Reggie2.0 toolbox

graph TD;
  gitlab_ci.py["gitlab_ci.py"]-->|call|A[reggie.py];
  repas.py-->|call|A[reggie.py];
  repas.py-->|read|parameter_rename.ini;
  repas.py-->|read|parameter_change.ini;
  repas.py-->|read/write|parameter[parameter.ini];
  A-->|read|builds.ini;
  A-->|read|analyze.ini;
  A-->|read|command_line.ini;
  A-->|read|excludeBuild.ini["excludeBuild.ini (optional)"];
  A-->|read|B["externals.ini (optional)"];
  A-->|read/write|parameter.ini;

Try typing the following

python reggie.py --help

python gitlab-ci.py --help

Python version compatibility

Reggie2.0 was originally desinged to be executed with Python 2, however, Python 3 is now mandated. The following two versions of Python 2 and 3 are recommended

Version
2.7.18
3.9.7

The following versions are known to cause problems

Version	Problem
3.8.10	subprocess.Popen cannot run mpirun correctly

For the sake of backward-compatibility, the following remarks should be considered.

print() function

In Python 3, print() is a function and if the line break is to be omitted, simply add , end='') to the print() call. In order for this command to work with Python 2, the following line must be added as the very first line of code in the file

from __future__ import print_function

Python 3 can't concat bytes to str

In Python 2

bufOut = bufOut + os.read(pipeOut_r, 1024)

is a valid command, where bufOut is of type str and os.read(pipeOut_r, 1024) is of type byte, however, in Python 3 the following line of code must be used

    out_s = os.read(pipeOut_r, 1024)
    if not isinstance(out_s, str):
        out_s = out_s.decode("utf-8")
    bufOut = bufOut + out_s

Lists of (key, value) pairs

In Python 2, .items() returned a list of (key, value) pairs. In Python 3, .items() is now an itemview object, which behaves different. Therefore it has to be iterated over (or materialised), which requires list(dict.items()). In Python 2

for key, value in parameters.items():

is valid, however, in Python 3 the following must be used

for key, value in list(parameters.items()):

Integer division

In Python 2

j = (i / option.base) % len(option.values)

returns an integer, however, in Python 3 a float is returned. Use

j = int((i / option.base) % len(option.values))

if an integer is required.

Items

In python3, use dict.items() instead of dict.iteritems() because iteritems() was removed in python3, so this method cannot be used anymore.

Take a look at Python 3.0 Wiki Built-in Changes section, where it is stated:

Removed dict.iteritems(), dict.iterkeys(), and dict.itervalues().

Instead: use dict.items(), dict.keys(), and dict.values() respectively.

Overview

General file and directory hierarchy in Reggie2.0
Analyze routines for post-processing in analyze.ini
Command line arguments for program execution in command_line.ini
Compile flag combinations for c-make in builds.ini
Exclude runs in parameter.ini

Code hierarchy and required .ini files

gitlab-ci.py
│   gitlab-ci.yml
│
└───reggie.py
    │   builds.ini
    │   analyze.ini;
    |   command_line.ini;
    |   excludeBuild.ini;
    |   externals.ini (opt);
    │
    └───flexi
    |   parameter_flexi.ini
    |   ...
    └───piclas
    │   parameter_piclas.ini
    │   ...
    └───hopr
        parameter_hopr.ini
        ...

Analyze routines for "analyze.ini"

L2 error file
L2 error upper limit
h-convergence test
p-convergence test
h5diff
1. h5diff (multiple files)
  1. Example with h5diff_one_diff_per_run = F
  2. Example with h5diff_one_diff_per_run = T
2. h5diff (additional options)
  1. Dataset Sorting
  2. Multiple dataset names
h5 array bounds check
Data file line comparison
integrate data columns
compare data columns
compare across commands
Clean-up files after each run

The parameters used in analyze.ini and example arguments are given in the following table. Note that if you intend to use white spaces in variable names they must be supplied in form of \s in the variable name. Example: "Initial Timestep" becomes "Initial\sTimestep" (or "Initial\s Timestep") because all white spaces are removed from the variable name automatically. The intention of a white space must be stated explicitly.

