mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-15 20:38:23 +01:00
new file describing output of POET + added target doxygen to CMake
This commit is contained in:
Max Lübke
parent
7fc3002b5d
commit
f7d94218c6
@ -23,3 +23,9 @@ find_package(RInside REQUIRED)
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add_subdirectory(src)
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add_subdirectory(R_lib)
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add_subdirectory(data)
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option(BUILD_DOC "Build documentation with doxygen" ON)
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if(BUILD_DOC)
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add_subdirectory(docs)
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endif(BUILD_DOC)
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18
docs/CMakeLists.txt
Normal file
18
docs/CMakeLists.txt
Normal file
@ -0,0 +1,18 @@
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find_package(Doxygen)
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if(DOXYGEN_FOUND)
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set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/./Doxyfile.in)
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set(DOXYGEN_OUT ${CMAKE_BINARY_DIR}/Doxyfile)
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configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
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add_custom_target(doc_doxygen ALL
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COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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COMMENT "Generating documantation with doxygen"
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VERBATIM)
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install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doxygen/ DESTINATION docs)
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else(DOXYGEN_FOUND)
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message("Doxygen not found. Please install.")
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endif(DOXYGEN_FOUND)
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@ -13,6 +13,58 @@
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# TAG += value [value, ...]
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# Values that contain spaces should be placed between quotes (\" \").
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###############################################################################
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#########################GENERATED BY CMAKE####################################
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###############################################################################
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# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
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# double-quotes, unless you are using Doxywizard) that should identify the
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# project for which the documentation is generated. This name is used in the
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# title of most generated pages and in a few other places.
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# The default value is: My Project.
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PROJECT_NAME = @CMAKE_PROJECT_NAME@
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# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
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# could be handy for archiving the generated documentation or if some version
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# control system is used.
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PROJECT_NUMBER = @CMAKE_PROJECT_VERSION@
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# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
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# into which the generated documentation will be written. If a relative path is
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# entered, it will be relative to the location where doxygen was started. If
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# left blank the current directory will be used.
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OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@/doxygen
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# The INPUT tag is used to specify the files and/or directories that contain
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# documented source files. You may enter file names like myfile.cpp or
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# directories like /usr/src/myproject. Separate the files or directories with
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# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
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# Note: If this tag is empty the current directory is searched.
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INPUT = @SRC_CODE_DIR@ \
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@PROJECT_SOURCE_DIR@/./README.md \
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@CMAKE_CURRENT_SOURCE_DIR@/./Output.md
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# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
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# is part of the input, its contents will be placed on the main page
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# (index.html). This can be useful if you have a project on for instance GitHub
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# and want to reuse the introduction page also for the doxygen output.
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USE_MDFILE_AS_MAINPAGE = @PROJECT_SOURCE_DIR@/./README.md
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# The EXCLUDE tag can be used to specify files and/or directories that should be
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# excluded from the INPUT source files. This way you can easily exclude a
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# subdirectory from a directory tree whose root is specified with the INPUT tag.
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#
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# Note that relative paths are relative to the directory from which doxygen is
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# run.
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EXCLUDE = @PROJECT_SOURCE_DIR@/src/util/argh.h
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#---------------------------------------------------------------------------
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# Project related configuration options
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#---------------------------------------------------------------------------
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@ -26,25 +78,11 @@
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DOXYFILE_ENCODING = UTF-8
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# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
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# double-quotes, unless you are using Doxywizard) that should identify the
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# project for which the documentation is generated. This name is used in the
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# title of most generated pages and in a few other places.
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# The default value is: My Project.
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PROJECT_NAME = POET
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# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
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# could be handy for archiving the generated documentation or if some version
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# control system is used.
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PROJECT_NUMBER =
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# Using the PROJECT_BRIEF tag one can provide an optional one line description
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# for a project that appears at the top of each page and should give viewer a
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# quick idea about the purpose of the project. Keep the description short.
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PROJECT_BRIEF =
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PROJECT_BRIEF = "A coupled reactive transport simulator"
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# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
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# in the documentation. The maximum height of the logo should not exceed 55
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@ -53,12 +91,6 @@ PROJECT_BRIEF =
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PROJECT_LOGO =
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# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
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# into which the generated documentation will be written. If a relative path is
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# entered, it will be relative to the location where doxygen was started. If
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# left blank the current directory will be used.
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OUTPUT_DIRECTORY = /tmp/doc
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# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
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# directories (in 2 levels) under the output directory of each output format and
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@ -858,13 +890,6 @@ WARN_LOGFILE =
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# Configuration options related to the input files
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#---------------------------------------------------------------------------
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# The INPUT tag is used to specify the files and/or directories that contain
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# documented source files. You may enter file names like myfile.cpp or
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# directories like /usr/src/myproject. Separate the files or directories with
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# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
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# Note: If this tag is empty the current directory is searched.
