CarpetIOHDF5

Erik Schnetter <schnetter@uni-tuebingen.de>
Christian D. Ott <cott@aei.mpg.de>
Thomas Radke <tradke@aei.mpg.de>

1 December 2004

Abstract

Thorn CarpetIOHDF5 provides HDF5-based output to the Carpet mesh refinement driver in Cactus. This document explains CarpetIOHDF5’s usage and contains a specification of the HDF5 file format that was adapted from John Shalf’s FlexIO library.

Contents

1 Introduction
2 CarpetIOHDF5 Parameters
3 Serial versus Parallel Output
4 Using the flesh I/O API to produce HDF5 output
5 Checkpointing & Recovery and Importing Data
6 CarpetIOHDF5 Utility Programs
 6.1 hdf5toascii_slicer
 6.2 hdf5_extract
7 Example Parameter File Excerpts
 7.1 Serial (unchunked) Output of Grid Variables
 7.2 Parallel (chunked) Output of Grid Variables
 7.3 Checkpointing & Recovery
 7.4 Importing Grid Variables via Filereader
8 Parameters
9 Interfaces
  9.0.1 PRIVATE GROUPS
10 Schedule

1 Introduction

Having encountered various problems with the Carpet I/O thorn CarpetIOFlexIO and the underlying FlexIO library, Erik Schnetter decided to write this thorn CarpetIOHDF5 which bypasses any intermediate binary I/O layer and outputs in HDF51 file format directly.

CarpetIOHDF5 provides output for the Carpet Mesh Refinement driver within the Cactus Code. Christian D. Ott added a file reader (analogous to Erik Schnetter’s implementation present in CarpetIOFlexIO) as well as checkpoint/recovery functionality to CarpetIOHDF5. Thomas Radke has taken over maintainence of this I/O thorn and is continuously working on fixing known bugs and improving the code functionality and efficiency.

The CarpetIOHDF5 I/O method can output any type of CCTK grid variables (grid scalars, grid functions, and grid arrays of arbitrary dimension); data is written into separate files named "<varname>.h5". It implements both serial and full parallel I/O – data files can be written/read either by processor 0 only or by all processors. Such datafiles can be used for further postprocessing (eg. visualization with OpenDX or DataVault2 ) or fed back into Cactus via the filereader capabilities of thorn IOUtil.

This document aims at giving the user a first handle on how to use CarpetIOHDF5. It also documents the HDF5 file layout used.

2 CarpetIOHDF5 Parameters

Parameters to control the CarpetIOHDF5 I/O method are:

3 Serial versus Parallel Output

According to the ouptput mode parameter settings of (IO::out_mode, IO::out_unchunked,
IO::out_proc_every) of thorn IOUtil, thorn CarpetIOHDF5 will output distributed grid variables either

Unchunked means that an entire Cactus grid array (gathered across all processors) is stored in a single HDF5 dataset whereas chunked means that all the processor-local patches of this array are stored as separate HDF5 datasets (called chunks). Consequently, for unchunked data all interprocessor ghostzones are excluded from the output. In contrast, for chunked data the interprocessor ghostzones are included in the output.

When visualising chunked datasets, they probably need to be recombined for a global view on the data. This needs to be done within the visualisation tool (see also below), Cactus itself does not provide its own recombiner utility program for CarpetIOHDF5’s output files.

The default is to output distributed grid variables in parallel, each processor writing a file <varname>.file_<processor ID>.h5. The chunked/unchunked mode can also be set individually in a key/value option string (with the key out_unchunked and possible string values "true|false|yes|no") appended to a group/variable name in the out_vars parameter, eg.

  IOHDF5::out_vars = "wavetoy::phi{out_unchunked = ’true’}  grid::coordinates"

will cause the variable phi to be output into a single unchunked file whereas other variables will still be output into separate chunked files (assuming the output mode is left to its default). Grid scalars and DISTRIB = CONST grid arrays are always output as unchunked data on processor 0 only.

