Meson sekelton code

This repository contains a Meson skeleton. It is used in the High-Performance Computiong: MD with C++ project.

Getting started

Click the Use this template button above, then clone the newly created repository, as described in the first milestone.

Compiling using CLion

Note: for Windows users, please follow these instructions in addition to the text below.

If you are using CLion, you can open your freshly cloned project by clicking on the "Open" button in the CLion welcome window. If prompted, trust the project.

You can change Meson build option in "File > Settings > Build, Execution, Deployment > Meson". This windows allows to set the buildtype option, which controls the level of optimization applied to the code. debug disables optimizations and turns on useful debugging features. This mode should be used when developing and testing code. release turns on aggressive optimization. This mode should be used when running production simulations. Add --buildtype=release or --buildtype=debug to "Setup options" to switch between the two.

To run the first milestone executable, click on the dialog directly right of the green hammer in the upper right toolbar, select "milestone01", and click the green arrow right of that dialog. You should see the output in the "Run" tab, in the lower main window.

To run the tests, select "tests" in the same dialog, then run. In the lower window, on the right, appears a panel that enumerates all the tests that were run and their results.

Try compiling and running for both debug and release configurations. Don't forget to switch between them when testing code or running production simulations.

Compiling from the command line

The command line (terminal) may look daunting at first, but it has the advantage of being the same across all UNIX platforms, and does not depend on a specific IDE. The standard Meson workflow is to create a builddir/ directory which will contain all the build files. To do that, and compile your project, run:

cd <your repository>

# Configure and create build directory
meson setup builddir

# Compile
cd builddir
meson compile

# Run executable and tests
./milestones/01/01
meson test

Note that CLion is by default configured to create a buildDir/ directory (with a capital D).

If there are no errors then you are all set! Note that the flag --buildtype=debug should be changed to --buildtype=release when you run a production simulation, i.e. a simulation with more than a few hundred atoms. This turns on aggressive compiler optimizations, which results in speedup. However, when writing the code and looking for bugs, debug should be used instead.

Try compiling and running tests with both compilation configurations.

Compiling on bwUniCluster, with MPI

The above steps should be done after loading the appropriate packages:

module load compiler/gnu mpi/openmpi

# then in build/
meson setup builddir --buildtype=release
cd builddir
meson compile

How to add code to the repository

There are three places where you are asked to add code:

• src/ is the core of the MD code. Code common to all the simulations you will run should be added here. This includes implementation of time stepping scheme, potentials, thermostats, neighbor lists, atom containers, and implementation files that will be provided by us (e.g. domain decomposition implementation). The meson.build file in src/ creates a static library which is linked to all the other targets in the repository, and which propagates its dependency, so that there is no need to explicitly link against Eigen or MPI.
• tests/ contains tests for the library code code. It uses GoogleTest to define short, simple test cases. This is where you will add tests for the time integration, potentials, thermostats, etc., but it should not contain "real physics" simulations, such as heat capacity calculations.
• milestones/ contains the "real physics" simulations that are required in milestones 04, 07, 08, 09. It should only contain code specific to the milestones, i.e. the main() function running the simulation, and input data files that we provide.

Adding to src/

Adding files to src/ is straightforward: create your files, e.g. lj.h and lj.cpp, then update the lib_sources variable in meson.build:

lib_sources = [  # All source files (excluding headers)
    'hello.cpp',
    'lj.cpp'
]

Adding to tests/

Create your test file, e.g. test_verlet.cpp in tests/, then modify the test_sources variable in tests/meson.build. Test that your test was correctly added by running meson compile in the build directory: your test should show up in the output.

Adding to milestones/

Create a new directory, e.g. with mkdir milestones/04, then add subdir('04') to milestones/meson.build, then create & edit milestones/04/meson.build:

executable(
    'milestone04',
    'main.cpp',
    include_directories : [lib_incdirs],
    link_with : [lib],
    dependencies : [eigen, mpi]
)

You can now create & edit milestones/04/main.cpp, which should include a main() function as follows:

int main(int argc, char* argv[]) {
    return 0;
}

The code of your simulation goes into the main() function.

Input files

We often provide input files (.xyz files) for your simulations, for example in milestone 4. You should place these in e.g. milestones/04/, and add the following to milestones/04/meson.build:

fs = import('fs')
fs.copyfile('lj54.xyz')

This will copy the file milestone/04/lj54.xyz to <build>/milestone/04/lj54.xyz, but only when the executable for the milestone is rebuilt. To trigger a rebuild you can erase the <build>/milestone/04 directory and meson compile again.

Note: .xyz files are ignored by Git. That's on purpose to avoid you staging very large files in the git tree.

Pushing code to GitHub

If you have added files to your local repositories, you should commit and push them to GitHub. To create a new commit (i.e. put your files in the repository's history), simply run:

git status
# Look at the files that need to be added
git add <files> ...
git commit -m '<a meaningful commit message!>'
git push

This repository is setup with continuous integration (CI), so all your tests will run automatically when you push. This is very handy to test if you have breaking changes.

Git in CLion

If you are using CLion, you can use Git directly from its interface. To add files, right click the file you wish to add, then "Git > Add". Once you are ready to commit, "Git > Commit" from the main menu bar. Add a message in the lower left window where it reads "Commit message", then click "Commit" or "Commit and Push...".