analyze	options	values (examples)	Default values	Description
L2 error in file	analyze_L2_file	L2error.txt	None	data file containing the L2 errors for comparing with
	analyze_L2_file_tolerance	6e-2	None	relative/absolute deviation between two L2 errors (from output and from reference file)
	analyze_L2_file_tolerance_type	relative	absolute	relative or absolute comparison
	analyze_L2_file_error_name	L_2_ERROR	L_2	string name of the L2 error in the std.out file
L2 error	analyze_L2	1e-5	None	L2 upper boundary for all nVar. If one L2 error is above the boundary, this test fails
	analyze_L2_error_name	L_2_ERROR	L_2	string name of the L2 error in the std.out file
h-convergence test	analyze_Convtest_h_cells	1,2,4,8	None	number of cells (in each direction, or in the direction of the convergence test variable)
	analyze_Convtest_h_tolerance	0.3	0.02	relative deviation from the p+1 convergence rate to the calculated one
	analyze_Convtest_h_rate	1.0	1.0	ratio of successful tests versus failed tests regarding the number of nVar
	analyze_Convtest_h_error_name	L_2_ERROR	L_2	string name of the L2 error in the std.out file
p-convergence test	analyze_Convtest_p_rate	0.6	None	ratio of successful tests versus failed tests regarding the number of nVar
	analyze_Convtest_p_percentage	0.5	0.75	ratio of increasing EOC samples vs. total number of samples (for the p-convergence, the EOC must increase with p)
	analyze_Convtest_p_error_name	L_2_ERROR	L_2	string name of the L2 error in the std.out file
h5diff	h5diff_file	particle_State_00.0000.h5	None	name of calculated .h5 file (output from current run)
	h5diff_reference_file	particle_State_00.0000.h5_ref	None	reference .h5 file (must be placed in repository) for comparing with the calculated one
	h5diff_data_set	DG_Solution or DG_Solution\sField1	None	name of dataset for comparing (e.g. DG_Solution or DG_Solution vs. Field1 when the datasets in the two files have different names)
	h5diff_tolerance_value	1.0e-2	1e-5	relative/absolute deviation between two elements in a .h5 array
	h5diff_tolerance_type	relative	absolute	relative or absolute comparison
	h5diff_one_diff_per_run	True	False	if multiple reference files are supplied, these can either be used in every run or one each run
	h5diff_sort	True	False	Sort h5 arrays before comparing them, which circumvents problems when comparing arrays that are written in arbitrary order due to multiple MPI processes writing the dataset (currently only 2-dimensional m x n arrays are implemented)
	h5diff_sort_dim	1	-1	Sorting dimension of a 2-dimensional m x n array (1: sort array by rows, 2: sort array by columns)
	h5diff_sort_var	0	-1	Sorting variable of the specified dimension. The array will be sorted for this variable in ascending order (note that variables start at 0)
	h5diff_reshape	True	False	Re-shape h5 arrays before comparing them, effectively removing rows or columns (for example). This is currently only implemented for 2-dimensional m x n arrays.
	h5diff_reshape_dim	1	-1	Select the dimension, which is to be changed (decreased, note that variables start at 0)
	h5diff_reshape_value	11	-1	Value to which the selected dimension is to be changed (decreased)
	h5diff_flip	True	False	Re-shape the h5 array before comparing it with the reference by transposing the array. This is currently only implemented for 2-dimensional m x n arrays.
	h5diff_max_differences	15	0	Maximum number of allowed differences that are detected by h5diff for the test to pass without failure
h5 array bounds check	check_hdf5_file	tildbox_State_01.0000.h5	None	name of calculated .h5 file (output from current run)
	check_hdf5_data_set	PartData	None	name of data set for comparing (e.g. DG_Solution)
	check_hdf5_span	1	2	Checks elements of a 2-dimensional m x n array (1: check array elements by rows, 2: check array elements by columns)
	check_hdf5_dimension	0:2	None	dimension of data set (note that dimensions start at 0)
