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blb/organizational/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: df447852406e9463907efbcfc12315b4
+tags: 645f666f9bcd5a90fca523b33c5a78b7

blb/organizational/_sources/index.rst.txt

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+.. Phoebus documentation master file, created by
+   sphinx-quickstart on Thu Sep 26 15:18:20 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Phoebus: Performance portable GRRMHD for supernovae, mergers, and more
+======================================================================
+
+`Phoebus`_ is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the `Parthenon`_ adaptive mesh refinement framework.
+
+.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon
+.. _Phoebus: https://github.com/lanl/phoebus
+
+Key Features
+^^^^^^^^^^^^^
+
+* Finite volume GRMHD
+* Neutrino transport with Monte Carlo and moment methods
+* Analytic and tabulated spacetimes
+* Monopolar general relativistic gravity for core-collapse supernovae
+* Lagrangian tracer particles
+* Support for arbitrary equations of state
+
+.. note::
+
+   These docs are under active development.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+   :glob:
+
+   src/*
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

blb/organizational/_sources/src/building.rst.txt

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+Building
+========
+
+Obtaining the Source Code
+-------------------------
+
+``phoebus`` uses submodules extensively. To make sure you get them all,
+clone it as
+
+.. code:: bash
+
+   git clone --recursive git@github.com:lanl/phoebus.git
+
+or as
+
+.. code:: bash
+
+   git clone git@github.com:lanl/phoebus.git
+   cd phoebus
+   git submodule update --init --recursive
+
+
+Prerequisites
+-------------
+
+To build ``phoebus``, you need to create a build directly, as in-source builds are not supported.
+After cloning the repository,
+
+.. code:: bash
+
+   cd phoebus
+   mkdir bin
+   cd bin
+
+Example builds
+--------------
+
+Below are some example build commands
+
+MPI-parallel only
+~~~~~~~~~~~~~~~~~
+
+The following will build ``phoebus`` with MPI parallelism but no shared
+memory parallelism
+
+.. code:: bash
+
+   cmake ..
+   make -j
+
+OpenMP-parallel
+~~~~~~~~~~~~~~~
+
+The following will build ``phoebus`` with OpenMP parallelism only
+
+.. code:: bash
+
+   cmake -DPHOEBUS_ENABLE_MPI=Off -DPHOEBUS_ENABLE_OPENMP=ON ..
+   make -j
+
+Cuda
+~~~~
+
+The following will build ``phoebus`` with no MPI or OpenMP parallelism.
+
+.. code:: bash
+
+   cmake -DPHOEBUS_ENABLE_CUDA=On -DCMAKE_CXX_COMPILER=${HOME}/phoebus/external/singularity-eos/utils/kokkos/bin/nvcc_wrapper -DKokkos_ARCH_HSW=ON -DKokkos_ARCH_VOLTA70=ON -DPHOEBUS_ENABLE_MPI=OFF ..
+
+A few notes for this one: - Note here the ``-DCMAKE_CXX_COMPILER`` flag.
+This is necessary. You *must* set the compiler to ``nvcc_wrapper``
+provided by Kokkos. - Note the ``-DKokkos_ARCH_*`` flags. Those set the
+host and device microarchitectures and are required. The choice here is
+on an ``x86_64`` machine with a ``volta`` GPU.
+
+Build Options
+-------------
+
+The build options explicitly provided by ``phoebus`` are:
+
++-----------------------+----------+-----------------------------------------------+
+| Option                | Default  | Comment                                       |
++=======================+==========+===============================================+
+| PHOEBUS_ENABLE_CUDA   | OFF      | Cuda                                          |
++-----------------------+----------+-----------------------------------------------+
+| PHOEBUS_ENABLE_HDF5   | ON       | HDF5. Required for output and restarts.       |
++-----------------------+----------+-----------------------------------------------+
+| PHOEBUS_ENABLE_MPI    | ON       | MPI. Required for distributed memory          |
+|                       |          | parallelism.                                  |
++-----------------------+----------+-----------------------------------------------+
+| PHOEBUS_ENABLE_OPENMP | OFF      | OpenMP. Required for shared memory            |
+|                       |          | parallelism.                                  |
++-----------------------+----------+-----------------------------------------------+
+| MACHINE_CFG           | None     | Machine-specific config file, optional.       |
++-----------------------+----------+-----------------------------------------------+
+
+Some relevant settings from Parthenon and Kokkos you may need to play
+with are:
+
