STREAM

This directory contains the STartup Runaway Electron Analysis Model (STREAM) code, designed to study the generation of runaway electrons during the startup phase of tokamak operation. The code is based on the Disruption Runaway Electron Avoidance Model (DREAM) code. STREAM works like DREAM to a large extent, and thus the guides regarding compilations and settings in the DREAM documentation also works for STREAM. The online documentation of DREAM is available at https://ft.nephy.chalmers.se/dream.

Requirements

To compile STREAM, you need to have the following software installed:

CMake >= 3.12
A C++17 compatible compiler (such as gcc >= 7.0)
GNU Scientific Library >= 2.0
HDF5
PETSc
OpenMP
MPI (for PETSc)
Python 3 (required for generating ADAS data)

Additionally, to use the STREAM Python interface, you need the following Python packages:

h5py
matplotlib
numpy
packaging
scipy

Notes on PETSc

While most of the software required by STREAM can be installed directly from your Linux distribution's package repository, PETSc usually requires a manual setup. To install PETSc, grab its sources from the PETSc website or clone the PETSc git repository:

$ git clone -b release https://gitlab.com/petsc/petsc.git petsc

After this, compiling PETSc should be a matter of running the following commands:

$ ./configure PETSC_ARCH=linux-c-opt
...
$ make PETSC_DIR=/path/to/petsc PETSC_ARCH=linux-c-opt all
...

Optionally, you can also run make check after make all.

Once PETSc has been compiled with the above commands, you only need to make sure that STREAM will be able to find your PETSc installation. The easiest way to achieve this is to add the PETSC_DIR and PETSC_ARCH environment variables used above to your ~/.bashrc file (if you use bash; if you're unsure, you probably do):

...
export PETSC_DIR="/path/to/petsc"
export PETSC_ARCH=linux-c-opt

Of course, the value for PETSC_DIR should be modified according to where you installed PETSc. An alternative to modifying your ~/.bashrc file is to just give these variables directly to CMake every time you reconfigure STREAM (which is usually not very often, unless you're a STREAM or DREAM developer).

Compilation

To compile STREAM, go to the root STREAM directory and run the following commands:

$ mkdir -p build
$ cd build
$ cmake ..
$ make -j NTHREADS

where NTHREADS is the number of CPU threads on your computer. If CMake can't find PETSc, you can change the cmake command above to read

$ cmake .. -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=linux-c-opt

where /path/to/petsc is the path to the directory containing your PETSc installation.

"PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"

This error can occur if you have only installed MPI locally for PETSc, or if you have multiple MPI implementations (e.g. MPICH and OpenMPI) installed on your system. If you installed MPICH automatically during the configuration of PETSc you should run cmake with the flag

$ cmake .. -DMPI_CXX_COMPILER=/path/to/petsc/linux-c-opt/bin/mpicxx

Alternatively, if you compiled PETSc with an MPI installation you should specify

$ cmake .. -DMPI_EXECUTABLE_SUFFIX=.mpich

if you compiled PETSc with MPICH, or

$ cmake .. -DMPI_EXECUTABLE_SUFFIX=.openmpi

if you compiled PETSc with OpenMPI.

Documentation