.. _outputs: Outputs ======= Outputs from Parthenon are controlled via ```` blocks, where ``*`` should be replaced by a unique integer for each block. To disable an output block without removing it from the input file set the block's ``dt < 0.0``. In addition to time base outputs, two additional options to trigger outputs (applies to HDF5, restart and histogram outputs) exist. - Signaling: If ``Parthenon`` catches a signal, e.g., ``SIGALRM`` which is often sent by schedulers such as Slurm to signal a job of exceeding the job's allocated walltime, ``Parthenon`` will gracefully terminate and write output files with a ``final`` id rather than a number. This also applies to the ``Parthenon`` internal walltime limit, e.g., when executing an application with the ``-t HH:MM:SS`` parameter on the command line. - File trigger: If a user places a file with the name ``output_now`` in the working directory of a running application, ``Parthenon`` will write output files with a ``now`` id rather than a number. After the output is being written the ``output_now`` file is removed and the simulation continues normally. The user can repeat the process any time by creating a new ``output_now`` file. Note, in both cases the original numbering of the output will be unaffected and the ``final`` and ``now`` files will be overwritten each time without warning. HDF5 ---- Parthenon allows users to select which fields are captured in the HDF5 (``.phdf``) dumps at runtime. In the input file, include a ```` block, list of variables, and specify ``file_type = hdf5``. A ``dt`` parameter controls the frequency of outputs for simulations involving evolution. If the optional parameter ``single_precision_output`` is set to ``true``, all variable data will be written in single precision. A ```` block might look like :: file_type = hdf5 write_xdmf = true # Determines whether xdmf annotations are output # nonexistent variables/swarms are ignored variables = density, velocity, & # comments are still ok energy # notice the & continuation character # for multiline lists swarms = tracers, photons # Particle swarms swarm_variables = x, y, z # swarm variables output for every swarm # Each swarm can sepcify in a separate list which additional # variables it would like to output. tracers_variables = x, y, z, rho, id photons_variables = x, y, z, frequency dt = 1.0 file_number_width = 6 # default: 5 use_final_label = true # default: true # Sparse variables may not be allocated on every block. By default # parthenon outputs de-allocated variables as 0 in the output # file. However, it is often convenient to output them as NaN # instead, marking deallocated and allocated but zero as # separate. This flag turns this functionality on. sparse_seed_nans = false # default false This will produce an hdf5 (``.phdf``) output file every 1 units of simulation time containing the density, velocity, and energy of each cell. The files will be identified by a 6-digit ID, and the output file generated upon completion of the simulation will be labeled ``*.final.*`` rather than with the integer ID. HDF5 and restart files write variable field data with inline compression by default. This is especially helpful when there are sparse variables allocated only in a few blocks, because all other blocks would write zeros of these variables, which can drastically increase output file size (and decrease I/O performance) without compression. The optional parameter ``hdf5_compression_level`` can be used to set the compression level (between 1 and 9, default is 5). If ``parthenon`` is compiled with support for compression, this also enables (logical) chunking of the data in blocks of ``nx1*nx2*nx3``. Compression (and thus chunking) can be disabled altogether with the CMake build option ``PARTHENON_DISABLE_HDF5_COMPRESSION``. See the :ref:`building` for more details. Tuning HDF5 Performance ----------------------- Tuning IO parameters can be passed to Parthenon through the use of environment variables. Available environment variables are: +---------------------------+---------------+------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Environment Variable | Initial State | Value Type | Description | +===========================+===============+============+============================================================================================================================================================================================================================================================================================================================================================================================================================================================+ || H5_sieve_buf_size || disabled || int || Sets the maximum size of the data sieve buffer, in bytes. The value should be equal to a multiple of the disk block size. If no value is set then the default is 256 KiB. | || H5_meta_block_size || disabled || int || Sets the minimum metadata block size, in bytes. If no value is set then the default is 8 MiB. May help performance if enabled. | || H5_alignment_threshold || disabled || int || The threshold value, in bytes, of H5Pset_alignment. Setting to 0 forces everything to be aligned. If a value is not set then the default is 0. Setting the environment variable automatically enables alignment. | || H5_alignment_alignment || disabled || int || The alignment value, in bytes, of H5Pset_alignment. If a value is not set then the default is 8 MiB. Setting the environment variable automatically enables alignment. H5Pset_alignment sets the alignment properties of a file access property list. Choose an alignment that is a multiple of the disk block size, enabling this usually shows better performance on parallel file systems. However, enabling may increase the file size significantly. | || H5_defer_metadata_flush || disabled || int || Value of 1 enables deferring metadata flush. Value of 0 disables. Experiment with before using. | || MPI_access_style || enabled || string || Specifies the manner in which the file will be accessed until the file is closed. Default is "write_once" | || MPI_collective_buffering || disabled || int || Value of 1 enables MPI collective buffering. Value of 0 disables. Experiment with before using. | || MPI_cb_block_size || N/A || int || Sets the block size, in bytes, to be used for collective buffering file access. Default is 1 MiB. | || MPI_cb_buffer_size || N/A || int || Sets the total buffer space, in bytes, that can be used for collective buffering on each target node, usually a multiple of cb_block_size. Default is 4 MiB. | +---------------------------+---------------+------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ Restart Files ------------- Parthenon allows users to output restart files for restarting a simulation. The restart file captures the input file, so no input file is required to be specified. Parameters for the input can be overridden in the usual way from the command line. At a future date we will allow for users the ability to extensively edit the parameters stored within the restart file. In the input file, include a ```` block and specify ``file_type = rst``. A ``dt`` parameter controls the frequency of outputs for simulations involving evolution. A ```` block might look like :: file_type = rst dt = 1.0 This will produce an hdf5 (``.rhdf``) output file every 1 units of simulation time that can be used for restarting the simulation. To use this restart file, simply specify the restart file with a ``-r `` at the command line. If both ``-r `` and ``-i `` are specified, the simulation will be restarted from the restart file with input parameters updated (or added) from the input file. For physics developers: The fields to be output are automatically selected as all the variables that have either the ``Independent`` or ``Restart`` ``Metadata`` flags specified. No other intervention is required by the developer. Additional user work at the per-mesh and per-meshblock levels can be performed immediately prior to restart files being written with the optional ``UserWorkBeforeRestart`` callbacks at either the per-Mesh (via ``ApplicationInput``) or the per-package level (via ``StateDescriptor``). Both callbacks (if provided) will be called in that order before restart files are written. Postprocessing/native analysis ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A rudimentary postprocessing option is available to analyze data in restart files within the downstream/Parthenon framework, i.e., making use of native compute capabilities. To trigger this kind of analysis, restart with ``-a restart.rhdf`` (instead of ``-r``). This will launch the standard driver as if a simulation would be restarted, but never call the main time loop. Only the callbacks ``UserWorkBeforeLoop`` are executed. Afterwards, all output blocks that have the parameter ``analysis_output=true`` are going to be processed including ``UserWorkBeforeOutput`` callbacks. Note, the standard modifications to