	check_hdf5_limits	-10.0:10.0	None	bounding interval for all elements in h5 array for all dimensions supplied under check_hdf5_dimension
data file line	compare_data_file_ one_diff_per_run	True	True	if multiple reference files are supplied, these can either be used in every run or one each run
	compare_data_file_ name	Database.csv	None	name of calculated ASCII data file (usually .csv file)
	compare_data_file_ reference	Database.csv_ref	None	name of reference file (must be placed in repository)
	compare_data_file_ tolerance	6e-2	None	relative/absolute deviation between two elements (in e.g. .csv file)
	compare_data_file_ tolerance_type	relative	absolute	relative or absolute comparison
	compare_data_file_ line	50	last	line number in calculated data file (e.g. .csv file)
	compare_data_file_ delimiter	:	,	delimiter symbol, default is comma ',' (note that a comma cannot be supplied in this file as it is a delimiter itself)
	compare_data_file_ max_differences	5	0	Maximum number of allowed differences that are detected by comparison with a reference value for the test to pass without failure
integrate data columns	integrate_line_file	Database.csv	None	name of calculated output file (e.g. .csv file)
	integrate_line_delimiter	:	,	delimiter symbol, default is comma ',' (note that a comma cannot be supplied in this file as it is a delimiter itself)
	integrate_line_columns	0:5	None	two columns for the values x and y supplied as 'x:y' (Note that columns start at 0)
	integrate_line_integral_value	44.00	None	integral value used for comparison
	integrate_line_tolerance_value	0.8e-2	None	tolerance that is used in comparison
	integrate_line_tolerance_type	relative	None	type of tolerance, either 'absolute' or 'relative'
	integrate_line_option	DivideByTimeStep	None	special option, e.g., calculating a rate by dividing the integrated values by the timestep which is used in the values 'x'
	integrate_line_multiplier	1	1	factor for multiplying the result (in order to acquire a physically meaning value for comparison)
	integrate_line_multiplier	1	1	factor for multiplying the result (in order to acquire a physically meaning value for comparison)
compare data column	compare_column_file	PartAnalyze.csv	None	name of calculated output file (e.g. .csv file)
	compare_column_reference_file	Reference.csv	None	name of of the reference file
	compare_column_delimiter	:	,	delimiter symbol, default is comma ',' (note that a comma cannot be supplied in this file as it is a delimiter itself)
	compare_column_index	0	None	column index for comparison (Note that the index of the column start at 0)
	compare_column_tolerance_value	0.8e-2	None	tolerance that is used in comparison
	compare_column_tolerance_type	relative	None	type of tolerance, either 'absolute' or 'relative'
	compare_column_multiplier	1	1	factor for multiplying the result (in order to acquire a physically meaning value for comparison)
compare across commands	compare_across_commands_ file	ElemTimeStatistics.csv	None	name of calculated output file (e.g. csv)
	compare_across_commands_ column_delimiter	:	,	delimiter symbol, default is comma ',' (note that a comma cannot be supplied in this file as it is a delimiter itself)
	compare_across_commands_ column_index	0	None	column index for comparison (note that first column has index 0)
	compare_across_commands_ line_number	1	last	line number for comparison (note that first line has number 1)
	compare_across_commands_ tolerance_value	0.1	0.1	tolerance value for deviation among the values to be compared
	compare_across_commands_ tolerance_type	absolute	relative	tolerance type to be used in comparison
	compare_across_commands_ reference	1	0	command number for taking reference value (according to numbering cmd_0001, cmd_0002,...) - default value 0 takes average of all calculated values
clean-up files after run	clean_up_files	State	None	remove all unwanted files directly after the run is completed. The wild card character is "*"

