C6 IOBasic

Chapter C6
IOBasic

Author(s):

Gabrielle Allen

Thomas Radke

Date:

Date

C6.1 Abstract

Thorn IOBasic provides I/O methods for outputting scalar values in ASCII format into files and for printing them as runtime information to screen.

C6.2 Purpose

Thorn IOBasic registers 2 I/O methods with the I/O interface in the flesh which both output the same following information:

for CCTK_SCALAR variables, the value of the scalar versus time
for CCTK_GF and CCTK_ARRAY variables, the values of global reduction operations (eg. minimum, maximum, L1, and L2 norm) versus time

The I/O methods differ in the destination the output is written to:

Scalar
This method outputs the information into ASCII files named "<scalar_name>.{asc|xg}" (for CCTK_SCALAR variables) and "<var_name>_<reduction>.{asc|xg}" (for CCTK_GF and CCTK_ARRAY variables where reduction would stand for the type of reduction value that is output).
The output data can be plotted by using either xgraph (for "*.xg" files) or gnuplot (for "*.asc" files). The output style can be selected via parameter settings.
Info
This method prints the data as runtime information to stdout.
The output occurs as a table with columns containing the current iteration number, the physical time at this iteration, and more columns for scalar/reduction values of each variable to be output.

C6.3 IOBasic Parameters

Parameters to control the Scalar I/O method are:

IOBasic::outScalar_criterion (steerable)
The criterion that decides when to Scalar output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_criterion parameter.
IOBasic::outScalar_every (steerable)
How often, in terms of iterations, to do Scalar output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_every parameter.
IOBasic::outScalar_dt (steerable)
How often, in terms of simulation time, to do Scalar output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_dt parameter.
IOBasic::out_dir
The directory in which to place the Scalar ASCII output files. If the directory doesn’t exist at startup it will be created.
If this paraeter is set to an empty string Scalar output will go to the standard output directory as specified in IO::out_dir.
IOBasic::outScalar_style
How to start comments in the Scalar ASCII output files.
Possible choices for this keywork parameter are xgraph and gnuplot.
IOBasic::out_format (steerable)
The output format for floating-point numbers in Scalar output.
This parameter conforms to the format modifier of the C library routine fprintf(3). You can set the format for outputting floating-point numbers (fixed or exponential) as well as their precision (number of digits).
IOBasic::outScalar_vars (steerable)
The list of variables to output into individual ASCII files.
The variables must be given by their fully qualified variable or group name. The special keyword all requests Scalar output for all variables. Multiple variables must be separated by spaces. For CCTK_GF and CCTK_ARRAY variables, an option string can be appended in curly braces to the name of the variable. The only option supported so far is an individual list of reductions for that variable which would take precedence over the default reduction operations to perform.
IOBasic::outScalar_reductions (steerable)
The list of global reduction operations to perform on CCTK_GF and CCTK_ARRAY variables for Scalar output. This setting can be overridden for individual variables using an option string.
Multiple reduction names must be separated by spaces.

Parameters to control the Info I/O method are:

IOBasic::outInfo_criterion (steerable)
The criterion that decides when to Info output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_criterion parameter.
IOBasic::outInfo_every (steerable)
How often, in terms of iterations, to do Info output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_every parameter.
IOBasic::outInfo_dt (steerable)
How often, in terms of simulation time, to do Info output. If this parameter is set in the parameter file, it will override the setting of the shared IO::out_dt parameter.
IOBasic::outInfo_vars (steerable)
The list of variables to output to screen.
The variables must be given by their fully qualified variable or group name. The special keyword all requests Info output for all variables. Multiple variables must be separated by spaces.
For CCTK_GF and CCTK_ARRAY variables, an option string can be appended in curly braces to the name of the variable. The only option supported so far is an individual list of reductions for that variable which would take precedence over the default reduction operations to perform.
IOBasic::outInfo_reductions (steerable)
The default list of global reduction operations to perform on CCTK_GF and CCTK_ARRAY variables. This setting can be overridden for individual variables using an option string.
Multiple reduction names must be separated by spaces.

All of the above parameters marked as steerable can be changed at runtime.

C6.4 Examples

C6.4.1 Example for Info Output

The following parameter settings request info output for variables grid::r, wavetoy::phi (both are CCTK grid functions) and mythorn::complex (a complex CCTK scalar) at every other iteration.

The minimum and maximum of grid::r is printed according to the list of default reductions for info output (parameter IOBasic::outInfo_reductions). This list is overridden for wavetoy::phi where only the L2 norm is output as specified in the option string for this variable. You can also add other reduction operators within the {} braces.

For the scalar variable mythorn::complex both the real and imaginary part are printed.

  IOBasic::outInfo_every      = 2
  IOBasic::outInfo_vars       = "grid::r
                                 wavetoy::phi{reductions = ’norm2’}
                                 mythorn::complex"
  IOBasic::outInfo_reductions = "minimum maximum"

The resulting screen output would look like this:

---------------------------------------------------------------------------------------------
  it  |          | GRID::r                     | WAVETOY::phi | MYTHORN::complex            |
      |    t     | minimum      | maximum      | norm2        | real part    | imag part    |
---------------------------------------------------------------------------------------------
    0 |    0.000 |   0.02986294 |   0.86602540 |   0.04217014 |   6.90359593 |   0.00000000 |
    2 |    0.034 |   0.02986294 |   0.86602540 |   0.00934749 |   6.90359593 |   0.00000000 |
    4 |    0.069 |   0.02986294 |   0.86602540 |   0.02989811 |   6.90359593 |   0.00000000 |
    6 |    0.103 |   0.02986294 |   0.86602540 |   0.05899959 |   6.90359593 |   0.00000000 |
    8 |    0.138 |   0.02986294 |   0.86602540 |   0.07351147 |   6.90359593 |   0.00000000 |
   10 |    0.172 |   0.02986294 |   0.86602540 |   0.07781795 |   6.90359593 |   0.00000000 |