the original input parameters via the command line or via an input file apply. A typical use case is, for example, to calculate histograms a posteriori, i.e., a new output block is specified in a file called ``sample_hist.in`` with all necessary details (particularly the ``analysis_output=true`` parameter within said block) and then the data can be processed via ``-a restart.rhdf -i sample_hist.in``. .. _output hist files: History Files ------------- In the input file, include a ```` block and specify ``file_type = hst``. A ``dt`` parameter controls the frequency of outputs for simulations involving evolution. The default behavior is to provide all enrolled history outputs, but output can be limited to a specific set of packages with an optional comma-separated list argument ``packages = package_a, package_b``. A ```` block might look like :: file_type = hst dt = 1.0 packages = advection_app This will produce a text file (``.hst``) output file every 1 units of simulation time. The content of the file is determined by the functions enrolled by specific packages, see :ref:`state history output`. Histograms ---------- Parthenon supports calculating flexible 1D and 2D histograms in-situ that are written to disk in HDF5 format. Currently supported are - 1D and 2D histograms (see examples below) - binning by variable or coordinate (x1, x2, x3 and radial distance) - counting samples and or summing a variable - weighting by volume and/or variable The output format follows ``numpy`` convention, so that plotting data with Python based machinery should be straightforward (see example below). In other words, 2D histograms use C-ordering corresponding to ``[x,y]`` indexing with ``y`` being the fast index. In general, histograms are calculated using inclusive left bin edges and data equal to the rightmost edge is also included in the last bin. A ```` block containing one simple and one complex example might look like:: file_type = histogram # required, sets the output type dt = 1.0 # required, sets the output interval hist_names = myname, other_name # required, specifies the names of the histograms # in this block (used a prefix below and in the output) # 1D histogram ("standard", i.e., counting occurance in bin) myname_ndim = 1 myname_x_variable = advected myname_x_variable_component = 0 myname_x_edges_type = log myname_x_edges_num_bins = 10 myname_x_edges_min = 1e-9 myname_x_edges_max = 1e0 myname_binned_variable = HIST_ONES # 2D histogram of volume weighted variable according to two coordinates other_name_ndim = 2 other_name_x_variable = HIST_COORD_X1 other_name_x_edges_type = list other_name_x_edges_list = -0.5, -0.25, 0.0, 0.25, 0.5 other_name_y_variable = HIST_COORD_X2 other_name_y_edges_type = list other_name_y_edges_list = -0.5, -0.1, 0.0, 0.1, 0.5 other_name_binned_variable = advected other_name_binned_variable_component = 0 other_name_weight_by_volume = true other_name_weight_variable = one_minus_advected_sq other_name_weight_variable_component = 0 with the following parameters - ``hist_names=STRING, STRING, STRING, ...`` (comma separated names) The names of the histograms in this block. Will be used as prefix in the block as well as in the output file. All histograms will be written to the same output file with the "group" in the output corresponding to the histogram name. - ``NAME_ndim=INT`` (either ``1`` or ``2``) Dimensionality of the histogram. - ``NAME_x_variable=STRING`` (variable name or special coordinate string ``HIST_COORD_X1``, ``HIST_COORD_X2``, ``HIST_COORD_X3`` or ``HIST_COORD_R``) Variable to be used as bin. If a variable name is given a component has to be specified, too, see next parameter. For a scalar variable, the component needs to be specified as ``0`` anyway. If binning should be done by coordinate the special strings allow to bin by either one of the three dimensions or by radial distance from the origin. - ``NAME_x_variable_component=INT`` Component index of the binning variable. Used/required only if a non-coordinate variable is used for binning. - ``NAME_x_edges_type=STRING`` (``lin``, ``log``, or ``list``) How the bin edges are defined in the first dimension. For ``lin`` and ``log`` direct indexing is used to determine the bin, which is significantly faster than specifying the edges via a ``list`` as the latter requires a binary search. - ``NAME_x_edges_min=FLOAT`` Minimum value (inclusive) of the bins in the first dim. Used/required only for ``lin`` and ``log`` edge type. - ``NAME_x_edges_max=FLOAT`` Maximum value (inclusive) of the bins in the first dim. Used/required only for ``lin`` and ``log`` edge type. - ``NAME_x_edges_num_bins=INT`` (must be ``>=1``) Number of equally spaced bins between min and max value in the first dim. Used/required only for ``lin`` and ``log`` edge type. - ``NAME_x_edges_list=FLOAT,FLOAT,FLOAT,...