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INPUT = /home/max/GFZ/POET/src
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# This tag can be used to specify the character encoding of the source files
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# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
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@ -945,14 +970,6 @@ FILE_PATTERNS = *.c \
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RECURSIVE = YES
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# The EXCLUDE tag can be used to specify files and/or directories that should be
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# excluded from the INPUT source files. This way you can easily exclude a
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# subdirectory from a directory tree whose root is specified with the INPUT tag.
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#
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# Note that relative paths are relative to the directory from which doxygen is
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# run.
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EXCLUDE = ../src/util/argh.h
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# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
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# directories that are symbolic links (a Unix file system feature) are excluded
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@ -1056,12 +1073,6 @@ FILTER_SOURCE_FILES = NO
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FILTER_SOURCE_PATTERNS =
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# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
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# is part of the input, its contents will be placed on the main page
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# (index.html). This can be useful if you have a project on for instance GitHub
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# and want to reuse the introduction page also for the doxygen output.
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USE_MDFILE_AS_MAINPAGE =
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#---------------------------------------------------------------------------
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# Configuration options related to source browsing
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@ -1752,7 +1763,7 @@ EXTRA_SEARCH_MAPPINGS =
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# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
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# The default value is: YES.
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GENERATE_LATEX = YES
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GENERATE_LATEX = NO
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# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
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# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
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66
docs/Output.md
Normal file
66
docs/Output.md
Normal file
@ -0,0 +1,66 @@
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# Output Files
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POET will place all simulation data and other files inside the given
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`<OUTPUT_DIRECTORY>`. The directory will look like this:
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``` {.example}
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.
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└── <OUTPUT_DIRECTORY>/
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├── iter000.rds
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├── iter000.dht
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├── ...
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├── iter<n>.rds
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├── iter<n>.dht
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├── setup.rds
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└── timings.rds
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```
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## Description
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All `.rds` file can be read inside a R runtime using e.g.
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`readRDS("<FILE>")`. The following description can be given to the
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files:
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| File | Description |
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|---------------|-------------------------------------------------------------------------------------------------------------------|
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| iter<*n*>.rds | Defines the state of the grid after *n* iteration, especially the state after transport (`T`) and chemistry (`C`) |
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| iter<*n*>.dht | DHT-snapshot of the *n* th iteration |
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| setup.rds | Summary of all simulation parameters given at startup |
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| timings.rds | Various measured timings by POET |
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## Timings
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POET provides built-in time measurements of (sub) routines. The
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corresponding values can be found in `<OUTPUT_DIRECTORY>/timings.rds`
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and possible to read out within a R runtime with
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`readRDS("timings.rds")`. There you will find the following values:
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| Value | Description |
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|--------------------|----------------------------------------------------------------------------|
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| simtime | time spent in whole simulation loop without any initialization and cleanup |
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| simtime\_transport | measured time in *transport* subroutine |
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| simtime\_chemistry | measured time in *chemistry* subroutine (actual parallelized part) |
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### chemistry subsetting
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If running parallel there are also measured timings which are subsets of
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*simtime\_chemistry*.
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| Value | Description |
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|----------------------------|----------------------------------------------------|
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| simtime\_workers | time spent in send/recv loop of master |
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| simtime\_chemistry\_master | sequential part of master chemistry |
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| phreeqc | measured time of each worker in PHREEQC subroutine |
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### DHT usage {#DHT-usage}
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If running parallel and with DHT activated two more timings and also
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some profiling about the DHT usage are given:
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| Value | Description |
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|-----------------|---------------------------------------------------------|
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| dht\_fill\_time | time to write data to DHT |
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| dht\_get\_time | time to retreive data from DHT |
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| dh\_hits | count of data points retrieved from DHT |
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| dht\_miss | count of misses/count of data points written to DHT |
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| dht\_evictions | count of data points evicted by another write operation |
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@ -1,7 +1,8 @@
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set(SRC_CODE_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE INTERNAL "directory indicating which source code version is used")
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configure_file(poet.h.in poet.h)
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add_executable(poet poet.cpp)
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target_include_directories(poet PUBLIC "${PROJECT_BINARY_DIR}/src")
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target_include_directories(poet PUBLIC "${PROJECT_CURRENT_BINARY_DIR}")
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target_link_libraries(poet PUBLIC POET_Model POET_Util MPI::MPI_C)
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target_compile_definitions(poet PRIVATE OMPI_SKIP_MPICXX)
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