Parallel output in a parallel simulation will ensure maximum I/O performance. Note that changing the output mode to serial I/O might only be necessary if the data analysis and visualisation tools cannot deal with chunked output files. Cactus itself, as well as many of the tools to visualise Carpet HDF5 data (see http://www.cactuscode.org/Visualization), can process both chunked and unchunked data. For instance, to visualise parallel output datafiles with DataVault, you would just send all the individual files to the DV server: hdf5todv phi.file_*.h5. In OpenDX the ImportCarpetIOHDF5 module can be given any filename from the set of parallel chunked files; the module will determine the total number of files in the set automatically and read them all.

4 Using the flesh I/O API to produce HDF5 output

Periodic output of grid variables is usually specified via I/O parameters in the parameter file and then automatically triggered by the flesh scheduler at each iteration step after analysis. If output should also be triggered at a different time, one can do that from within an application thorn by invoking one of the CCTK_OutputVar*() I/O routines provided by the flesh I/O API (see chapter B8.2 “IO” in the Cactus Users Guide). In this case, the application thorn routine which calls CCTK_OutputVar*() must be scheduled in level mode.

It should be noted here that – due to a restriction in the naming scheme of objects in an HDF5 data file – CarpetIOHDF5 can output a given grid variable with given refinement level only once per timestep. Attempts of application thorns to trigger the output of the same variable multiple times during an iteration will result in a runtime warning and have no further effect. If output for a variable is required also for intermediate timesteps this can be achieved by calling CCTK_OutputVarAs*() with a different alias name; output for the same variable is then written into different HDF5 files based on the alias argument.

5 Checkpointing & Recovery and Importing Data

Thorn CarpetIOHDF5 can also be used to create HDF5 checkpoint files and to recover from such files later on. In addition it can read HDF5 datafiles back in using the generic filereader interface described in the thorn documentation of IOUtil.

Checkpoint routines are scheduled at several timebins so that you can save the current state of your simulation after the initial data phase, during evolution, or at termination. Checkpointing for thorn CarpetIOHDF5 is enabled by setting the parameter IOHDF5::checkpoint = "yes".

A recovery routine is registered with thorn IOUtil in order to restart a new simulation from a given HDF5 checkpoint. The very same recovery mechanism is used to implement a filereader functionality to feed back data into Cactus.

Checkpointing and recovery are controlled by corresponding checkpoint/recovery parameters of thorn IOUtil (for a description of these parameters please refer to this thorn’s documentation).

6 CarpetIOHDF5 Utility Programs

6.1 hdf5toascii_slicer

This utility program extracts 1D lines and 2D slices from 3D HDF5 datasets produced by CarpetIOHDF5 and outputs them in CarpetIOASCII format (suitable to be further processed by gnuplot).

The hdf5toascii_slicer program is contained in the src/utils/ subdirectory of thorn CarpetIOHDF5. It is built with

  make <configuration>-utils

where the executable ends up in the subdirectory exe/<configuration>/.

For details on how to use the hdf5toascii_slicer program, run it with no command-line options (or with the --help option).

hdf5toascii_slicer can be used on either chunked or unchunked data:

6.2 hdf5_extract

This utility program extracts selected datasets from any given HDF5 output file which may be useful when only certain parts (eg. a specific timestep) of large files are required (eg. for copying to some other location for further processing).

The hdf5_extract program is contained in the src/utils/ subdirectory of thorn CactusPUGHIO/IOHDF5. It is built with

  make <configuration>-utils

where the executable ends up in the subdirectory exe/<configuration>/.

7 Example Parameter File Excerpts

7.1 Serial (unchunked) Output of Grid Variables

  # how often to output and where output files should go  
  IO::out_every = 2  
  IO::out_dir   = "wavetoy-data"  
 
  # request output for wavetoy::psi at every other iteration for timelevel 0,  
  #                for wavetoy::phi every 4th iteration with timelevels 1 and 2  
  IOHDF5::out_vars = "wavetoy::phi{ out_every = 4 refinement_levels = { 1 2 } }  
                      wavetoy::psi"  
 
  # we want unchunked output  
  # (because the visualisation tool cannot deal with chunked data files)  
  IO::out_mode      = "onefile"  
  IO::out_unchunked = 1

