Install

Before installing Smilei, you need to install a few dependencies:

  • A C++11 compiler, optionally implementing openMP version > 4.5 (gcc users: v6.0 or newer recommended)

  • an MPI library (by default a version supporting MPI_THREAD_MULTIPLE is required: v4.0 or newer recommended)

  • an HDF5 library compatible with your versions of C++ and MPI

  • Python 2.7 or Python 3+ (with header files)

Optional dependencies are:

Install the dependencies

There are various ways to install all dependencies, depending on the platform:

The command make help can give you some information about your environment.

If you have successfully installed these dependencies on other platforms, please contact us and share!

Setup environment variables for compilation

Several environment variables may be required, depending on your setup.

  • SMILEICXX: the MPI-C++ compiler. Defaults to mpicxx.

  • HDF5_ROOT_DIR: the folder for the HDF5 library. Defaults to $HDF5_ROOT.

  • BUILD_DIR: the folder where the compilation should occur. Defaults to ./build.

  • PYTHONEXE: the python executable to use in smilei. Defaults to python.

  • PICSAR: set to TRUE to enable the PSATD solver from picsar. Defaults to FALSE.

The usual CXXFLAGS and LDFLAGS can also be used to pass other arguments to the compiler and linker.

Download and compile

  1. Clone the latest Smilei version from Github:

    cd /path/of/your/choice/
git clone https://github.com/SmileiPIC/Smilei.git

    If you do not have git, you can dowload a tarball here and extract it in a new folder.

  2. In a terminal, go to that location and compile:

    cd Smilei
make

    If the compilation is successful, you should now have a new smilei executable.

  3. The next step is to write a namelist.

Advanced compilation options

Compile with several processors (fast compilation)

make -j 4

Compilation configuration with keyword “config”

make config=debug           # With debugging output (slow execution)
make config=noopenmp        # Without OpenMP support
make config=no_mpi_tm       # Without a MPI library which supports MPI_THREAD_MULTIPLE
make config=scalasca        # For the Scalasca profiler
make config=advisor         # For Intel Advisor
make config=vtune           # For Intel Vtune
make config=inspector       # For Intel Inspector
make config=detailed_timers # More detailed timers, but somewhat slower execution

It is possible to combine arguments above within quotes, for instance:

make config="debug noopenmp" # With debugging output, without OpenMP

Obtain some information about the compilation

make print-XXX               # Prints the value of makefile variable XXX
make env                     # Prints the values of all makefile variables
make help                    # Gets some help on compilation

Machine-specific compilation

Each machine may require a specific configuration (environment variables, modules, etc.). These instructions may be included in a file of your choice, via the machine argument:

make machine=my_machine_file

where my_machine_file is a file, located in scripts/compile_tools/machine, containing the lines of command to be executed before compilation. If you successfully write such a file for a common supercomputer, please share it with developpers so that it can be included in the next release of Smilei.

Optimization and vectorization options explained

To tune optimization and vectorization options, Smilei uses the machine files described above. They contain compiler options for specific hardware architectures or processor families.

This page explains in detail optimization flags used in machine files and therefore how to generate your own machine file.

Create the documentation

If you have installed the python module sphinx, you can create the documentation (which you are currently reading) with:

make doc

This creates a local html website accessible in your build/html/ folder.

Install the happi module

A python module, happi, is provided to view, extract and post-process data from all the diagnostics. There are several ways to load this module in python.

  1. Recommended:

make happi

This has to be done only once, unless you move the smilei directory elsewhere. This command creates a small file in the Python user-site directory that tells python where to find the module. To remove it use the command make uninstall_happi.

The module will directly be accessible from python:

>>> import happi

  1. Alternative: Execute the Diagnostics.py script from python

Adding a new python module is not always possible. Instead, we provide the script Diagnostics.py which is able to find the happi module and import it into python.

You may add the following command in your own python script:

>>> execfile("/path/to/Smilei/scripts/Diagnostics.py")

Install the smilei_tables tool

Generation of the tables is handled by an external tools. A full documentation is available on the dedicated page.