C6.4.2 Example for Scalar Output

The following parameter settings request scalar output for all grid function variables in the group grid::coordinates and for the scalar variable grid::coarse_dx.
Output occurs every 10th iteration. gnuplot output style is selected for the ASCII files which are placed into a subdirectory scalar_output. The minimum and maximum of grid::r is printed according to the list of default reductions for scalar output (parameter IOBasic::outScalar_reductions). This list is overridden for wavetoy::phi where only the L1 norm is output as specified in the option string for this variable. You can also add other reduction operators within the {} braces.

  IOBasic::outScalar_every      = 10
  IOBasic::outScalar_vars       = "grid::coordinates grid::coarse_dx wavetoy::phi{reductions = ’norm1’}"
  IOBasic::outScalar_reductions = "minimum maximum"
  IOBasic::outScalar_style      = "gnuplot"
  IOBasic::out_dir              = "scalar_output"

This would create the following ASCII files:

  ~/Cactus/par> ls scalar_output
  coarse_dx.asc  r_minimum.asc  x_minimum.asc  y_minimum.asc  z_minimum.asc
  r_maximum.asc  x_maximum.asc  y_maximum.asc  z_maximum.asc  phi_norm1.asc

C6.5 Comments

Possible Reduction Operations
In order to get output of reduction values for CCTK_GF and CCTK_ARRAY variables you need to activate a thorn which provides reduction operators (eg. thorn PUGHReduce in the CactusPUGH arrangement). For a list of possible reduction operations please refer to the documention of this reduction thorn.
Getting Output from IOBasic’s I/O Mehtods
You obtain output by an I/O method by either

setting the appropriate I/O parameters
calling one of the routines of the I/O function interface provided by the flesh

For a description of basic I/O parameters and the I/O function interface to invoke I/O methods by application thorns please see the documentation of thorn IOUtil and the flesh.
Building Cactus configurations with IOBasic
Since IOBasic uses parameters from IOUtil it also needs this I/O helper thorn be compiled into Cactus and activated at runtime in the ActiveThorns parameter in your parameter file.

C6.6 Parameters


out_dir	Scope: private	STRING

Description: Output directory for IOBasic’s scalar files, overrides IO::out_dir

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


out_format	Scope: private	STRING

Description: Which format for Scalar floating-point number output

Range		Default: .13f
see [1] below	output with given precision in exponential / floating point notation

[1]

\^({\textbackslash}.[1]?[0-9])?[EGefg]\$


outinfo_criterion	Scope: private	KEYWORD

Description: Criterion to select Info output intervals

Range		Default: iteration
never	Never output
iteration	Output every so many iterations
time	Output every that much coordinate time


outinfo_dt	Scope: private	REAL

Description: How often to do Info output

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


outinfo_every	Scope: private	INT

Description: How often to do Info output

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


outinfo_reductions	Scope: private	STRING

Description: List of reductions to output as Info to screen

Range		Default: minimum maximum
.+	Space-separated list of reduction operators


outinfo_vars	Scope: private	STRING

Description: Variables to output as Info to screen

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


outscalar_criterion	Scope: private	KEYWORD

Description: Criterion to select Scalar output intervals

Range		Default: iteration
never	Never output
iteration	Output every so many iterations
time	Output every that much coordinate time


outscalar_dt	Scope: private	REAL

Description: How often to do Scalar output

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


outscalar_every	Scope: private	INT

Description: How often to do Scalar output

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


outscalar_reductions	Scope: private	STRING

Description: List of reductions to output into files

Range		Default: minimum maximum norm1 norm2
.+	Space-separated list of reduction operators


outscalar_style	Scope: private	KEYWORD

Description: Which style for Scalar output

Range		Default: xgraph
gnuplot	1D output readable by gnuplot
xgraph	1D output readable by xgraph


outscalar_vars	Scope: private	STRING

Description: Variables to output into files

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


io_out_dir	Scope: shared from IO	STRING


new_filename_scheme	Scope: shared from IO	BOOLEAN


out_criterion	Scope: shared from IO	KEYWORD


out_dt	Scope: shared from IO	REAL


out_every	Scope: shared from IO	INT


out_fileinfo	Scope: shared from IO	KEYWORD


strict_io_parameter_check	Scope: shared from IO	BOOLEAN


verbose	Scope: shared from IO	KEYWORD

C6.7 Interfaces

General

Implements:

iobasic

Inherits:

Grid Variables

PRIVATE GROUPS


Group Names	Variable Names	Details

next_info_output_time		compact	0
	next_info_output_time	dimensions	0
		distribution	CONSTANT
		group type	SCALAR
		stagger type	NONE
		timelevels	1
		variable type	REAL

next_scalar_output_time		compact	0
	next_scalar_output_time	dimensions	0
		distribution	CONSTANT
		group type	SCALAR
		stagger type	NONE
		timelevels	1
		variable type	REAL

C6.8 Schedule

This section lists all the variables which are assigned storage by thorn CactusBase/IOBasic. 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_info_output_time next_scalar_output_time

Scheduled Functions

CCTK_STARTUP

iobasic_startup

startup routine

	After:	ioutil_startup
	Language:	c
	Type:	function

CCTK_INITIAL

iobasic_init

initialisation routine

	Language:	c
	Type:	function

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Chapter C6IOBasic