7.2 Parallel (chunked) Output of Grid Variables

  # how often to output  
  IO::out_every = 2  
 
  # each processor writes to its own output directory  
  IOHDF5::out_dir = "wavetoy-data-proc%u"  
 
  # request output for wavetoy::psi at every other iteration for timelevel 0,  
  #                for wavetoy::phi every 4th iteration with timelevels 1 and 2  
  IOHDF5::out_vars = "wavetoy::phi{ out_every = 4 refinement_levels = { 1 2 } }  
                      wavetoy::psi"  
 
  # we want parallel chunked output (note that this already is the default)  
  IO::out_mode = "proc"

7.3 Checkpointing & Recovery

  # say how often we want to checkpoint, how many checkpoints should be kept,  
  # how the checkpoints should be named, and they should be written to  
  IO::checkpoint_every = 100  
  IO::checkpoint_keep  = 2  
  IO::checkpoint_file  = "wavetoy"  
  IO::checkpoint_dir   = "wavetoy-checkpoints"  
 
  # enable checkpointing for CarpetIOHDF5  
  IOHDF5::checkpoint = "yes"  
 
  #######################################################  
 
  # recover from the latest checkpoint found  
  IO::recover_file = "wavetoy"  
  IO::recover_dir  = "wavetoy-checkpoints"  
  IO::recover      = "auto"

7.4 Importing Grid Variables via Filereader

  # which data files to import and where to find them  
  IO::filereader_ID_files = "phi psi"  
  IO::filereader_ID_dir   = "wavetoy-data"  
 
  # what variables and which timestep to read  
  # (if this parameter is left empty, all variables and timesteps found  
  #  in the data files will be read)  
  IO::filereader_ID_vars  = "WaveToyMoL::phi{ cctk_iteration = 0 }  
                             WaveToyMoL::psi"

8 Parameters




checkpoint
Scope: private  BOOLEAN



Description: Do checkpointing with CarpetIOHDF5 ?



  Default: no






checkpoint_every_divisor
Scope: private  INT



Description: Checkpoint if (iteration % out_every) == 0



Range   Default: -1
1:*
Every so many iterations
-1:0
Disable periodic checkpointing






checkpoint_next
Scope: private  BOOLEAN



Description: Checkpoint at next iteration ?



  Default: no






compression_level
Scope: private  INT



Description: Compression level to use for writing HDF5 data



Range   Default: (none)
0:9
Higher numbers compress better, a value of zero disables compression






minimum_size_for_compression
Scope: private  INT



Description: Only compress datasets larger than this many bytes



Range   Default: 32768
0:*
This should to be large enough so that compression gains outweigh the overhead






one_file_per_group
Scope: private  BOOLEAN



Description: Write one file per group instead of per variable



  Default: no






open_one_input_file_at_a_time
Scope: private  BOOLEAN



Description: Open only one HDF5 file at a time when reading data from multiple chunked checkpoint/data files



Range   Default: no
no
Open all input files first, then import data (most efficient)
yes
Process input files one after another (reduces memory requirements)






out0d_criterion
Scope: private  KEYWORD



Description: Criterion to select 0D HDF5 slice output intervals, overrides out_every



Range   Default: default
default
Use IO::out_criterion
never
Never output
iteration
Output every so many iterations
divisor
Output if iteration mod divisor == 0.
time
Output every that much coordinate time






out0d_dir
Scope: private  STRING



Description: Name of 0D HDF5 slice output directory, overrides IO::out_dir



Range   Default: (none)
Empty: use IO::out_dir
.+
Not empty: directory name






out0d_dt
Scope: private  REAL



Description: How often to do 0D HDF5 slice output, overrides IO::out_dt



Range   Default: -2
(0:*
In intervals of that much coordinate time
As often as possible
-1
Disable output
-2
Default to IO::out_dt






out0d_every
Scope: private  INT



Description: How often to do 0D HDF5 slice output, overrides out_every



Range   Default: -2
1:*
Output every so many time steps
-1:0
No output
-2
Use IO::out_every






