IOHDF5

Thomas Radke

Date

Abstract

Thorn IOHDF5 provides an I/O method to output variables in HDF5 file format. It also implements checkpointing/recovery functionality using HDF5.

1 Purpose

Thorn IOHDF5 uses the standard I/O library HDF51 to output any type of CCTK grid variables (grid scalars, grid functions, and grid arrays of arbitrary dimension) in the HDF5 file format.

Output is done by invoking the IOHDF5 I/O method which thorn IOHDF5registers with the flesh’s I/O interface at startup.

Data is written into files named "<varname>.h5". Such datafiles can be used for further postprocessing (eg. visualization) or fed back into Cactus via the filereader capabilities of thorn IOUtil.

2 IOHDF5 Parameters

Parameters to control the IOHDF5 I/O method are:

3 Serial versus Parallel Output

According to the ouptput mode parameter settings (IO::out_mode, IO::out_unchunked,
IO::out_proc_every) of thorn IOUtil, thorn IOHDF5 will output distributed data either

The default is to output data in parallel, in order to get maximum I/O performance. If needed, you can recombine the resulting chunked datafiles into a single unchunked file using the recombiner utility program. See section 9 for information how to build the recombiner program.

4 Output of Hyperslab Data

By default, thorn IOHDF5 outputs multidimensional Cactus variables with their full contents resulting in maximum data output. This can be changed for individual variables by specifying a hyperslab as a subset of the data within the N-dimensional volume. Such a subset (called a hyperslab) is generally defined as an orthogonal region into the multidimensional dataset, with an origin (lower left corner of the hyperslab), direction vectors (defining the number of hyperslab dimensions and spanning the hyperslab within the N-dimensional grid), an extent (the length of the hyperslab in each of its dimensions), and an optional downsampling factor.

Hyperslab parameters can be set for individual variables using an option string appended to the variables’ full names in the IOHDF5::out_vars parameter.

Here is an example which outputs two 3D grid functions Grid::r and Wavetoy::phi. While the first is output with their full contents at every 5th iteration (overriding the IOHDF5::out_every parameter for this variable), a two-dimensional hyperslab is defined for the second grid function. This hyperslab defines a subvolume to output, starting with a 5 grid points offset into the grid, spanning in the yz-plane, with an extent of 10 and 20 grid points in y- and z-direction respectively. For this hyperslab, only every other grid point will be output.

  IOHDF5::out_every = 1  
  IOHDF5::out_vars  = "Grid::x{ out_every = 5 }  
                       Wavetoy::phi{ origin     = {4 4 4}  
                                     direction  = {0 1 0  
                                                   0 0 1}  
                                     extent     = {10 20}  
                                     downsample = {2 2}   }"

The hyperslab parameters which can be set in an option string are:

5 IOHDF5 Output Restrictions

Due to the naming scheme used to build unique names for HDF5 datasets (see 7, the IOHDF5 I/O method currently has the restriction that it can output a given variable (with a specific timelevel) – or a hyperslab of it – only once per iteration.

As a workaround, you should request output in such a case by using the flesh’s I/O API CCTK_OutputVarAsByMethod() routine with a different alias name for each output. Note that this will create multiple output files for the same variable then.

6 Checkpointing & Recovery

Thorn IOHDF5 can also be used for creating HDF5 checkpoint files and recovering from such files later on.

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 IOHDF5 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). The parameter IO::checkpoint_every_walltime_hours is not (yet) supported.

7 Importing External Data Into Cactus With IOHDF5

In order to import external data into Cactus (eg. to initialize some variable) you first need to convert this data into an HDF5 datafile which then can be processed by the registered recovery routine of thorn IOHDF5.

The following description explains the HDF5 file layout of an unchunked datafile which thorn IOHDF5 expects in order to restore Cactus variables from it properly. There is also a well-documented example C program provided (IOHDF5/doc/CreateIOHDF5datafile.c) which illustrates how to create a datafile with IOHDF5 file layout. This working example can be used as a template for building your own data converter program.

  1. Actual data is stored as multidimensional datasets in an HDF5 file. There is no nested grouping structure, every dataset is located in the root group.
    A dataset’s name must match the following naming pattern which guarantees to generate unique names:
      "<full variable name> timelevel <timelevel> at iteration <iteration>"

    IOHDF5’s recovery routine parses a dataset’s name according to this pattern to determine the Cactus variable to restore, along with its timelevel. The iteration number is just informative and not needed here.