L2 error file

Compare all L2 errors calculated for all nVar against supplied values in a data file
relative or absolute comparison possible

Template for copying to analyze.ini

 ! L2 error from file
analyze_L2_file                = L2error.txt
analyze_L2_file_tolerance      = 1e-2
analyze_L2_file_tolerance_type = relative

Note that the errors (in this example in L2error.txt) must be supplied in the following format

L_2       :    1.5942413E+09   1.9238600E+09   1.2437159E+10   7.1690941E+01   1.4439652E+02   1.4360107E-01   1.5516452E+09   3.2439672E-02

L2 error upper limit

Compare all L2 errors calculated for all nVar against an upper boundary analyze_L2

Template for copying to analyze.ini

!L2 error norm
analyze_L2=1e7

h-convergence test

Determine the rate of convergence versus decreasing the average spacing between two DOF by running multiple different grids
Requires multiple mesh files

Template for copying to analyze.ini

! h-convergence test
analyze_Convtest_h_cells=1,2,4,8
analyze_Convtest_h_tolerance=0.3
analyze_Convtest_h_rate=1

p-convergence test

Determine an increasing rate of convergence by increasing the polynomial degree (for a constant mesh)

Template for copying to analyze.ini

! p-convergence test
analyze_Convtest_p_rate=0.8
analyze_Convtest_p_percentage=0.75

h5diff

Compares two arrays from two .h5 files element-by-element either with an absolute or relative difference (when comparing with zero, h5diff automatically uses an absolute comparison).
Requires h5diff, which is compiled within the HDF5 package (set the corresponding environment variable).
```
`export PATH=/opt/hdf5/X.X.XX/bin/:$PATH`
```
Requires h5py for checking if the datasets which are to be compared by h5diff are of the same dimensions.

http://docs.h5py.org/en/2.5.0/build.html

Template for copying to analyze.ini

! hdf5 diff
h5diff_file            =          single-particle_State_000.00000005000000000.h5
h5diff_reference_file  = single-particle_reference_State_000.0000000500000000.h5
h5diff_data_set        = DG_Source
h5diff_tolerance_value = 1.0e-2
h5diff_tolerance_type  = relative

h5diff (multiple files)

Compares multiple arrays from multiple .h5 files element-by-element either with an absolute or relative difference (when comparing with zero, h5diff automatically uses an absolute comparison).
Requires h5diff, which is compiled within the HDF5 package.

Example with `h5diff_one_diff_per_run = F`

This setup considers 2 runs and compares two files with two different reference files in each run, hence, multiple file output can be analyzed.

Template for copying to analyze.ini

! hdf5 diff
h5diff_file            = sharpSOD_State_0000000.100000000.h5        , sharpSOD_QDS_0000000.100000000.h5
h5diff_reference_file  = reggie_sharpSOD_State_0000000.100000000.h5 , reggie_sharpSOD_QDS_0000000.100000000.h5
h5diff_data_set        = DG_Solution                                , FieldData
h5diff_tolerance_value = 1.0e-12                                    , 1.0e-12
h5diff_tolerance_type  = absolute                                   , absolute

Example with `h5diff_one_diff_per_run = T`

This setup considers 4 runs (the polynomial degree is varied) and in every run only one file is compared with a reference file. In the next run, a different reference file is used.

Template for copying to analyze.ini

! hdf5 diff
h5diff_one_diff_per_run= T
h5diff_file            = hdg_slab_DielectricGlobal_000.00000000000000000.h5        , hdg_slab_DielectricGlobal_000.00000000000000000.h5        , hdg_slab_DielectricGlobal_000.00000000000000000.h5        , hdg_slab_DielectricGlobal_000.00000000000000000.h5
h5diff_reference_file  = hdg_slab_DielectricGlobal_000.00000000000000000_ref_N3.h5 , hdg_slab_DielectricGlobal_000.00000000000000000_ref_N5.h5 , hdg_slab_DielectricGlobal_000.00000000000000000_ref_N7.h5 , hdg_slab_DielectricGlobal_000.00000000000000000_ref_N9.h5
h5diff_data_set        = DG_Solution                                               , DG_Solution                                               , DG_Solution                                               , DG_Solution
h5diff_tolerance_value = 1.0e-2                                                    , 1.0e-2                                                    , 1.0e-2                                                    , 1.0e-2
h5diff_tolerance_type  = relative                                                  , relative                                                  , relative                                                  , relative

h5diff (additional options)

Dataset Sorting

Further options include the pre-sorting of a dataset before the actual comparison via h5diff is performed. This circumvents problems when comparing arrays that are written in arbitrary order due to multiple MPI processes writing the dataset (currently only 2-dimensional m x n arrays are implemented)
The sorting can be performed for rows m by setting h5diff_sort_dim=1 or columns n by h5diff_sort_dim=2
The corresponding variable is selected via h5diff_sort_var. Note that variables start at 0 and end at m-1 or n-1 for rows or columns, respectively.

The following example considers an 8 x 4481 array PartData, which is to be sorted by the values in the first row (select the rows via h5diff_sort_dim=1 and the variable h5diff_sort_var=0)

Template for copying to analyze.ini

! hdf5 diff
h5diff_file             = sphere_PartStateBoundary_000.00000010000000000.h5
h5diff_reference_file   = sphere_PartStateBoundary_000.00000010000000000_ref.h5
h5diff_data_set         = PartData
h5diff_tolerance_value  = 1.0e-2
h5diff_tolerance_type   = relative
h5diff_sort             = T
h5diff_sort_dim         = 1
h5diff_sort_var         = 0

Dataset Re-Shaping

datasets may be reshaped prior to comparison, e.g., made smaller by decreasing a dimension

The following example considers an 14497 x 12 array PartData, which is to be re-shaped to an 14497 x 11 array, effectively removing the 12th column.