`` (comma separated list of increasing values) Arbitrary definition of edge values with inclusive innermost and outermost edges. Used/required only for ``list`` edge type. - ``NAME_y_edges...`` Same as the ``NAME_x_edges...`` parameters except for being used in the second dimension for ``ndim=2`` histograms. - ``NAME_accumulate=BOOL`` (``true`` or ``false`` default) Accumulate data that is outside the binning range in the outermost bins. - ``NAME_binned_variable=STRING`` (variable name or ``HIST_ONES``) Variable to be binned. If a variable name is given a component has to be specified, too, see next parameter. For a scalar variable, the component needs to be specified as ``0`` anyway. If sampling (i.e., counting the number of value inside a bin) is to be used the special string ``HIST_ONES`` can be set. - ``NAME_binned_variable_component=INT`` Component index of the variable to be binned. Used/required only if a variable is binned and not ``HIST_ONES``. - ``NAME_weight_by_volume=BOOL`` (``true`` or ``false``) Apply volume weighting to the binned variable. Can be used simultaneously with binning by a different variable. Note that this does *not* include any normalization (e.g., by total volume or the sum of the weight variable in question) and is left to the user during post processing. - ``NAME_weight_variable=STRING`` Variable to be used as weight. Can be used together with volume weighting. For a scalar variable, the component needs to be specified as ``0`` anyway. - ``NAME_weight_variable_component=INT`` Component index of the variable to be used as weight. Note, weighting by volume and variable simultaneously might seem counterintuitive, but easily allows for, e.g., mass-weighted profiles, by enabling weighting by volume and using a mass density field as additional weight variable. In practice, a 1D histogram in the astrophysical context may look like (top panel from Fig 4 in `Curtis et al 2023 ApJL 945 L13 `_): .. figure:: figs/Curtis_et_al-ApJL-2023-1dhist.png :alt: 1D histogram example from Fig 2 in Curtis et al 2023 ApJL 945 L13 Translating this to the notation used for Parthenon histogram outputs means specifying for each histogram - the field containing the Electron fraction as ``x_variable``\ , - the field containing the traced mass density as ``binned_variable``\ , and - enable ``weight_by_volume`` (to get the total traced mass). Similarly, a 2D histogram (also referred to as phase plot) example may look like (from the `yt Project documentation `_): .. figure:: figs/yt_doc-2dhist.png :alt: 2D histogram example from the yt documentation Translating this to the notation used for Parthenon histogram outputs means using - the field containing the density as ``x_variable``\ , - the field containing the temperature as ``y_variable``\ , - the field containing the mass density as ``binned_variable``\ , and - enable ``weight_by_volume`` (to get the total mass). The following is a minimal example to plot a 1D and 2D histogram from the output file: .. code:: python with h5py.File("parthenon.out8.histograms.00040.hdf", "r") as infile: # 1D histogram x = infile["myname/x_edges"][:] y = infile["myname/data"][:] plt.plot(x, y) plt.show() # 2D histogram x = infile["other_name/x_edges"][:] y = infile["other_name/y_edges"][:] z = infile["other_name/data"][:].T # note the transpose here (so that the data matches the axis for the pcolormesh) plt.pcolormesh(x,y,z,) plt.show() Ascent (optional) ----------------- Parthenon supports in situ visualization and analysis via the external `Ascent `__ library. Support for Ascent is disabled by default and must be enabled via ``PARTHENON_ENABLE_ASCENT=ON`` during configure. In the input file, include a ```` block and specify ``file_type = ascent``. A ``dt`` parameter controls the frequency of outputs for simulations involving evolution. *Note* that in principle Ascent can control its own output cadence (including automated triggers). If you want to call Ascent on every cycle, set ``dt`` to a value smaller than the actual simulation ``dt``. The mandatory ``actions_file`` parameter points to a separate file that defines Ascent actions in ``.yaml`` or ``.json`` format, see `Ascent documentation `__ for a complete list of options. Parthenon currently only publishes cell-centered variables to Ascent. Moreover, the published name of the field always starts with the base name (to avoid name clashes between multiple fields that may have the same [component] labels). If component label(s) are provided, they will be added as a suffix, e.g,. ``basename_component-label`` for all variable types (even scalars). Otherwise, an integer index is added for vectors/tensors with more than one component, i.e., vectors/tensors with a single component and without component labels will not contain a suffix. The definition of component labels for variables is typically done by downstream codes so that the downstream documentation should be consulted for more specific information. A ```` block might look like:: file_type = ascent dt = 1.0 actions_file = my_actions.yaml see also the advection example `input file `__ and `actions file `__. *Note* by default "field filtering" is enabled for Ascent in Parthenon, i.e., only fields that are used in Ascent actions are published. There may be cases, where Ascent cannot determine which fields it needs for an action and will fail. In this case, add an ``ascent_options.yaml`` file to the run directory containing:: field_filtering: false to override at runtime. See `Ascent documenation `__ for more information. Python scripts -------------- The ``scripts/python`` folder includes scripts that may be useful for visualizing or analyzing data in the ``.phdf`` files. The ``phdf.py`` file defines a class to read in and query data. The ``movie2d.py`` script shows an example of using this class, and also provides a convenient means of making movies of 2D simulations. The script can be invoked as :: python3 /path/to/movie2d.py name_of_variable *.phdf which will produce a ``png`` image per dump suitable for encoding into a movie. Visualization software ---------------------- Both `ParaView `__ and `VisIt `__ are capable of opening and visualizing Parthenon graphics dumps. In both cases, the ``.xdmf`` files should be opened. In ParaView, select the “XDMF Reader” when prompted. .. warning:: Currently parthenon face- and edge- centered data is not supported for ParaView and VisIt. However, our python tooling does support all mesh locations. Tying non-standard coordinates to visualization tools ------------------------------------------------------ By default, Parthenon outputs the positions of faces on each block in ``X1``, ``X2`` and ``X3`` and assumes these correspond to the ``x``, ``y``, and ``z`` components of the nodes on the mesh. However, some applications may apply cooridnate transformations or use moving meshes. In these cases, the above strategy will not provide intuitive plots. For these applications we provide a special ``Metadata`` flag. If you mark a node-centered 3-vector variable with the the flag ``Metadata::CoordinatesVec``, and fill it with the ``x``, ``y``, and ``z`` values of your node positions, Parthenon will specify these values should be used by visualization software such as Visit or Paraview. For example, in your package ``Initialize`` function, you might declare something like: .. code:: cpp pkg->AddField("locations", Metadata({Metadata::Node, Metadata::CoordinatesVec, Metadata::Derived, Metadata::OneCopy}, std::vector{3})); and then (trivially) if you set .. code:: cpp pman.app_input->InitMeshBlockUserData = SetGeometryBlock; for .. code:: cpp void SetGeometryBlock(MeshBlock *pmb, ParameterInput *pin) { /* boiler plate to build a pack object */ parthenon::par_for(DEFAULT_LOOP_PATTERN, "positions", DevExecSpace(), 0, pack.GetNBlocks() - 1, kb.s, kb.e, jb.s, jb.e, ib.s, ib.e, KOKKOS_LAMBDA(const int b, const int k, const int j, const int i) { const auto &coords = pack.GetCoordinates(b); pack(b, 0, k, j, i) = coords.X(k, j, i); pack(b, 1, k, j, i) = coords.X(k, j, i); pack(b, 2, k, j, i) = coords.X(k, j, i); }); return; } then the code will set the nodal values to their trivial coordinate values and these will be used for visualization. In a more non-trivial example, ``SetGeometryBlock`` might apply a coordinate transformation. Or actually evolve ``"locations"``. .. warning:: Non-standard coordinates are not supported in XDMF for 1D meshes and Parthenon will revert to the traditional output in 1D. Preparing outputs for ``yt`` ---------------------------- Parthenon HDF5 outputs can be read with the python visualization library `yt `__ as certain variables are named when adding fields via ``StateDescriptor::AddField`` and ``StateDescriptor::AddSparsePool``. Variable names are added as a ``std::vector`` in the variable metadata. These labels are optional and are only used for output to HDF5. 