out0d_point_x
Scope: private  REAL



Description: x coordinate for 0D points



Range   Default: (none)
*:*






out0d_point_xi
Scope: private  INT



Description: x-index (counting from 0) for 0D points



Range   Default: (none)
0:*






out0d_point_y
Scope: private  REAL



Description: y coordinate for 0D points



Range   Default: (none)
*:*






out0d_point_yi
Scope: private  INT



Description: y-index (counting from 0) for 0D points



Range   Default: (none)
0:*






out0d_point_z
Scope: private  REAL



Description: z coordinate for 0D points



Range   Default: (none)
*:*






out0d_point_zi
Scope: private  INT



Description: z-index (counting from 0) for 0D points



Range   Default: (none)
0:*






out0d_vars
Scope: private  STRING



Description: Variables to output in 0D HDF5 file format



Range   Default: (none)
List of group or variable names






out1d_criterion
Scope: private  KEYWORD



Description: Criterion to select 1D HDF5 slice output intervals, overrides out_every



Range   Default: default
default
Use IO::out_criterion
never
Never output
iteration
Output every so many iterations
divisor
Output if (iteration % out_every) == 0.
time
Output every that much coordinate time






out1d_d
Scope: private  BOOLEAN



Description: Do output along the diagonal



  Default: yes






out1d_dir
Scope: private  STRING



Description: Name of 1D HDF5 slice output directory, overrides IO::out_dir



Range   Default: (none)
Empty: use IO::out_dir
.+
Not empty: directory name






out1d_dt
Scope: private  REAL



Description: How often to do 1D HDF5 slice output, overrides IO::out_dt



Range   Default: -2
(0:*
In intervals of that much coordinate time
As often as possible
-1
Disable output
-2
Default to IO::out_dt






out1d_every
Scope: private  INT



Description: How often to do 1D HDF5 slice output, overrides out_every



Range   Default: -2
1:*
Output every so many time steps
-1:0
No output
-2
Use IO::out_every






out1d_vars
Scope: private  STRING



Description: Variables to output in 1D HDF5 file format



Range   Default: (none)
List of group or variable names






out1d_x
Scope: private  BOOLEAN



Description: Do 1D HDF5 slice output in the x-direction



  Default: yes






out1d_xline_y
Scope: private  REAL



Description: y coordinate for 1D lines in x-direction



Range   Default: (none)
*:*






out1d_xline_yi
Scope: private  INT



Description: y-index (counting from 0) for 1D lines in x-direction



Range   Default: (none)
0:*






out1d_xline_z
Scope: private  REAL



Description: z coordinate for 1D lines in x-direction



Range   Default: (none)
*:*






out1d_xline_zi
Scope: private  INT



Description: z-index (counting from 0) for 1D lines in x-direction



Range   Default: (none)
0:*






out1d_y
Scope: private  BOOLEAN



Description: Do 1D HDF5 slice output in the y-direction



  Default: yes






out1d_yline_x
Scope: private  REAL



Description: x coordinate for 1D lines in y-direction



Range   Default: (none)
*:*






out1d_yline_xi
Scope: private  INT



Description: x-index (counting from 0) for 1D lines in y-direction



Range   Default: (none)
0:*






out1d_yline_z
Scope: private  REAL



Description: z coordinate for 1D lines in y-direction



Range   Default: (none)
*:*






out1d_yline_zi
Scope: private  INT



Description: z-index (counting from 0) for 1D lines in y-direction



Range   Default: (none)
0:*






out1d_z
Scope: private  BOOLEAN



Description: Do 1D HDF5 slice output in the z-direction



  Default: yes






out1d_zline_x
Scope: private  REAL



Description: x coordinate for 1D lines in z-direction



Range   Default: (none)
*:*






out1d_zline_xi
Scope: private  INT



Description: x-index (counting from 0) for 1D lines in z-direction



Range   Default: (none)
0:*






out1d_zline_y
Scope: private  REAL



Description: y coordinate for 1D lines in z-direction



Range   Default: (none)
*:*






out1d_zline_yi
Scope: private  INT



Description: y-index (counting from 0) for 1D lines in z-direction



Range   Default: (none)
0:*






out2d_criterion
Scope: private  KEYWORD



Description: Criterion to select 2D HDF5 slice output intervals, overrides out_every



