diff --git a/Docs/sphinx_documentation/source/BuildingCMake.rst b/Docs/sphinx_documentation/source/BuildingCMake.rst deleted file mode 100644 index 5b72568a..00000000 --- a/Docs/sphinx_documentation/source/BuildingCMake.rst +++ /dev/null @@ -1,279 +0,0 @@ -Building incflo with CMake -============================ - -CMake build is a two-steps process. First ``cmake`` is invoked to create -configuration files and makefiles in a chosen directory (``builddir``). -Next, the actual build is performed by invoking ``make`` from within ``builddir``. -The CMake build process is summarized as follows: - -.. highlight:: console - -:: - - mkdir /path/to/builddir - cd /path/to/builddir - cmake [options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] /path/to/incflo - make - -In the above snippet, ``[options]`` indicates one or more options for the -customization of the build, as described later in this section. -If the option ``CMAKE_BUILD_TYPE`` is omitted, -``CMAKE_BUILD_TYPE=Release`` is assumed. - -There are two modes to build incflo with CMake: - -o **SUPERBUILD (recommended):** AMReX is built as part -of the incflo build process. This method is strongly encouraged as it -ensures that the configuration options for incflo and AMReX are consistent. - -o **STANDALONE:** incflo source code is built separately and linked to an existing -AMReX installation. This is ideal for continuous integration severs (CI) -and regression testing applications. AMReX library version and configuration options -must meet incflo requirements. - - - -.. note:: - **incflo requires CMake 3.14 or higher.** - -.. _sec:build:superbuild: - -SUPERBUILD Instructions (recommended) -------------------------------------- - -In this mode, incflo CMake inherents AMReX CMake targets and configuration options, that is, incflo and AMReX are configured and built as a single entity. - -First you need to download the AMReX source code as shown in -`AMReX user guide - Downloading the code `_. - -Next, clone the incflo repository and build the incflo executable: - -.. code:: shell - - > git clone http://github.com/amrex-codees/incflo.git - > cd incfo - > mkdir build - > cd build - > cmake -DAMREX_HOME=/path/to/amrex/source/directory [amrex options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. - > make -j - -``AMREX_HOME`` in the snippet above is a CMake variable pointing to the top-level source directory of the AMReX distribution you downloaded earlier. -``[amrex options]`` is a list of any of the AMReX configuration options listed in the -`AMReX user guide - Building with CMake `_ - - -.. _sec:build:standalone: - -**STANDALONE** instructions ---------------------------------------------------------------------- - -If ``AMREX_HOME`` is not set (see :ref:`sec:build:superbuild`), incflo CMake will look for an existing -AMReX installation on the system and link the incflo binaries against it. . - -Building AMReX -~~~~~~~~~~~~~~~~~~~ - -Clone AMReX from the official Git repository and checkout the -*development* branch: - -.. code:: shell - - > git clone https://github.com/AMReX-Codes/amrex.git - > cd amrex - > git checkout development - -Next, configure, build and install AMReX as follows: - -.. code:: shell - - > mkdir build - > cd build - > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir .. - > make install - -``[amrex options]`` is a list of any of the AMReX configuration options listed in the -`AMReX user guide - Building with CMake `_. -We suggest to always use the option ``-DUSE_XSDK_DEFAULTS=yes`` when building AMReX for incflo. - - -Building incflo -~~~~~~~~~~~~~~~~~ - - -Clone and build incflo: - -.. code:: shell - - > git clone https://github.com/amrex-codes/incflo.git - > mkdir build - > cd build - > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [incflo options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir .. - > make -j - - -Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search -``/absolute/path/to/amrex/installdir`` before searching system paths -for an available AMReX installation. -``AMReX_ROOT`` can also be set as an environmental variable instead of passing it as a command line option. - - -``[incflo options]`` indicates any of the configuration option listed in the table below. - -+-----------------+------------------------------+------------------+-------------+ -| Option name | Description | Possible values | Default | -| | | | value | -+=================+==============================+==================+=============+ -| CMAKE\_CXX\ | User-defined C++ flags | valid C++ | None | -| _FLAGS | | compiler flags | | -+-----------------+------------------------------+------------------+-------------+ -| CMAKE\_CUDA\ | User-defined CUDA flags | valid CUDA | None | -| _FLAGS | | compiler flags | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_DIM | Dimensionality of the build | 2/3 | 3 | -| | | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_MPI | Enable build with MPI | no/yes | yes | -| | | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_OMP | Enable build with OpenMP | no/yes | no | -| | | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_CUDA | Enable build with CUDA | no/yes | no | -| | | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_EB | Build Embedded Boundary | no/yes | no | -| | support | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_HYPRE | Enable HYPRE support | no/yes | no | -| | | | | -+-----------------+------------------------------+------------------+-------------+ -| INCFLO\_FPE | Build with Floating-Point | no/yes | no | -| | Exceptions checks | | | -+-----------------+------------------------------+------------------+-------------+ - - - - -Few more notes on building incflo ------------------------------------ - -The system default C++ compiler can be overwritten as follows: - -.. code:: shell - - > cmake -DCMAKE_CXX_COMPILER= [options] .. - -When building on a platform that uses the ``module`` utility, use either -the above command (with full path to the compilers) or the following: - -.. code:: shell - - > cmake -DCMAKE_CXX_COMPILER=CC [options] .. - -incflo uses the same compiler flags used to build AMReX, unless -``CMAKE_CXX_FLAGS`` is explicitly provided, or -the environmental variables ``CXXFLAGS`` is set. - - -Building incflo for Cori (NERSC) ------------------------------------ - -Standard build -~~~~~~~~~~~~~~~~~~~ - -For the Cori cluster at NERSC, you first need to load/unload modules required to build incflo. - -.. code:: shell - - > module unload altd - > module unload darshan - > module load cmake/3.14.0 - -The default options for Cori are the **Haswell** architecture and **Intel** compiler, if you want to compile with the **Knight's Landing (KNL)** architecture: - -.. code:: shell - - > module swap craype-haswell craype-mic-knl - -Or use the **GNU** compiler: - -.. code:: shell - - > module swap PrgEnv-intel PrgEnv-gnu - -Now incflo can be built following the :ref:`sec:build:superbuild`. - -.. note:: - - The load/unload modules options could be saved in the `~/.bash_profile.ext` - - -GPU build -~~~~~~~~~~~~~~~~~~~ - -To compile on the GPU nodes in Cori, you first need to purge your modules, most of which won't work on the GPU nodes - -.. code:: shell - - > module purge - -Then, you need to load the following modules: - -.. code:: shell - - > module load modules esslurm gcc cuda openmpi/3.1.0-ucx cmake/3.14.0 - -Currently, you need to use OpenMPI; mvapich2 seems not to work. - -Then, you need to use slurm to request access to a GPU node: - -.. code:: shell - - > salloc -N 1 -t 02:00:00 -c 80 -C gpu -A m1759 --gres=gpu:8 --exclusive - -This reservers an entire GPU node for your job. Note that you can’t cross-compile for the GPU nodes - you have to log on to one and then build your software. - -Finally, navigate to the base of the incflo repository and compile in GPU mode: - -.. code:: shell - - > cd incflo - > mdkir build - > cd build - > cmake -DINCFLO_CUDA=yes -DAMReX_CUDA_ARCH=Volta -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran .. - > make -j - -For more information about GPU nodes in Cori -- ``_ - -Building incflo for Summit (OLCF) ------------------------------------ - -For the Summit cluster at OLCF, you first need to load/unload modules required to build incflo. - -.. code:: shell - - > module unload xalt - > module unload darshan - > module load gcc - > module load cmake/3.14.0 - -Now incflo can be built following the :ref:`sec:build:superbuild`. - -To build incflo for GPUs, you need to load cuda module: - -.. code:: shell - - > module load cuda/10.1.105 - -To compile for GPUs: - -.. code:: shell - - > cd incflo - > mdkir build - > cd build - > cmake -DCMAKE_CXX_COMPILER=g++ -DINCFLO_CUDA=yes - > make -j - -An example of a *submission_script* for using the GPUs on Summit can be found in ``incflo/summit_script.sh``. -For more information about Summit cluster: ``_ diff --git a/Docs/sphinx_documentation/source/BuildingGMake.rst b/Docs/sphinx_documentation/source/BuildingGMake.rst deleted file mode 100644 index 8be70c6a..00000000 --- a/Docs/sphinx_documentation/source/BuildingGMake.rst +++ /dev/null @@ -1,64 +0,0 @@ -Building incflo with gmake -============================ - -Building incflo with gmake - -If you want to use gmake to build incflo, you will need to have already -cloned amrex into a local directory: - -.. code:: shell - - > git clone https://github.com/amrex-codes/amrex - -Then, - -.. code:: shell - - > git clone http://github.com/amrex-codes/incflo.git - > cd incflo - -Now decide whether you want to build the executable in 2-D vs 3-D, -with EB (embedded boundaries / cut cells) or not. For this example, -let's say you want to build in 2-D with cut cells. Then - -.. code:: shell - - > git clone http://github.com/amrex-codes/incflo.git - > cd test_2d - -(The other directories are test_3d, test_no_eb, and test_no_eb_2d.) - -Edit the GNUmakefile to set AMREX_HOME to be the path to the directory -where you have put amrex. Other options that you can set include - -+-----------------+------------------------------+------------------+-------------+ -| Option name | Description | Possible values | Default | -| | | | value | -+=================+==============================+==================+=============+ -| COMP | Compiler (gnu or intel) | gnu / intel | None | -+-----------------+------------------------------+------------------+-------------+ -| USE_MPI | Whether to enable MPI | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| USE_OMP | Whether to enable OpenMP | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| USE_CUDA | Whether to enable CUDA | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| DEBUG | Whether to use DEBUG mode | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| PROFILE | Include profiling info | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| TINY_PROFILE | Include tiny profiling info | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| COMM_PROFILE | Include comm profiling info | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ -| TRACE_PROFILE | Include trace profiling info | TRUE / FALSE | FALSE | -+-----------------+------------------------------+------------------+-------------+ - -.. note:: - **Do not set both USE_OMP and USE_CUDA to true.** - -Then type - -.. code:: shell - - > make diff --git a/Docs/sphinx_documentation/source/GettingStarted.rst b/Docs/sphinx_documentation/source/GettingStarted.rst index 02de2396..1dc4f6b6 100644 --- a/Docs/sphinx_documentation/source/GettingStarted.rst +++ b/Docs/sphinx_documentation/source/GettingStarted.rst @@ -1,10 +1,375 @@ .. _Chap:GettingStarted: Getting Started -=============== +*************** +This section walks you through a brief introduction to using incflo. + +.. + alternative to `` `` is :code:` ` + + +.. _sec:Download: + +Downloading the code +==================== +incflo is built on top of the AMReX framework. In order to run +incflo, you must download separate git modules for incflo, AMReX +and AMReX-Hydro. + +First, make sure that git is installed on your machine. + +#. Download the AMReX repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Codes/amrex.git + + This will create a folder called ``amrex/`` on your machine. + For additional information on downloading the AMReX source code see `AMReX user guide - Downloading the code `_. + + +#. Download the AMReX-Hydro repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Codes/AMReX-Hydro.git + + This will create a folder called ``AMReX-Hydro/`` on your machine. + +#. Download the incflo repository by typing: + + .. code:: shell + + git clone https://github.com/AMReX-Codes/incflo.git + + This will create a folder called ``incflo/`` on your machine. + +You will want to periodically update each of these repositories +by typing ``git pull`` within each repository. + +Next, you can choose to either :ref:`sec:GNUMake` or :ref:`sec:CMake`. + + +.. _sec:GNUMake: + +Building