++---------------------+----------+---------------------------------------------+
+| Option              | Default  | Comment                                     |
++=====================+==========+=============================================+
+| CMAKE_CXX_COMPILER  | None     | Must be set to ``nvcc_wrapper`` with cuda   |
+|                     |          | backend                                     |
++---------------------+----------+---------------------------------------------+
+| Kokkos_ARCH_XXXX    | OFF      | You must set the GPU architecture when      |
+|                     |          | compiling for Cuda                          |
++---------------------+----------+---------------------------------------------+
+
+You can see all the Parthenon build options
+`here <https://github.com/lanl/parthenon/blob/develop/docs/building.md>`__
+and all the Kokkos build options
+`here <https://github.com/kokkos/kokkos/wiki/Compiling>`__
+
+Cmake machine configs
+---------------------
+
+If you are proficient with ``cmake`` You can optionally write a
+``cmake`` file that sets the configure parameters that you like on a
+given machine. Both ``phoebus`` and ``parthenon`` can make use of it.
+You can point to the file with
+
+::
+
+   -DMACHINE_CFG=path/to/machine/file
+
+at config time or by setting the environment variable ``MACHINE_CFG`` to
+point at it, e.g.,
+
+.. code:: bash
+
+   export MACHINE_CFG=path/to/machine/file
+
+An example machine file might look like
+
+::
+
+   # Machine file for x86_64-volta on Darwin
+   message(STATUS "Loading machine configuration for Darwin x86-volta node")
+   message(STATUS "Assumes: module load module load gcc/7.4.0 cuda/10.2 openmpi/4.0.3-gcc_7.4.0 anaconda/Anaconda3.2019.10 cmake && spack load hdf5")
+   message(STATUS "Also assumes you have a valid spack installation loaded.")
+
+   set(PHOEBUS_ENABLE_CUDA ON CACHE BOOL "Cuda backend")
+   set(PHOEBUS_ENABLE_MPI OFF CACHE BOOL "No MPI")
+   set(Kokkos_ARCH_HSW ON CACHE BOOL "Haswell target")
+   set(Kokkos_ARCH_VOLTA70 ON CACHE BOOL "volta target")
+   set(CMAKE_CXX_COMPILER /home/jonahm/phoebus/external/parthenon/external/Kokkos/bin/nvcc_wrapper CACHE STRING "nvcc wrapper")
+
+you could then configure and compile as
+
+.. code:: bash
+
+   cmake -DMACHINE_CFG=path/to/machine/file ..
+   make -j
+
+Running
+-------
+
+Run phoebus from the ``build`` directory as
+
+.. code:: bash
+
+   ./src/phoebus -i path/to/input/file.pin
+
+The input files are in ``phoebus/inputs/*``. There’s typically one input
+file per problem setup file.
+
+Submodules
+----------
+
+-  ``parthenon`` asynchronous tasking and block-AMR infrastructure
+-  ``singularity-eos`` provides performance-portable equations of state
+   and PTE solvers
+-  ``singularity-opac`` provides performance-portable opacities and
+   emissivities
+-  ``Kokkos`` provides performance portable shared-memory parallelism.
+   It allows our loops to be CUDA, OpenMP, or something else. By default
+   we use the ``Kokkos`` shipped with ``parthenon``.
+
+External (Required)
+-------------------
+
+-  ``cmake`` for building
+
+Optional
+--------
+
+-  ``hdf5`` for output (must be parallel if MPI is enabled)
+-  ``MPI`` for distributed memory parallelism
+-  ``python3`` for visualization

blb/organizational/_sources/src/code_of_conduct.rst.txt

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+.. _lanlcode: https://lanl.github.io/singularity-eos
+
+Code of Conduct
+=====================================
+
+We as users, members, contributors, and leaders agree to make participation in our
+community a harassment-free experience for everyone.
+We will interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+We agree to uphold the `LANL Code of Conduct <lanlcode>`_ in all spaces relevant.
+Of note:
+
+::
+
+   -  Foster a mutually respectful working environment that is free from
+      discrimination, intimidation, and harassment (including sexual
+      harassment).
+   -  Do not discriminate against others on the basis of any
+      characteristic protected by law or LANL policy.
+   -  Do not engage in behaviors that create an offensive, hostile, or
+      intimidating work environment, including shouting, abusive
+      language, threats of violence, the use of obscenities or other
+      non-verbal expressions of aggression, horseplay such as kicking
+      co-workers’ chairs or using personal insults, or the use of
+      offensive nicknames or other derogatory remarks.
+   -  Avoid behavior that a reasonable person would find to be demeaning
+      or humiliating.