4D variables are named with a list of names for each row while 3D variables are named with a single name. For example, the following configurations are acceptable: .. code:: cpp auto pkg = std::make_shared("Hydro"); /* ... */ const int nhydro = 5; std::vector cons_labels(nhydro); cons_labels[0]="Density"; cons_labels[1]="MomentumDensity1"; cons_labels[2]="MomentumDensity2"; cons_labels[3]="MomentumDensity3"; cons_labels[4]="TotalEnergyDensity"; Metadata m({Metadata::Cell, Metadata::Independent, Metadata::FillGhost}, std::vector({nhydro}), cons_labels); pkg->AddField("cons", m); const int ndensity = 1; std::vector density_labels(ndensity); density_labels[0]="Density"; m = Metadata({Metadata::Cell, Metadata::Derived}, std::vector({ndensity}), density_labels); pkg->AddField("dens", m); const int nvelocity = 3; std::vector velocity_labels(nvelocity); velocity_labels[0]="Velocity1"; velocity_labels[1]="Velocity2"; velocity_labels[2]="Velocity3"; m = Metadata({Metadata::Cell, Metadata::Derived}, std::vector({nvelocity}), velocity_labels); pkg->AddField("vel", m); const int npressure = 1; std::vector pressure_labels(npressure); pressure_labels[0]="Pressure"; m = Metadata({Metadata::Cell, Metadata::Derived}, std::vector({npressure}), pressure_labels); pkg->AddField("pres", m); The ``yt`` frontend needs either the hydrodynamic conserved variables or primitive compute derived quantities. The conserved variables must have the names ``"Density"``, ``"MomentumDensity1"``, ``"MomentumDensity2"``, ``"MomentumDensity3"``, ``"TotalEnergyDensity"`` while the primitive variables must have the names ``"Density"``, ``"Velocity1"``, ``"Velocity2"``, ``"Velocity3"``, ``"Pressure"``. Either of these sets of variables must be named and present in the output, with the primitive variables taking precedence over the conserved variables when computing derived quantities such as specific thermal energy. In the above example, including either ``"cons"`` or ``"dens"``, ``"vel"``, and ``"pres"`` in the HDF5 output would allow ``yt`` to read the data. Additional parameters can also be packaged into the HDF5 file to help ``yt`` interpret the data, namely adiabatic index and code unit information. These are identified by passing ``true`` as an optional boolean argument when adding parameters via ``StateDescriptor::AddParam``. For example, .. code:: cpp pkg->AddParam("CodeLength", 100,true); pkg->AddParam("CodeMass", 1000,true); pkg->AddParam("CodeTime", 1,true); pkg->AddParam("AdibaticIndex", 5./3.,true); pkg->AddParam("IntParam", 0,true); pkg->AddParam("EquationOfState", "Adiabatic",true); adds the parameters ``CodeLength``, ``CodeMass``, ``CodeTime``, ``AdiabaticIndex``, ``IntParam``, and ``EquationOfState`` to the HDF5 output. Currently, only ``int``, ``float``, and ``std::string`` parameters can be included with the HDF5. Code units can be defined for ``yt`` by including the parameters ``CodeLength``, ``CodeMass``, and ``CodeTime``, which specify the code units used by Parthenon in terms of centimeters, grams, and seconds by writing the parameters. In the above example, these parameters dictate ``yt`` to interpret code lengths in the data in units of 100 centimeters (or 1 meter per code unit), code masses in units of 1000 grams (or 1 kilogram per code units) and code times in units of seconds (or 1 second per code time). Alternatively, this unit information can also be supplied to the ``yt`` frontend when loading the data. If code units are not defined in the HDF5 file or at load time, ``yt`` will assume that the data is in ``CGS``. The adiabatic index can also be specified via the parameter ``AdiabaticIndex``, defined at load time for ``yt``, or left as its default ``5./3.``. For example, the following methods are valid to load data with ``yt`` .. code:: python filename = "parthenon.out0.00000.phdf" #Read units and adiabatic index from the HDF5 file or use defaults ds = yt.load(filename) #Specify units and adiabatic index explicitly units_override = {"length_unit" : (100, "cm"), "time_unit" : (1, "s"), "mass_unit" : (1000,"g")} ds = yt.load(filename,units_override=units_override,gamma=5./3.) Currently, the ``yt`` frontend for Parthenon is hosted on the ``parthenon-frontend`` branch of this `yt fork `_. In the future, the Parthenon frontend will be included in the main ``yt`` repo.