with GNU Make +====================== + +Here, we walk you through compiling an incflo executable. +Decide whether you want to build the executable in 2-D vs 3-D, +with or without EB (embedded boundaries / cut cells), and choose the corresponding +directory: ``test_2d``, ``test_3d``, ``test_no_eb_2d``, or ``test_no_eb``. +For this example, let's say you want to build in 2-D with cut cells. +Then to build the code: + +#. ``cd`` to the desired build directory; e.g. + + .. code:: shell + + cd incflo/test_2d + + +#. Edit the ``GNUmakefile``: + + Set AMREX_HOME to be the path to the directory where you have put amrex. NOTE: when setting ``AMREX_HOME`` in the ``GNUmakefile``, be aware that ``~`` does not expand, so ``AMREX_HOME=~/amrex/`` will yield an error. + + Alternatively, the path to AMReX can be set up as an environment variable, ``AMREX_HOME``, on your machine to point to the path name where you have put AMReX. For example, if you are using the bash shell, you can add this to your ``.bashrc`` as: + + .. highlight:: bash + + :: + + export AMREX_HOME=/path/to/amrex + + alternatively, in tcsh one can set + + .. highlight:: tcsh + + :: + + setenv AMREX_HOME /path/to/amrex + + + Common options that you can set in the GNUMakefile include + + +-----------------+------------------------------+------------------+-------------+ + | Option name | Description | Possible values | Default | + | | | | value | + +=================+==============================+==================+=============+ + | COMP | Compiler (gnu or intel) | gnu / intel | None | + +-----------------+------------------------------+------------------+-------------+ + | USE_MPI | Whether to enable MPI | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | USE_OMP | Whether to enable OpenMP | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | USE_CUDA | Whether to enable CUDA | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | DEBUG | Whether to use DEBUG mode | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | PROFILE | Include profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | TINY_PROFILE | Include tiny profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | COMM_PROFILE | Include comm profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + | TRACE_PROFILE | Include trace profiling info | TRUE / FALSE | FALSE | + +-----------------+------------------------------+------------------+-------------+ + + .. note:: + **Do not set both USE_OMP and USE_CUDA to true.** + + Additional options and information on using other compilers can be found in the + AMReX documentation at + https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html . + + +#. Make the executable: + + Now type + + .. code:: shell + + make + + The name of the resulting executable (generated by the make system) encodes several of the build characteristics, including dimensionality of the problem, compiler name, and whether MPI and/or OpenMP were linked with the executable. + Thus, several different build configurations may coexist simultaneously in a problem folder. + For example, the default build in ``incflo/test_2d`` will look + like ``incflo2d.gnu.MPI.EB.ex``, indicating that this is a 2-d version of the code, made with + ``COMP=gnu``, ``USE_MPI=TRUE`` and support for embedded boundaries (EB). + + +.. _sec:CMake: + +Building with CMake +=================== + +CMake build is a two-steps process. First ``cmake`` is invoked to create +configuration files and makefiles in a chosen directory (``builddir``). +Next, the actual build is performed by invoking ``make`` from within ``builddir``. +The CMake build process is summarized as follows: + +.. highlight:: console + +:: + + mkdir /path/to/builddir + cd /path/to/builddir + cmake [options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] /path/to/incflo + make + +In the above snippet, ``[options]`` indicates one or more options for the +customization of the build, as described later in this section. +If the option ``CMAKE_BUILD_TYPE`` is omitted, +``CMAKE_BUILD_TYPE=Release`` is assumed. + +There are two modes to build incflo with CMake: + + o **SUPERBUILD (recommended):** AMReX and AMReX-Hydro are built as part + of the incflo build process. This method is strongly encouraged as it + ensures that the configuration options are consistent. + + o **STANDALONE:** incflo source code is built separately and linked to an existing + AMReX installation. This is ideal for continuous integration severs (CI) + and regression testing applications. AMReX library version and configuration options + must meet incflo requirements. + + + +.. note:: + **incflo requires CMake 3.14 or higher.