Template for copying to analyze.ini

! hdf5 diff
h5diff_file             = sphere_PartStateBoundary_000.00000010000000000.h5
h5diff_reference_file   = sphere_PartStateBoundary_000.00000010000000000_ref.h5
h5diff_data_set         = PartData
h5diff_tolerance_value  = 1.0e-2
h5diff_tolerance_type   = relative
h5diff_reshape          = T
h5diff_reshape_dim      = 0
h5diff_reshape_value    = 11

Multiple dataset names

When the datasets in the file and reference differ, simply supply both names. Instead of

h5diff_data_set        = DG_Solution

simply add the second name and add the "\s" delimiter, because white spaces are always removed by default

h5diff_data_set        = DG_Solution\sField1

where "DG_Solution" corresponds to the dataset name in h5diff_file and "Field1" to the dataset in h5diff_reference_file.

h5 array bounds check

Check if all elements of a h5 array are within a supplied interval
Requires h5py python module (analyze will fail if the module cannot be found)

Template for copying to analyze.ini

! check if particles are outside of domain at tEnd
check_hdf5_file        = tildbox_State_001.00000000000000000.h5
check_hdf5_data_set    = PartData
check_hdf5_span        = 2 ! 1: check array elements by rows, 2: check array elements by columns
check_hdf5_dimension   = 0:2
check_hdf5_limits      = -10.0:10.0

Data file line comparison

Compare a single line in, e.g., a .csv file element-by-elements
The data is delimited by a comma on default but can be changed by setting "compare_data_file_delimiter = :" (when, e.g., ":" is to be used as the delimiter)
relative of absolute comparison

Example 1 of 4

Template for copying to analyze.ini

! compare the last row in Database.csv with a reference file
compare_data_file_name      = Database.csv
compare_data_file_reference = Database_reference.csv
compare_data_file_tolerance = 2.0
compare_data_file_tolerance_type = relative

Note that a comma is the default delimiter symbol for reading the data from the supplied file. The variable "compare_data_file_delimiter" cannot be set as custom delimiter symbol "," because the comma is used for splitting the keywords in analyze.ini. However, other symbols can be supplied using "compare_data_file_delimiter" instead of a comma.

Example 2 of 4

When different runs produce different output (e.g. changing the initial conditions, here, the temperature is varied), multiple reference files can be supplied. The following example produces the same output file (Database.csv) but compares with different reference files (Database_TX000K_ref.csv).

! compare the last row in Database.csv with a reference file
compare_data_file_name      = Database.csv
compare_data_file_reference = Database_T1000K_ref.csv, Database_T2000K_ref.csv, Database_T3000K_ref.csv, Database_T4000K_ref.csv, Database_T5000K_ref.csv
compare_data_file_tolerance = 2.0
compare_data_file_tolerance_type = relative

Example 3 of 4

Additionally, multiple output files (Database_TX000K.csv) can be supplied in combination with multiple reference files (Database_TX000K_ref.csv). See the following example.

! compare the last row in Database.csv with a reference file
compare_data_file_name      = Database_T1000K.csv, Database_T2000K.csv, Database_T3000K.csv, Database_T4000K.csv, Database_T5000K.csv
compare_data_file_reference = Database_T1000K_ref.csv, Database_T2000K_ref.csv, Database_T3000K_ref.csv, Database_T4000K_ref.csv, Database_T5000K_ref.csv
compare_data_file_tolerance = 2.0
compare_data_file_tolerance_type = relative

Note that for this example, the number of supplied output files, reference files and runs must be the same.

Example 4 of 4

Additionally, the tolerance type and value can be altered.