Range   Default: default
default
Use IO::out_criterion
never
Never output
iteration
Output every so many iterations
divisor
Output if (iteration % out_every) == 0.
time
Output every that much coordinate time






out2d_dir
Scope: private  STRING



Description: Name of 2D HDF5 slice output directory, overrides IO::out_dir



Range   Default: (none)
Empty: use IO::out_dir
.+
Not empty: directory name






out2d_dt
Scope: private  REAL



Description: How often to do 2D HDF5 slice output, overrides IO::out_dt



Range   Default: -2
(0:*
In intervals of that much coordinate time
As often as possible
-1
Disable output
-2
Default to IO::out_dt






out2d_every
Scope: private  INT



Description: How often to do 2D HDF5 slice output, overrides out_every



Range   Default: -2
1:*
Output every so many time steps
-1:0
No output
-2
Use IO::out_every






out2d_vars
Scope: private  STRING



Description: Variables to output in 2D HDF5 file format



Range   Default: (none)
List of group or variable names






out2d_xy
Scope: private  BOOLEAN



Description: Do 2D HDF5 slice output in the xy-direction



  Default: yes






out2d_xyplane_z
Scope: private  REAL



Description: z coordinate for 2D planes in xy-direction



Range   Default: (none)
*:*






out2d_xyplane_zi
Scope: private  INT



Description: z-index (counting from 0) for 2D planes in xy-direction



Range   Default: (none)
0:*






out2d_xz
Scope: private  BOOLEAN



Description: Do 2D HDF5 slice output in the xz-direction



  Default: yes






out2d_xzplane_y
Scope: private  REAL



Description: y coordinate for 2D planes in xz-direction



Range   Default: (none)
*:*






out2d_xzplane_yi
Scope: private  INT



Description: y-index (counting from 0) for 2D planes in xz-direction



Range   Default: (none)
0:*






out2d_yz
Scope: private  BOOLEAN



Description: Do 2D HDF5 slice output in the yz-direction



  Default: yes






out2d_yzplane_x
Scope: private  REAL



Description: x coordinate for 2D planes in yz-direction



Range   Default: (none)
*:*






out2d_yzplane_xi
Scope: private  INT



Description: x-index (counting from 0) for 2D planes in yz-direction



Range   Default: (none)
0:*






out3d_criterion
Scope: private  KEYWORD



Description: Criterion to select 3D HDF5 slice output intervals, overrides out_every



Range   Default: default
default
Use IO::out_criterion
never
Never output
iteration
Output every so many iterations
divisor
Output if (iteration % out_every) == 0.
time
Output every that much coordinate time






out3d_dir
Scope: private  STRING



Description: Name of 3D HDF5 slice output directory, overrides IO::out_dir



Range   Default: (none)
Empty: use IO::out_dir
.+
Not empty: directory name






out3d_dt
Scope: private  REAL



Description: How often to do 3D HDF5 slice output, overrides IO::out_dt



Range   Default: -2
(0:*
In intervals of that much coordinate time
As often as possible
-1
Disable output
-2
Default to IO::out_dt






out3d_every
Scope: private  INT



Description: How often to do 3D HDF5 slice output, overrides out_every



Range   Default: -2
1:*
Output every so many time steps
-1:0
No output
-2
Use IO::out_every






out3d_ghosts
Scope: private  BOOLEAN



Description: Output ghost zones (DEPRECATED)



  Default: yes






out3d_outer_ghosts
Scope: private  BOOLEAN



Description: Output outer boundary zones (assuming that there are nghostzones boundary points) (DEPRECATED)



  Default: yes






out3d_vars
Scope: private  STRING



Description: Variables to output in 3D HDF5 file format



Range   Default: (none)
List of group or variable names






out_criterion
Scope: private  KEYWORD



Description: Criterion to select CarpetIOHDF5 output intervals, overrides out_every