** + +.. _sec:build:superbuild: + +SUPERBUILD Instructions (recommended) +------------------------------------- + +In this mode, incflo CMake inherents AMReX CMake targets and configuration options, as well as AMRex-Hydro CMake targets; that is, incflo, AMReX and AMReX-Hydro are configured and built as a single entity. + +First, make sure you've downloaded all the source code (see :ref:`Download`). + +Next, build the incflo executable: + + .. code-block:: console + + > cd incflo + > mkdir build + > cd build + > cmake -DAMREX_HOME=/path/to/amrex/source/directory [amrex options] -DAMREX_HYDRO_HOME=/path/to/AMReX-Hydro/source/directory -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. + > make -j + + +where ``AMREX_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX distribution you downloaded earlier; ``[amrex options]`` is a list of any of the AMReX configuration options listed in the `AMReX user guide - Building with CMake `_; ``AMREX_HYDRO_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX-Hydro distribution you downloaded earlier; and ``..`` is the relative path pointing to the top-level source directory of incflo or this example. + + +.. _sec:build:standalone: + +**STANDALONE** instructions +--------------------------------------------------------------------- + +For a stand alone build, incflo CMake will look for an existing +AMReX installation on the system and link the incflo binaries against it. + +Building AMReX +~~~~~~~~~~~~~~~~~~~ + +First, make sure you've downloaded all the source code (see :ref:`Download`). + +Next, configure, build and install AMReX as follows: + +.. code:: shell + + > cd /path/to/amrex + > mkdir build + > cd build + > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute/path/to/installdir -DAMREX_HYDRO_HOME=/path/to/AMReX-Hydro/source/directory .. + > make install + +``[amrex options]`` is a list of any of the AMReX configuration options listed in the +`AMReX user guide - Building with CMake `_. +We suggest to always use the option ``-DUSE_XSDK_DEFAULTS=yes`` when building AMReX for incflo. ``AMREX_HYDRO_HOME`` is a CMake variable pointing to the top-level source directory of the AMReX-Hydro distribution you downloaded earlier + + +Building incflo +~~~~~~~~~~~~~~~~~ + + +Build incflo: + +.. code:: shell + + > cd /path/to/incflo + > mkdir build + > cd build + > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [incflo options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir .. + > make -j + + +Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search +``/absolute/path/to/amrex/installdir`` before searching system paths +for an available AMReX installation. +``AMReX_ROOT`` can also be set as an environmental variable instead of passing it as a command line option. + + +``[incflo options]`` indicates any of the configuration option listed in the table below. + ++-----------------+------------------------------+------------------+-------------+ +| Option name | Description | Possible values | Default | +| | | | value | ++=================+==============================+==================+=============+ +| CMAKE\_CXX\ | User-defined C++ flags | valid C++ | None | +| _FLAGS | | compiler flags | | ++-----------------+------------------------------+------------------+-------------+ +| CMAKE\_CUDA\ | User-defined CUDA flags | valid CUDA | None | +| _FLAGS | | compiler flags | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_DIM | Dimensionality of the build | 2/3 | 3 | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_MPI | Enable build with MPI | no/yes | yes | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_OMP | Enable build with OpenMP | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_CUDA | Enable build with CUDA | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_EB | Build Embedded Boundary | no/yes | no | +| | support | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_HYPRE | Enable HYPRE support | no/yes | no | +| | | | | ++-----------------+------------------------------+------------------+-------------+ +| INCFLO\_FPE | Build with Floating-Point | no/yes | no | +| | Exceptions checks | | | ++-----------------+------------------------------+------------------+-------------+ + + + + +Few more notes on building incflo +----------------------------------- + +The system default C++ compiler can be overwritten as follows: + +.. code:: shell + + > cmake -DCMAKE_CXX_COMPILER= [options] .. + +When building on a platform that uses the ``module`` utility, use either +the above command (with full path to the compilers) or the following: + +.. code:: shell + + > cmake -DCMAKE_CXX_COMPILER=CC [options] .. + +incflo uses the same compiler flags used to build AMReX, unless +``CMAKE_CXX_FLAGS`` is explicitly provided, or +the environmental variables ``CXXFLAGS`` is set. + + + +Building incflo for Summit (OLCF) +----------------------------------- + +For the Summit cluster at OLCF, you first need to load/unload modules required to build incflo. + +.. code:: shell + + > module unload xalt + > module unload darshan + > module load gcc + > module load cmake/3.14.0 + +Now incflo can be built following the :ref:`sec:build:superbuild`. + +To build incflo for GPUs, you need to load cuda module: + +.. code:: shell + + > module load cuda/10.1.105 + +To compile for GPUs: + +.. code:: shell + + > cd incflo + > mdkir build + > cd build + > cmake -DCMAKE_CXX_COMPILER=g++ -DINCFLO_CUDA=yes + > make -j + +An example of a *submission_script* for using the GPUs on Summit can be found in ``incflo/summit_script.sh``. +For more information about Summit cluster: ``_ + + +Running the code +================ +incflo takes an input file as its first command-line argument. The file may +contain a set of parameter definitions that will override defaults set in the code. +Many example inputs files can be found in the ``incflo/test_XXX`` directories. +For example, to run the Taylor-Green vortices example in ``incflo/test_2d``, assuming your executable is named ``incflo.ex`` +and is located in the ``test_2d`` directory, then you can simply type: + +.. code:: shell + + > cd incflo/test_2d + > ./incflo.ex benchmark.taylor_green_vortices + + +For more information on inputs options, see the :ref:`Chap:Inputs` section. + +incflo can generate subfolders in the current folder +named ``plt00000``, ``plt00010``, etc, and ``chk00000``, +``chk00010``, etc. These are called plotfiles and checkpoint +files. The plotfiles are used for visualization of derived fields; the checkpoint +files are used for restarting the code. For more information see the AMReX Documentation on +:ref:`amrex:Chap:IO`. + + +Visualizing the Results +======================= + +Options for visualizing the data are discussed in the AMReX Documenation on :ref:`amrex:Chap:Visualization`. -.. toctree:: - :maxdepth: 1 - BuildingCMake - BuildingGMake diff --git a/Docs/sphinx_documentation/source/conf.py b/Docs/sphinx_documentation/source/conf.py index 508b07a4..66e8ff61 100644 --- a/Docs/sphinx_documentation/source/conf.py +++ b/Docs/sphinx_documentation/source/conf.py @@ -44,9 +44,9 @@ def get_incflo_version(): 'breathe'] intersphinx_mapping = { - 'incflo_tutorials': ('https://incflo-codes.github.io/incflo/tutorials_html/', None) - # 'incflo_tutorials': ('../../../sphinx_tutorials/build/html/', - # '../../sphinx_tutorials/build/html/objects.inv') + 'amrex': ('https://amrex-codes.github.io/amrex/docs_html/', None), + 'hydro': ('https://amrex-codes.github.io/amrex/hydro_html/', None) + # 'incflo_tutorials': ('https://incflo-codes.github.io/incflo/tutorials_html/', None) } # Add any paths that contain templates here, relative to this directory. diff --git a/Docs/sphinx_documentation/source/index.rst b/Docs/sphinx_documentation/source/index.rst index e2f8989a..4b8063e4 100644 --- a/Docs/sphinx_documentation/source/index.rst +++ b/Docs/sphinx_documentation/source/index.rst @@ -6,7 +6,7 @@ the variable density incompressible Navier-Stokes equations in the presence of complex geometries. It includes adaptive mesh refinement (AMR) but without subcycling in time. -For an AMReX-based incompressible flow code with subcycling in time, please go to +For an AMReX-based incompressible flow code with subcycling in time, please see IAMR at https://amrex-codes.github.io/IAMR/