  2. The type of your data as well as its dimensions are already inherited by a dataset itself as metainformation. But this is not enough for IOHDF5 to safely match it against a specific Cactus variable. For that reason, the variable’s groupname, its grouptype, and the total number of timelevels must be attached to every dataset as attribute information.
  3. Finally, the recovery routine needs to know how the datafile to recover from was created:

    Such information is put into as attributes into a group named "Global Attributes". Since we assume unchunked data here the processor information isn’t relevant — unchunked data can be fed back into a Cactus simulation running on an arbitrary number of processors.
    The Cactus version ID must be present to indicate that grid variables with multiple timelevels should be recovered following the new timelevel scheme (as introduced in Cactus beta 10).

The example C program goes through all of these steps and creates a datafile x.h5 in IOHDF5 file layout which contains a single dataset named "grid::x timelevel 0 at iteration 0", with groupname "grid::coordinates", grouptype CCTK_GF (thus identifying the variable as a grid function), and the total number of timelevels set to 1.

The global attributes are set to "unchunked" = "yes", nprocs = 1, and ioproc_every = 1.

Once you’ve built and ran the program you can easily verify if it worked properly with

  h5dump x.h5

which lists all objects in the datafile along with their values. It will also dump the contents of the 3D dataset. Since it only contains zeros it would probably not make much sense to feed this datafile into Cactus for initializing your x coordinate grid function :-)

8 Building A Cactus Configuration with IOHDF5

The Cactus distribution does not contain the HDF5 header files and library which is used by thorn IOHDF5. You have to include the thorn HDF5 (located in the Cactus ExternalLibraries arrangement). This thorn will either build its own HDF5 library, or use an installed version in some cases.

Thorn IOHDF5 inherits from IOUtil and IOHDF5Util so you need to include these thorns in your thorn list to build a configuration with IOHDF5.

9 Utility Programs provided by IOHDF5

Thorn IOHDF5 provides the following utility programs:

All utility programs are located in the src/util/ subdirectory of thorn IOHDF5. To build the utilities just do a

  make <configuration>-utils

in the Cactus toplevel directory. The executables will then be placed in the exe/<configuration>/ subdirectory.

All utility programs are self-explaining – just call them without arguments to get a short usage info. If any of these utility programs is called without arguments it will print a usage message.

10 Parameters




checkpoint
Scope: private  BOOLEAN



Description: Do checkpointing with HDF5



  Default: no






checkpoint_next
Scope: private  BOOLEAN



Description: Checkpoint at next iteration



  Default: no






out_dir
Scope: private  STRING



Description: Output directory for IOHDF5 files, overrides IO::out_dir



Range   Default: (none)
.+
A valid directory name
An empty string to choose the default from IO::out_dir






out_every
Scope: private  INT



Description: How often to do IOHDF5 output, overrides IO::out_every



Range   Default: -1
1:*
Every so many iterations
0:
Disable IOHDF5 output
-1:
Default to IO::out_every






out_vars
Scope: private  STRING



Description: Variables to output in HDF5 file format



Range   Default: (none)
.+
Space-separated list of fully qualified variable/group names
An empty string to output nothing






checkpoint_every
Scope: shared from IO INT






checkpoint_id
Scope: shared from IO BOOLEAN






checkpoint_keep
Scope: shared from IO INT






checkpoint_on_terminate
Scope: shared from IO BOOLEAN






io_out_dir
Scope: shared from IO STRING






io_out_every
Scope: shared from IO INT






out_mode
Scope: shared from IO KEYWORD






out_save_parameters
Scope: shared from IO KEYWORD






out_timesteps_per_file
Scope: shared from IO INT






print_timing_info
Scope: shared from IO BOOLEAN






recover
Scope: shared from IO KEYWORD






recover_and_remove
Scope: shared from IO BOOLEAN






recover_file
Scope: shared from IO STRING






strict_io_parameter_check
Scope: shared from IO BOOLEAN






verbose
Scope: shared from IO KEYWORD



11 Interfaces

General

Implements:

iohdf5

12 Schedule

This section lists all the variables which are assigned storage by thorn CactusPUGHIO/IOHDF5. 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

NONE

Scheduled Functions

CCTK_STARTUP

  iohdf5_startup

  iohdf5 startup routine

 

 After: iohdf5util_startup
 Language:c
 Type: function

CCTK_CPINITIAL

  iohdf5_initialdatacheckpoint

  initial data checkpoint routine

 

 Language:c
 Type: function

CCTK_CHECKPOINT

  iohdf5_evolutioncheckpoint

  evolution data checkpoint routine

 

 Language:c
 Type: function

CCTK_TERMINATE

  iohdf5_terminationcheckpoint

  termination checkpoint routine

 

 Before: iohdf5util_terminate
  Language:c
 Type: function

CCTK_RECOVER_PARAMETERS (conditional)

  iohdf5_recoverparameters

  parameter recovery routine

 

 Language:c
 Type: function