diff --git a/Dockerfile b/Dockerfile index 612bf24..9bcb986 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,53 +1,58 @@ FROM debian:stable-slim ## Singularity build steps: ## $ docker build -t tamaas --build-arg USE_MPI=True [--build-arg ...] . ## $ docker save -o tamaas.tar ## $ singularity build tamaas.sif docker-archive://tamaas.tar MAINTAINER Lucas Frérot # Add contrib and non-free RUN sed -i 's/main/main contrib non-free/' /etc/apt/sources.list # Install build and runtime dependencies RUN apt-get -qq update && apt-get install -qq -y \ g++ \ git \ libboost-dev \ libthrust-dev \ libfftw3-dev \ libfftw3-mpi-dev \ libopenmpi-dev \ python3-dev \ python3-numpy \ python3-pip \ python3-scipy \ python3-h5py \ python3-netcdf4 \ python3-mpi4py \ scons \ && rm -rf /var/lib/apt/lists/* RUN python3 -m pip install uvw # Basic setup RUN mkdir -p /src/tamaas COPY . /src/tamaas RUN rm -rf /src/tamaas/build-* # Build arguments ARG BACKEND=cpp ARG FFTW_THREADS=none ARG USE_MPI=False # Compiling and installing RUN cd /src/tamaas \ && scons \ backend=$BACKEND \ fftw_threads=$FFTW_THREADS \ use_mpi=$USE_MPI \ verbose=true \ prefix=/usr/local \ && scons install \ && cd / && rm -rf /src/tamaas + +# Do not use modules in ~/.local +# Singularity mounts the entire $HOME by default which conflicts if Tamaas +# is already installed there +ENV PYTHONNOUSERSITE=1 diff --git a/doc/sphinx/source/quickstart.rst b/doc/sphinx/source/quickstart.rst index 88d8e29..777c8af 100644 --- a/doc/sphinx/source/quickstart.rst +++ b/doc/sphinx/source/quickstart.rst @@ -1,237 +1,257 @@ Quickstart ---------- Here is a quick introduction to get you started with Tamaas. Installation from PyPI ^^^^^^^^^^^^^^^^^^^^^^ If you have a Linux system, you can simply run ``python3 -m pip install tamaas``. This installs the latest stable version of Tamaas from `PyPI `_. You can get the latest cutting-edge build of Tamaas with: .. code-block:: bash python3 -m pip install \ --extra-index-url https://gitlab.com/api/v4/projects/19913787/packages/pypi/simple \ tamaas .. note:: To limit the number of statically linked dependencies in the wheel package, the builds that can be installed via PyPI or the GitLab package registery do not include parallelism or architecture specific optimizations. If you want to execute Tamaas in parallel, or want to improve performance, it is highly recommanded that you compile from source with the instructions below. Docker image ^^^^^^^^^^^^ Docker images are automatically built and pused to the Gitlab registry. To get the latest image simply run: .. code-block:: bash docker pull registry.gitlab.com/tamaas/tamaas # to rename for convenience docker tag registry.gitlab.com/tamaas/tamaas tamaas Then you can run scripts directly: .. code-block:: bash docker run -v $PWD:/app -t tamaas python3 /app/your_script.py # or docker run tamaas tamaas surface --sizes 16 16 --cutoffs 4 4 8 --hurst 0.8 | docker run -i tamaas tamaas contact 0.1 > results.npy The ``Dockerfile`` at the root of the Tamaas repository can be used to build an image containing Tamaas with a full set of dependencies and customize the build options. Simply run: .. code-block:: bash docker build -t tamaas . .. tip:: The following arguments can be passed to docker to customize the Tamaas build (with the ``--build-arg`` flag for ``docker build``): - ``BACKEND``: parallelism model for loops - ``FFTW_THREADS``: parallelism model for FFTW3 - ``USE_MPI``: compile an MPI-parallel version of Tamaas See below for explanations. + +Singularity container +^^^^^^^^^^^^^^^^^^^^^ + A `singularity `_ container can be created from the docker image with: .. code-block:: bash singularity build tamaas.sif docker://registry.gitlab.com/tamaas/tamaas +To run the image with MPI: + +.. code-block:: bash + + mpirun singularity exec --home=$PWD tamaas.sif python3 + +.. warning:: + + The Docker image on Gitlab is built with MPI support with OpenMPI from the + latest Debian stable. If running the singularity container is run in a cluster + environment, make sure the vendored MPI is compatible with the one `provided + by Debian + `_. + Otherwise you will have to build the singularity container yourself with the + proper MPI version. + Installation from source ^^^^^^^^^^^^^^^^^^^^^^^^ First make sure the following dependencies are installed for Tamaas: - a **C++ compiler** with full **C++14** and **OpenMP** support - **SCons** (python build system) - **FFTW3** - **thrust** (1.9.2+) - **boost** (pre-processor) - **python 