Install using Docker

If you don't want to do the compilation yourself and just want to quickly try STEPS, we provide a prebuilt Docker image for you. Please check https://github.com/CNS-OIST/STEPS_Docker and follow the instructions.

Install from source code

To facilitate new requirements from the parallel TetOpSplit solver, STEPS 3.0 and above uses CMake system to replace the Python distutils system in previous releases. Please follow the instructions below.

Minimum Prerequisites

C++ compiler supporting c++17 (e.g. gcc 7.4, clang 6)
Python3 (3.6.x or above)
NumPy (http://www.numpy.org/)
CMake (https://cmake.org/)
Cython (http://www.cython.org/)
BLAS/OpenBLAS ( http://www.openblas.net/ )

See install Dependencies sections

Optional Prerequisites

To use the parallel SSA solver TetOpSplit: MPI libraries (e.g. MPICH https://www.mpich.org/)
To use the parallel EField solver: PETSc (https://www.mcs.anl.gov/petsc/)

Installation From Source code

please avoid using the "Download ZIP" feature, as submodules are currently not packed in the zip file. This includes the master branch as well as all previous releases in https://github.com/CNS-OIST/STEPS/releases.

Clone the repository using git clone in terminal, and change to the directory.

git clone --recursive https://github.com/CNS-OIST/STEPS.git
cd STEPS

(optional): To checkout a previous release, for example release with tag 3.5.0 (Release tags can be found here, type in

git checkout tags/3.5.0 -b steps_3.5.0
git submodule update --recursive

run the following commands to compile the source code and install

git submodule update --init --recursive
mkdir build
cd build
cmake ..
make
[sudo] make install

After installation, you can check the STEPS installation with the following commands

python3 -c "import steps; steps._greet()"

If STEPS is installed successfully, you should be able to see similar information as below

STochastic Engine for Pathway Simulation
Version:  3.6.0
License:  GPL2.0
Website:  steps.sourceforge.net
CXX Binding: Cython

You can change the installation location by changing the prefix in CMake

cmake -DCMAKE_INSTALL_PREFIX:PATH=/MY_INSTALL_LOCATION ..

MPI and PETSc libraries are automatically detected in the system. If the user wants to manually choose to build STEPS with / without them it can set

cmake -DUSE_MPI=[True|False] -DUSE_PETSC=[True|False] ..

Please refer to CMAKE documentation for customizing your installation

Simulation with serial solvers

STEPS 3.0 and above contain all serial solvers in previous releases, to run STEPS in serial interactive mode, open Python and import the steps module

import steps

Scripts of serial STEPS simulations can be executed in terminal

python3 sim_script.py

Script migration in 3.6

A new python API is available but scripts that worked with STEPS 3.5 should still work without any modification in STEPS 3.6.

Detailed guides for the new API can be found in the documentation.

Simulation with parallel TetOpSplit

At the moment STEPS does not provide the interactive interface for parallel TetOpSplit solver, thus parallel simulations need to be executed via scripts in terminal with "mpirun" command

mpirun -n N_PROCS python3 parallel_sim_script.py

N_PROCS is the number of MPI processes to be created for the parallel simulation.

Please refer to the documentation of your MPI solution for further customization.

Dependencies and build instructions

Linux Debian based:

You can follow the installation procedure performed by the Docker image recipe

OSX:

Use Anaconda or Miniconda: conda install scipy numpy matplotlib cmake cython openblas openmpi llvm-openmp

Full example to build STEPS on Apple M1 Silicon with Python 3.8 through Miniconda

Prerequisites:

Install latest XCode
Install Miniconda3 macOS Apple M1 64-bit

CONDA_DIR=/path/to/miniconda
export PATH=$CONDA_DIR/bin:$PATH
conda install -c conda-forge \
  boost-cpp   \
  cmake       \
  cython      \
  gfortran    \
  gmsh        \
  llvm-openmp \
  matplotlib  \
  mpi4py      \
  mpich       \
  nose        \
  numpy       \
  openblas    \
  pkg-config  \
  scipy
export MPICH_FC=$CONDA_DIR/bin/gfortran
export MPICH_CC=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
export MPICH_CXX=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++

# Fetch and build PETSc
cd /path/to/src
git clone -b release https://gitlab.com/petsc/petsc.git petsc
pushd petsc
./configure --prefix=/path/to/petsc/installation --with-64-bit-indices=1 --with-debugging=0 \
            --with-scalar-type=real --with-x=0 --CC=mpicc --CXX=mpicxx --F77=mpif77 --FC=mpif90 \
            "MAKEFLAGS=$MAKEFLAGS"
make
make install
export PKG_CONFIG_PATH="/path/to/petsc/installation/lib/pkgconfig:$PKG_CONFIG_PATH"
popd

cd /path/to/src
git clone -b tags/4.0.0 --recursive https://github.com/CNS-OIST/STEPS.git
cd STEPS
mkdir __build
cd __build
export CC=mpicc
export CXX=mpicxx
cmake ..
make
make install

Validation and Examples

Short validation tests (running in a few minutes, using serial solvers only) can be found in this repository, under test/validation
Longer validation tests (using serial and parallel solvers) can be found in the STEPS_Validation repository
Examples scripts (including tutorials and papers models) can be found in the STEPS_Example repository

Code Formatting and Static Analysis

The hpc-coding-conventions submodule is responsible for the code formatting and static analysis.

To activate code formatting of both C/C++ and CMake files, enable the CMake variable STEPS_FORMATTING (-DSTEPS_FORMATTING:BOOL=ON). This will add the following make targets: clang-format, check-clang-format, cmake-format, check-cmake-format.
To activate static analysis of C++ files with clang-tidy, enable the CMake variable STEPS_STATIC_ANALYSIS (-DSTEPS_STATIC_ANALYSIS:BOOL=ON). This will add the following make target: clang-tidy.

Thorough instructions on how to perform code formatting and static analysis can be found in the submodule's repository.

Documentation

You can find STEPS user manual and other documentation from the STEPS official website http://steps.sourceforge.net

musicinmybrain / steps Goto Github PK

steps's Introduction