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Prepare project to transfer to svn + set poet version with help of
git/textfiles
This commit is contained in:
Max Lübke
parent
a5f95c328d
commit
8b9450d3c0
28
CMake/POET_Scripts.cmake
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28
CMake/POET_Scripts.cmake
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@ -0,0 +1,28 @@
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# Set or get version
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macro(get_POET_version)
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if(EXISTS ${PROJECT_SOURCE_DIR}/.git)
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find_program(GIT_EXECUTABLE git DOC "git executable")
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mark_as_advanced(GIT_EXECUTABLE)
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execute_process(
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COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
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WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
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OUTPUT_VARIABLE POET_GIT_BRANCH
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OUTPUT_STRIP_TRAILING_WHITESPACE)
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execute_process(
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COMMAND ${GIT_EXECUTABLE} describe --always
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WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
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OUTPUT_VARIABLE POET_GIT_VERSION
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OUTPUT_STRIP_TRAILING_WHITESPACE)
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if(NOT POET_GIT_BRANCH STREQUAL "master")
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set(POET_VERSION "${POET_GIT_BRANCH}/${POET_GIT_VERSION}")
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else()
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set(POET_VERSION "${POET_GIT_VERSION}")
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endif()
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elseif(EXISTS ${PROJECT_SOURCE_DIR}/.svn)
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file(STRINGS .gitversion POET_VERSION)
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else()
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set(POET_VERSION "0.1")
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endif()
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message(STATUS "Configuring POET version ${POET_VERSION}")
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endmacro(get_POET_version)
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@ -1,7 +1,7 @@
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# Version 3.9+ offers new MPI package variables
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cmake_minimum_required(VERSION 3.9)
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project(POET VERSION 0.1 LANGUAGES CXX C)
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project(POET CXX C)
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# specify the C++ standard
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set(CMAKE_CXX_STANDARD 14)
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@ -9,10 +9,10 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
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set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
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include("CMake/POET_Scripts.cmake")
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list(APPEND CMAKE_MODULE_PATH "${POET_SOURCE_DIR}/CMake")
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# set(GCC_CXX_FLAGS "-D STRICT_R_HEADERS")
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# add_definitions(${GCC_CXX_FLAGS})
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# set(GCC_CXX_FLAGS "-D STRICT_R_HEADERS") add_definitions(${GCC_CXX_FLAGS})
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find_package(MPI REQUIRED)
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93
README.md
93
README.md
@ -1,4 +1,3 @@
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<!--
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Time-stamp: "Last modified 2021-02-08 13:46:00 mluebke"
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-->
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@ -22,7 +21,7 @@ To compile POET you need several software to be installed:
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- C/C++ compiler (tested with GCC)
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- MPI-Implementation (tested with OpenMPI and MVAPICH)
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- R language and environment
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- R language and environment
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- CMake 3.9+
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If documantiation should be build during compilation `doxygen`and `graphviz`
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@ -38,31 +37,43 @@ The following R libraries must then be installed:
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### Compiling source code
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The generation of makefiles is done with CMake. So, running
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The generation of makefiles is done with CMake. If you obtain POET from a git repository you should be able to generate Makefiles by running
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```
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cmake . -B build
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```sh
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mkdir build && cd build
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cmake ..
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```
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will create the directory `build`. `cd` into it and run `make` to start build
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This will create the directory `build` and processes the CMake files and generate Makefiles from it. You're now able to run `make` to start build
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process.
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If everything went well you'll find the executable at `build/src/poet`.
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If POET was obtained from the official SVN repository or the redmine at <https://redmine.cs.uni-potsdam.de/projects/poet> the branch or tag to be used have to be set via
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During the generation of Makefiles, various options can be specified via `cmake
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-D <option>=<value> [...]`. Currently there are the following available options:
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```sh
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mkdir build && cd build
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cmake -D POET_SET_BRANCH="<BRANCH>" ..
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```
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- **DHT_Debug**=*boolean* - toggles the output of detailed statistics about DHT
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usage (`cmake -D DHT_Debug=ON`). Defaults to *OFF*.
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- **BUIL_DOC**=*boolean* - toggles the generation of documantiation during
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compilation process. Defaults to *ON*.
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where currently available branches/tags are:
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- dev
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If everything went well you'll find the executable at `build/src/poet`, but it is recommended to install the POET project structure to a desired `CMAKE_INSTALL_PREFIX` with `make install`.
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During the generation of Makefiles, various options can be specified via `cmake -D <option>=<value> [...]`. Currently there are the following available options:
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- **DHT_Debug**=_boolean_ - toggles the output of detailed statistics about DHT
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usage (`cmake -D DHT_Debug=ON`). Defaults to _OFF_.
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- **BUILD_DOC**=_boolean_ - toggles the generation of documantiation during
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compilation process. Defaults to _ON_.
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- _only from svn version:_ **POET_SET_BRANCH**=_string_ - set branch or tag whose code is used
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### Example: Build from scratch
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Assuming that only the C/C++ compiler, MPI libraries, R runtime environment and
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CMake have been installed, POET can be installed as follows:
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``` sh
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```sh
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# start R environment
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$ R
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@ -88,14 +99,14 @@ recommend to install to hierarchies like `/usr/local/` etc.
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The correspondending directory tree would look like this:
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``` sh
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```sh
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.