3+** with **numpy** - **pybind11** (included as submodule) - **expolit** (included as submodule) Optional dependencies are: - an MPI implementation - **FFTW3** with MPI/threads/OpenMP (your pick) support - **scipy** (for nonlinear solvers) - **uvw**, **h5py**, **netCDF4** (for dumpers) - **googletest** and **pytest** (for tests) - **Doxygen** and **Sphinx** (for documentation) .. tip:: On a HPC environment, use the following variables to specify where the dependencies are located: - ``FFTW_ROOT`` - ``THRUST_ROOT`` - ``BOOST_ROOT`` - ``PYBIND11_ROOT`` - ``GTEST_ROOT`` .. note:: You can use the provided Dockerfile to build an image with the external dependencies installed. You should first clone the git repository with the submodules that are dependencies to tamaas (`pybind11 `_ and `googletest `_):: git clone --recursive https://gitlab.com/tamaas/tamaas.git The build system uses `SCons `_. In order to compile Tamaas with the default options:: scons After compiling a first time, you can edit the compilation options in the file ``build-setup.conf``, or alternatively supply the options directly in the command line: .. code-block:: bash scons option=value [...] To get a list of **all** build options and their possible values, you can run ``scons -h``. You can run ``scons -H`` to see the SCons-specific options (among them ``-j n`` executes the build with ``n`` threads and ``-c`` cleans the build). Note that the build is aware of the ``CXX`` and ``CXXFLAGS`` environment variables. Once compiled, you can install the python module with: .. code-block:: bash scons install prefix=/your/prefix The above command automatically calls ``pip(3)`` if it is installed, and falls back on ``setuptools`` otherwise. If you do not want to install Tamaas, you can use the following command:: scons dev This creates a symlink in ``~/.local/lib//site-packages`` and is equivalent to ``pip(3) install -e`` or ``./setup.py develop``. You can check that everything is working fine with: .. code-block:: bash python3 -c 'import tamaas; print(tamaas)' Important build options ....................... Here are a selected few important compilation options: ``build_type`` Controls the type of build, which essentially changes the optimisation level (``-O0`` for ``debug``, ``-O2`` for ``profiling`` and ``-O3`` for ``release``) and the amount of debug information. Default type is ``release``. Accepted values are: - ``release`` - ``debug`` - ``profiling`` ``CXX`` Compiler (uses the environment variable ``CXX`` by default). ``CXXFLAGS`` Compiler flags (uses the environment variable ``CXXFLAGS`` by default). Useful to add tuning flags (e.g. ``-march=native -mtune=native`` for GCC or ``-xHOST`` for Intel), or additional optimisation flags (e.g. ``-flto`` for link-time optimization). ``backend`` Controls the Thrust parallelism backend. Defaults to ``omp`` for OpenMP. Accepted values are: - ``omp``: OpenMP - ``cpp``: Sequential - ``tbb`` (unsupported): Threading Building Blocks ``fftw_threads`` Controls the FFTW thread model. Defaults to ``omp`` for OpenMP. Accepted values are: - ``omp``: OpenMP - ``threads``: PThreads - ``none``: Sequential ``use_mpi`` Activates MPI-parallelism (boolean value). More details on the above options can be found in :doc:`performance`. Building the docs ^^^^^^^^^^^^^^^^^ Documentation is built using ``scons doc``. Make sure to have the correct dependencies installed (they are already provided in the Docker image). Running the contact pipe tools ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Once installed, the python package provides a `tamaas` command, which defines three subcommands that can be used to explore the mechanics of elastic rough contact: - ``surface`` generates randomly rough surfaces (see :doc:`rough_surfaces`) - ``contact`` solves an elastic contact problem with a surface read from ``stdin`` (see :doc:`contact`) - ``plot`` plots the surface tractions and displacements read from ``stdin`` Here's a sample command line for you to try out: .. code-block:: bash tamaas surface --cutoffs 2 4 64 --size 512 512 --hurst 0.8 | tamaas contact 1 | tamaas plot Check out the help of each command (e.g. ``tamaas surface -h``) for a description of the arguments. Running the tests ^^^^^^^^^^^^^^^^^ You need to activate the ``build_tests`` option to compile the tests: .. code-block:: bash scons build_tests=True Tests can then be run with the ``scons test`` command. Make sure you have `pytest `_ installed.