! compare the last row in Database.csv with a reference file
compare_data_file_name           = Database_T1000K.csv, Database_T2000K.csv, Database_T3000K.csv, Database_T4000K.csv, Database_T5000K.csv
compare_data_file_reference      = Database_T1000K_ref.csv, Database_T2000K_ref.csv, Database_T3000K_ref.csv, Database_T4000K_ref.csv, Database_T5000K_ref.csv
compare_data_file_tolerance      = 1e-2    , 5e-2    , 1e-10    , 1e-10
compare_data_file_tolerance_type = relative, relative, absolute, absolute

Note that for this example, the number of all varied parameters must be the same (in this case 4) otherwise it will not work.

integrate data columns

Integrate the data in a column over another column, e.g., x:y in a data file as integral(y(x), x, x(1), x(end)) via the trapezoid rule
The data is delimited by a comma on default but can be changed by setting "integrate_line_delimiter = :" (when, e.g., ":" is to be used as the delimiter)
special options are available for calculating, e.g., rates (something per second)

Template for copying to analyze.ini

! ===================================================================================================================
! integrate columns x:y in a data file as integral(y(x), x, x(1), x(end))
! check the emission current of electrons: Current = Q*MPF*q/delta_t_database = 44 A
! ===================================================================================================================
! with   Q = integrate nPartIn(t) from t=0 to t=3E-11 = 4.500111958051274e-10 for p=9 (integrate nPartIN over time)
!      MPF = 1e6
!        q = 1.6022e-19 (charge of one electron)
!       dt = ? (depends on polynomial degree and mesh)
! ===================================================================================================================
! for p = 9: 551 timesteps  -->  0.44769549409291E-09*IntegrateLineMultiplier = 44 A
integrate_line_file            = Database.csv          ! data file name
integrate_line_columns         = 0:5                   ! columns x:y
integrate_line_integral_value  = 44.00                 ! Ampere
integrate_line_tolerance_value = 0.8e-2                ! tolerance
integrate_line_tolerance_type  = relative              ! absolute or relative comparison
integrate_line_option          = DivideByTimeStep      ! the first column in Database.csv is used for this option
integrate_line_multiplier      = 5.340588433333334e-03 ! = MPF*q/tend = 1e6*1.60217653E-19/3E-11

Note that a comma is the default delimiter symbol for reading the data from the supplied file. The variable "integrate_line_delimiter" cannot be set as custom delimiter symbol "," because the comma is used for splitting the keywords in analyze.ini. However, other symbols can be supplied using "integrate_line_delimiter" instead of a comma.

compare data column

compares the data in a column with a reference file
The data is delimited by a comma on default but can be changed by setting "compare_column_delimiter = :" (when, e.g., ":" is to be used as the delimiter)

Template for copying to analyze.ini

! compare columns in a data file
compare_column_file            = PartAnalyze.csv ! data file name
compare_column_reference_file  = reference.csv   ! reference data file name
compare_column_index           = 0               ! columns index (starts at 0)
compare_column_tolerance_value = 0.8e-2          ! tolerance
compare_column_tolerance_type  = relative        ! absolute or relative comparison
compare_column_multiplier      = 5e-3            ! fixed factor

Note that a comma is the default delimiter symbol for reading the data from the supplied file. The variable "compare_column_delimiter" cannot be set as custom delimiter symbol "," because the comma is used for splitting the keywords in analyze.ini. However, other symbols can be supplied using "compare_column_delimiter" instead of a comma.

Compare across commands

Description: compare data from corresponding runs of different commands, e.g. cmd_*/run_0001 (= cmd_0001/run_0001 vs. cmd_0002/run_0001 vs. cmd_0003/run_0001 vs. ...), cmd_*/run_0002, cmd_*/run_0003, etc.
Purpose: allows to investigate e.g. the parallel efficiency in a strong scaling test, if the different command directories originate from an increasing number of MPI threads (command_line.ini: MPI=2,4,6,...) and the PID is written to the csv-file
data to be compared is a singular value per run, written to a csv-file and specified through row number (first line = 1) and column index (first column = 0)
two referencing types are supported, specified through compare_across_commands_reference:
- a value ≥ 1 is interpreted as command index (cf. directory names cmd_0001, cmd_0002, etc.), e.g. the value 1 would compare all data against that of the first command
- the value 0 takes the average (arithmetic mean) of all extracted data as reference
Caution: The default delimiter symbol for reading the data from the supplied csv-file is a comma. The variable compare_across_commands_column_delimiter cannot be set to character "," because the comma is used for splitting the keywords in analyze.ini. Any other delimiter symbol, however, is acceptable.