Range   Default: default
default
Use ’IO::out_criterion’
never
Never output
iteration
Output every so many iterations
divisor
Output if (iteration % out_every) == 0.
time
Output every that much coordinate time






out_dir
Scope: private  STRING



Description: Name of CarpetIOHDF5 output directory, overrides ’IO::out_dir’



Range   Default: (none)
Empty: use IO::out_dir
.+
Not empty: directory name






out_dt
Scope: private  REAL



Description: How often to do CarpetIOHDF5 output, overrides ’IO::out_dt’



Range   Default: -2
(0:*
In intervals of that much coordinate time
As often as possible
-1
Disable output
-2
Default to ’IO::out_dt’






out_every
Scope: private  INT



Description: How often to do CarpetIOHDF5 output, overrides out_every



Range   Default: -2
1:*
Output every so many time steps
-1:0
No output
-2
Use ’IO::out_every’






out_extension
Scope: private  STRING



Description: File extension to use for CarpetIOHDF5 output



Range   Default: .h5
File extension (including a leading dot, if desired)






out_vars
Scope: private  STRING



Description: Variables to output in CarpetIOHDF5 file format



Range   Default: (none)
List of group or variable names






output_all_timelevels
Scope: private  BOOLEAN



Description: Output all timelevels instead of only the current



  Default: no






output_boundary_points
Scope: private  BOOLEAN



Description: Output outer boundary points (assuming that there are nghostzones boundary points)



  Default: yes






output_buffer_points
Scope: private  BOOLEAN



Description: Output refinement buffer points



  Default: yes






output_ghost_points
Scope: private  BOOLEAN



Description: Output ghost points



  Default: yes






output_index
Scope: private  BOOLEAN



Description: Output an index file for each output file



  Default: no






output_symmetry_points
Scope: private  BOOLEAN



Description: Output symmetry points (assuming that there are nghostzones symmetry points)



  Default: yes






skip_recover_variables
Scope: private  STRING



Description: Skip these variables while recovering



Range   Default: (none)






use_checksums
Scope: private  BOOLEAN



Description: Use checksums for the HDF5 data



  Default: no






use_grid_structure_from_checkpoint
Scope: private  BOOLEAN



Description: Use the grid structure stored in the checkpoint file



  Default: yes






use_reflevels_from_checkpoint
Scope: private  BOOLEAN



Description: Use ’CarpetRegrid::refinement_levels’ from the checkpoint file rather than from the parameter file ?



