5 (Parallel)#

Download the source from [here][source-hdf5].

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.gz
tar -xzf hdf5-1.12.1.tar.gz
cd hdf5-1.12.1
CC=mpicc ./configure --prefix=$PWD/build --enable-parallel --enable-shared
make && make check
make install && make check-install

H5PY#

CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/Users/skim0119/github/hdf5-1.12.1/build pip install --no-binary=h5py h5py

Install/Build Python Dependencies#

make poetry-download
make install

Building NEURON simulator#

git clone https://github.com/neuronsimulator/nrn.git
cd nrn
git submodule update --init --recursive
mkdir build
cd build
cmake .. -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_CORENEURON=ON -DPYTHON_EXECUTABLE=$(which python3) -DNRN_ENABLE_PYTHON=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_INSTALL_PREFIX=../install
cmake --build . --parallel 8 --target install

export PATH=<Installation path>/bin:$PATH
export PYTHONPATH=<Installation path>/lib/python:$PYTHONPATH
Possible Issues

  • Readline cannot be found:

    • Try to install Readline using apt or yum. It can also be installed using conda.

    • Readline might already exist on the system. Search in /usr/lib or /usr/lib64.

    • Pass environment variable directly: cmake -DReadline_INCLUDE_DIR=/usr/lib64 -DReadline_LIBRARY=/usr/lib64/libreadline.so.7 ....


Install NeuroH5#

# get the source
git clone https://github.com/soltesz-lab/neuroh5.git
cd neuroh5

# add HDF5 build to PATH
export HDF5_SOURCE=<HDF5 installation directory>
export PATH=$PATH:$HDF5_SOURCE/build

# (make sure the node has enough RAM and cores, otherwise the compilation will fail)
CMAKE_BUILD_PARALLEL_LEVEL=8 pip install .

Other CLI tools in NeuroH5 can be installed using cmake.

cmake .
make -j4
export PATH=<NeuroH5 installation path>/bin:$PATH

Tools and scripts to aid cluster usage#