Template for copying to analyze.ini

compare_across_commands_file            = ElemTimeStatistics.csv    ! name of output file
compare_across_commands_column_index    = 5                         ! column index (starts at 0)
compare_across_commands_line_number     = 3                         ! line number (starts at 1)
compare_across_commands_tolerance_value = 0.2                       ! tolerance
compare_across_commands_tolerance_type  = relative                  ! absolute or relative comparison
compare_across_commands_reference       = 1                         ! command number for taking reference value (1,2,...), or 0 for average

Make sure to provide a file command_line.ini with multiple commands, e.g. for a strong scaling test

MPI=2,4,6,8

Clean-up files

remove all unwanted files directly after the run is completed. The wild card character is "*"

Template for copying to analyze.ini

clean_up_files = *_State_*, *.csv, *.dat

Command Line

parameters used in command_line.ini and example arguments

function	options	values	Default values	Description
mpirun	MPI	1,2,4,8	None	number of MPI threads with which the runs are repeated
additional info	cmd_suffix	DSMC.ini	None	additional information that is appended to the command line argument that is used for running a program
restart from file	restart_file	My_State_000.0000005123.h5	None	supply the name of a state file from which all simulations are to be re-started

Example

run multiple different MPI threads
use additional parameter file DSMC.ini

Template for copying to command_line.ini

! command line parameters
MPI=2
cmd\_suffix=DSMC.ini

Externals

parameters used in externals.ini

function	options	values	Default values	Description
mpirun	MPI	1,2,4,8	None	number of MPI threads with which the runs are repeated
name of external binary in bin folder	externalbinary	hopr	None	supply the external binary name (the binary is assumed to lie in each "build/bin/" directory
directory of ini-files for external binary	externaldirectory	hopr	None	supply the relative path (starting from each example folder) to the directory of the parameterfiles for the external binary
runtime of external (pre or post)	externalruntime	pre,post	None	supply the runtime of the external binary and its parameterfiles as pre- or postprocessing
Pre-execution command	cmd_pre_execute	ln\s-s\s../cube_mesh.h5	None	Run additional script before external in executed (e.g. create an symbolic link)

Example

supply two external binaries: hopr and posti
supply two directories with parameter files for each external tool
different run times for hopr and posti
(optional: run different MPI threads with hopr and posti, see above)

Template for copying to command\_line.ini

! external parameters
externalbinary    = hopr,posti
externaldirectory = hopr,posti
externalruntime   = pre,post
MPI               = 1,2

! do not mix multiple definitions for binary, directory and runtime
nocrosscombination:externalbinary,externaldirectory,externalruntime,MPI

Builds

parameters used in builds.ini and example arguments

function	options	values	Default values	Description
program to execute	binary	./bin/flexi	None	set the relative binary path in build directory
compile flags	CMAKE_BUILD_TYPE	DEBUG	None	set compile flags to the corresponding settings
exclude combinations	EXCLUDE:	FLEXI_VISCOSITY=sutherland,FLEXI_PARABOLIC=OFF	None	exclude specific combinations of compile flags, these will be skipped

Runs

Exclude runs directly

In order to exclude runs see the following example

! =============================================================================== !
! Species1 - CH4
! =============================================================================== !
Part-Species1-MWTemperatureIC=1000,4000
Part-Species1-TempVib=2000,3000

! exclude combinations
EXCLUDE:Part-Species1-MWTemperatureIC=1000,Part-Species1-TempVib=3000

Use the same parameter list for multiple parameters in parameter.ini

In order to exclude runs see the following example in which 10 runs are performed, but the parameters are exchanged parallely. Modify the parameter.ini file.

! =============================================================================== !
! Species1 - CH4
! =============================================================================== !
Part-Species1-MWTemperatureIC=crosscombinations
Part-Species1-TempVib=crosscombinations
Part-Species1-TempRot=crosscombinations
Part-Species1-TempElec=crosscombinations
! =============================================================================== !
! Species2 - CH3
! =============================================================================== !
Part-Species2-MWTemperatureIC=crosscombinations
Part-Species2-TempVib=crosscombinations
Part-Species2-TempRot=crosscombinations
Part-Species2-TempElec=crosscombinations
! =============================================================================== !
! Species3 - H2
! =============================================================================== !