  Default: no






abort_on_io_errors
Scope: shared from IO BOOLEAN






checkpoint_dir
Scope: shared from IO STRING






checkpoint_every
Scope: shared from IO INT






checkpoint_every_walltime_hours
Scope: shared from IO REAL






checkpoint_file
Scope: shared from IO STRING






checkpoint_id
Scope: shared from IO BOOLEAN






checkpoint_id_file
Scope: shared from IO STRING






checkpoint_keep
Scope: shared from IO INT






checkpoint_on_terminate
Scope: shared from IO BOOLEAN






filereader_id_dir
Scope: shared from IO STRING






io_out_criterion
Scope: shared from IO KEYWORD






io_out_dir
Scope: shared from IO STRING






io_out_dt
Scope: shared from IO REAL






io_out_every
Scope: shared from IO INT






io_out_unchunked
Scope: shared from IO BOOLEAN






out_group_separator
Scope: shared from IO STRING






out_mode
Scope: shared from IO KEYWORD






out_save_parameters
Scope: shared from IO KEYWORD






out_single_precision
Scope: shared from IO BOOLEAN






out_timesteps_per_file
Scope: shared from IO INT






out_xline_y
Scope: shared from IO REAL






out_xline_yi
Scope: shared from IO INT






out_xline_z
Scope: shared from IO REAL






out_xline_zi
Scope: shared from IO INT






out_xyplane_z
Scope: shared from IO REAL






out_xyplane_zi
Scope: shared from IO INT






out_xzplane_y
Scope: shared from IO REAL






out_xzplane_yi
Scope: shared from IO INT






out_yline_x
Scope: shared from IO REAL






out_yline_xi
Scope: shared from IO INT






out_yline_z
Scope: shared from IO REAL






out_yline_zi
Scope: shared from IO INT






out_yzplane_x
Scope: shared from IO REAL






out_yzplane_xi
Scope: shared from IO INT






out_zline_x
Scope: shared from IO REAL






out_zline_xi
Scope: shared from IO INT






out_zline_y
Scope: shared from IO REAL






out_zline_yi
Scope: shared from IO INT






recover
Scope: shared from IO KEYWORD






recover_and_remove
Scope: shared from IO BOOLEAN






recover_dir
Scope: shared from IO STRING






recover_file
Scope: shared from IO STRING






strict_io_parameter_check
Scope: shared from IO BOOLEAN






verbose
Scope: shared from IO KEYWORD



9 Interfaces

General

Implements:

iohdf5

Grid Variables

9.0.1 PRIVATE GROUPS




  Group Names     Variable Names     Details   




next_output_iteration   compact0
next_output_iteration   dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 variable typeINT




next_output_time   compact0
next_output_time   dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 variable typeREAL




this_iteration   compact0
this_iteration   dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 variable typeINT




last_output_iteration_slice   compact0
last_output_iteration_slice  dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 vararray_size4
 variable typeINT




last_output_time_slice   compact0
last_output_time_slice   dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 vararray_size4
 variable typeREAL




this_iteration_slice   compact0
this_iteration_slice   dimensions0
  distributionCONSTANT
  group typeSCALAR
  timelevels1
 vararray_size4
 variable typeINT




Adds header:

CarpetIOHDF5.hh

Uses header:

Timer.hh

carpet.hh

defs.hh

bbox.hh

vect.hh

data.hh

gdata.hh

ggf.hh

gh.hh

typecase.hh

typeprops.hh

Provides:

IO_SetCheckpointGroups to

10 Schedule

This section lists all the variables which are assigned storage by thorn Carpet/CarpetIOHDF5. Storage can either last for the duration of the run (Always means that if this thorn is activated storage will be assigned, Conditional means that if this thorn is activated storage will be assigned for the duration of the run if some condition is met), or can be turned on for the duration of a schedule function.

Storage

 

Always:  
next_output_iteration next_output_time this_iteration  
last_output_iteration_slice last_output_time_slice this_iteration_slice 
   

Scheduled Functions

CCTK_STARTUP

  carpetiohdf5_startup

  startup routine

 

 After: ioutil_startup
 Language:c
 Type: function

CCTK_INITIAL

  carpetiohdf5_init

  initialisation routine

 

 Language:c
 Options: global
 Type: function

CCTK_POST_RECOVER_VARIABLES

  carpetiohdf5_initcheckpointingintervals

  initialisation of checkpointing intervals after recovery

 

 Language:c
 Options: global
 Type: function

CCTK_CPINITIAL

  carpetiohdf5_initialdatacheckpoint

  initial data checkpoint routine

 

 Language:c
 Options: meta
 Type: function

CCTK_CHECKPOINT

  carpetiohdf5_evolutioncheckpoint

  evolution checkpoint routine

 

 Language:c
 Options: meta
 Type: function

CCTK_TERMINATE

  carpetiohdf5_terminationcheckpoint

  termination checkpoint routine

 

 Language:c
 Options: meta
 Type: function

CCTK_POSTINITIAL

  carpetiohdf5_closefiles

  close all filereader input files

 

 Language:c
 Options: global
 Type: function

CCTK_RECOVER_PARAMETERS (conditional)

  carpetiohdf5_recoverparameters

  parameter recovery routine

 

 Language:c
 Options: meta
 Type: function

CCTK_STARTUP (conditional)

  carpetiohdf5_setnumrefinementlevels

  overwrite ’carpetregrid::refinement_levels’ with the number of levels found in the checkpoint file

 

 Before: carpetiohdf5_startup
 Language:c
 Options: meta
 Type: function

CCTK_POST_RECOVER_VARIABLES (conditional)

  carpetiohdf5_closefiles

  close all initial data checkpoint files after recovery

 

 Language:c
 Options: meta
 Type: function