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└── poet/
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├── bin/
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│ └── poet
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├── data/
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│ └── SimDol2D.R
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├── docs/
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├── docs/
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│ └── html/
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│ ├── index.html
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│ └── ...
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@ -130,17 +141,17 @@ Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>` where:
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The following parameters can be set:
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| Option | Value | Description |
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|-------------------------|--------------|-----------------------------------------------------------------|
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| **-work-package-size=** | *1..n* | size of work packages (defaults to *5*) |
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| **-ignore-result** | | disables store of simulation resuls |
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| **-dht** | | enabling DHT usage (defaults to *OFF*) |
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| **-dht-nolog** | | disabling applying of logarithm before rounding |
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| **-dht-signif=** | *1..n* | set rounding to number of significant digits (defaults to *5*) |
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| **-dht-strategy=** | *0-1* | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to *0*) |
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| **-dht-size=** | *1-n* | size of DHT per process involved in byte (defaults to *1 GiB*) |
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| **-dht-snaps=** | *0-2* | disable or enable storage of DHT snapshots |
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| **-dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
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| Option | Value | Description |
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| ----------------------- | ------------ | -------------------------------------------------------------- |
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| **-work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
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| **-ignore-result** | | disables store of simulation resuls |
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| **-dht** | | enabling DHT usage (defaults to _OFF_) |
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| **-dht-nolog** | | disabling applying of logarithm before rounding |
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| **-dht-signif=** | _1..n_ | set rounding to number of significant digits (defaults to _5_) |
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| **-dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
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| **-dht-size=** | _1-n_ | size of DHT per process involved in byte (defaults to _1 GiB_) |
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| **-dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
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| **-dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
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#### Additions to `dht-signif`
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@ -148,26 +159,25 @@ Only used if no vector is given in setup file. For individual valuies per column
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use R vector `signif_vector` in `SIMFILE`.
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#### Additions to `dht-snaps`
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Following values can be set:
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- *0* = snapshots are disabled
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- *1* = only stores snapshot at the end of the simulation with name
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`<OUTPUT_DIRECTORY>.dht`
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- *2* = stores snapshot at the end and after each iteration iteration
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snapshot files are stored in <DIRECTORY>/iter<n>.dht
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- _0_ = snapshots are disabled
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- _1_ = only stores snapshot at the end of the simulation with name
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`<OUTPUT_DIRECTORY>.dht`
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- _2_ = stores snapshot at the end and after each iteration iteration
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snapshot files are stored in `<DIRECTORY>/iter<n>.dht`
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### Example: Running from scratch
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We will continue the above example and start a simulation with `SimDol2D.R`,
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which is the only simulation supported at this moment. To start the simulation
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with 4 processes `cd` into your previously installed POET-dir
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`<POET_INSTALL_DIR>/bin` and run:
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``` sh
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```sh
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mpirun -n 4 ./poet ../data/SimDol2D.R output
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```
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After a finished simulation all data generated by POET will be found in the
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directory `output`.
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@ -176,20 +186,21 @@ You might want to use the DHT to cache previously simulated data points and
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reuse them in further time-steps. Just append `-dht` to the options of POET to
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activate the usage of the DHT. The resulting call would look like this:
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``` sh
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```sh
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mpirun -n 4 ./poet -dht SimDol2D.R output
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```
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## Examples included (more to come)
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- **SimDol2D.R** - simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20
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time steps 2)
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time steps 2)
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- ~~**SimDolKtz.R** - simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k
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elements), 20 time steps The flow snapshots are **NOT INCLUDED** in project
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directory but must be provided separately.~~ At this moment **SimDolKtz.R** is
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not supported.
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elements), 20 time steps The flow snapshots are **NOT INCLUDED** in project
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directory but must be provided separately.~~ At this moment **SimDolKtz.R** is
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not supported.
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## About the usage of MPI_Wtime()
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Implemented time measurement functions uses `MPI_Wtime()`. Some important
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informations from the OpenMPI Man Page:
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@ -63,7 +63,7 @@ USE_MDFILE_AS_MAINPAGE = @PROJECT_SOURCE_DIR@/./README.md
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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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EXCLUDE = @SRC_CODE_DIR@/./util/argh.h
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#---------------------------------------------------------------------------
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# Project related configuration options
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@ -1,8 +1,13 @@
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set(SRC_CODE_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE INTERNAL "directory indicating which source code version is used")
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set(SRC_CODE_DIR
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${CMAKE_CURRENT_SOURCE_DIR}
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CACHE INTERNAL "directory indicating which source code version is used")
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get_poet_version()
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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 "${PROJECT_CURRENT_BINARY_DIR}")
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target_include_directories(poet PUBLIC "${CMAKE_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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@ -58,9 +58,7 @@ int main(int argc, char *argv[]) {
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}
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if (world_rank == 0) {
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cout << "Running POET in version " << poet_version_major << "."
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<< poet_version_minor << endl
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<< endl;
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cout << "Running POET in version " << poet_version << endl << endl;
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}
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/* initialize R runtime */
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@ -1,7 +1,6 @@
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#ifndef POET_H
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#define POET_H
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const int poet_version_major = @POET_VERSION_MAJOR@;
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const int poet_version_minor = @POET_VERSION_MINOR@;
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const char *poet_version = "@POET_VERSION@";
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#endif // POET_H
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