Part-Species3-MWTemperatureIC=crosscombinations
Part-Species3-TempVib=crosscombinations
Part-Species3-TempRot=crosscombinations
Part-Species3-TempElec=crosscombinations
! =============================================================================== !
! Species4 - H
! =============================================================================== !
Part-Species4-MWTemperatureIC=crosscombinations
Part-Species4-TempElec=crosscombinations

crosscombinations=1000,2000,3000,4000,5000,6000,7000,8000,9000,10000

Example

Template for copying to builds.ini

! relative binary path in build directory
binary=./bin/flexi

! fixed compiler flags
CMAKE_BUILD_TYPE=DEBUG
FLEXI_BUILD_HDF5=OFF
FLEXI_PAPI=OFF
FLEXI_POLYNOMIAL_DEGREE=N
FLEXI_MKL=OFF
FLEXI_SPLIT_DG=OFF

! include combinations
FLEXI_2D=OFF,ON
FLEXI_EQNSYSNAME=navierstokes,linearscalaradvection
FLEXI_LIFTING=br1,br2
FLEXI_MPI=ON!,OFF
FLEXI_NODETYPE=GAUSS,GAUSS-LOBATTO
FLEXI_PARABOLIC=ON,OFF
FLEXI_VISCOSITY=constant,sutherland,powerlaw
FLEXI_FV=ON,OFF
FLEXI_FV_RECONSTRUCTION=ON,OFF
FLEXI_GCL=ON,OFF

! exclude combinations
EXCLUDE:FLEXI_VISCOSITY=sutherland,FLEXI_PARABOLIC=OFF
EXCLUDE:FLEXI_VISCOSITY=powerlaw,FLEXI_PARABOLIC=OFF
EXCLUDE:FLEXI_VISCOSITY=sutherland,FLEXI_EQNSYSNAME=linearscalaradvection
EXCLUDE:FLEXI_VISCOSITY=powerlaw,FLEXI_EQNSYSNAME=linearscalaradvection
EXCLUDE:FLEXI_LIFTING=br2,FLEXI_EQNSYSNAME=linearscalaradvection
EXCLUDE:FLEXI_FV=ON,FLEXI_FV_RECONSTRUCTION=OFF,FLEXI_PARABOLIC=ON
EXCLUDE:FLEXI_FV=OFF,FLEXI_FV_RECONSTRUCTION=ON
EXCLUDE:FLEXI_GCL=ON,FLEXI_FV=ON ! Not yet implemented
EXCLUDE:FLEXI_NODETYPE=GAUSS-LOBATTO,FLEXI_VISCOSITY=sutherland
EXCLUDE:FLEXI_NODETYPE=GAUSS-LOBATTO,FLEXI_VISCOSITY=powerlaw
EXCLUDE:FLEXI_LIFTING=br2,FLEXI_VISCOSITY=sutherland
EXCLUDE:FLEXI_LIFTING=br2,FLEXI_VISCOSITY=powerlaw

Name		Name	Last commit message	Last commit date
Latest commit History 483 Commits
.gitlab/merge_request_templates		.gitlab/merge_request_templates
gitlab_ci		gitlab_ci
repas		repas
.gitignore		.gitignore
.gitlab-ci.yml		.gitlab-ci.yml
CONTRIBUTORS.md		CONTRIBUTORS.md
LICENCE.md		LICENCE.md
README.md		README.md
analysis.py		analysis.py
analyze_functions.py		analyze_functions.py
args_parser.py		args_parser.py
check.py		check.py
combinations.py		combinations.py
externalcommand.py		externalcommand.py
outputdirectory.py		outputdirectory.py
reggie.py		reggie.py
summary.py		summary.py
tools.py		tools.py

License

reggie-framework/reggie2.0

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Reggie2.0 toolbox

Python version compatibility

print() function

Python 3 can't concat bytes to str

Lists of (key, value) pairs

Integer division

Items

Overview

Code hierarchy and required .ini files

Analyze routines for "analyze.ini"

L2 error file

L2 error upper limit

h-convergence test

p-convergence test

h5diff

h5diff (multiple files)

Example with h5diff_one_diff_per_run = F

Example with h5diff_one_diff_per_run = T

h5diff (additional options)

Dataset Sorting

Dataset Re-Shaping

Multiple dataset names

h5 array bounds check

Data file line comparison

Example 1 of 4

Example 2 of 4

Example 3 of 4

Example 4 of 4

integrate data columns

compare data column

Compare across commands

Clean-up files

Command Line

Example

Externals

Example

Builds

Runs

Exclude runs directly

Use the same parameter list for multiple parameters in parameter.ini

Example

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Example with `h5diff_one_diff_per_run = F`

Example with `h5diff_one_diff_per_run = T`

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