added CMake install process + rearrange data dir

CMakeLists.txt

@@ -7,6 +7,8 @@ project(POET VERSION 0.1 LANGUAGES CXX C)
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
 list(APPEND CMAKE_MODULE_PATH "${POET_SOURCE_DIR}/CMake")
 
 # set(GCC_CXX_FLAGS "-D STRICT_R_HEADERS")
@@ -18,4 +20,6 @@ find_package(R REQUIRED)
 find_package(Rcpp REQUIRED)
 find_package(RInside REQUIRED)
 
-add_subdirectory(src)
+add_subdirectory(src)
+add_subdirectory(R_lib)
+add_subdirectory(data)

README.md

@@ -8,6 +8,12 @@
 POET is a coupled reactive transport simulator implementing a parallel
 architecture and a fast distributed hash table.
 
+## External Libraries
+
+We use external libraries:
+
+- **argh** - https://github.com/adishavit/argh (BSD license)
+
 ## Installation
 
 ### Requirements
@@ -65,29 +71,42 @@ $ R
 $ cd <POET_dir>
 
 # Build process
-$ cmake . -B build
-$ cd build
-$ make
-
-# move poet executable into POET project root
-$ mv src/poet ..
-$ cd ..
+$ mkdir build && cd build
+$ cmake -DCMAKE_INSTALL_PREFIX=/home/<user>/poet ..
+$ make -j<max_numprocs>
+$ make install
 ```
 
-The executable can now be found in the POET project root. 
+This will install a POET project structure into `/home/<user>/poet` which is
+called hereinafter `<POET_INSTALL_DIR>`. With this version of POET I would not
+recommend to install to hierarchies like `/usr/local/` etc.
+
+The correspondending directory tree would be look like this:
+
+``` sh
+.
+└── poet/
+    ├── bin/
+    │   └── poet
+    ├── data/
+    │   └── SimDol2D.R
+    └── R_lib/
+        ├── kin_r_library.R
+        └── parallel_r_library.R
+```
+
+The R libraries will be read in during runtime and the paths are hardcoded
+absolute paths inside `poet.cpp`. So, if you consider to move `bin/poet` either
+change paths of the R source files and recompile POET or also move `R_lib/*`
+according to the binary.
 
 ## Running
 
-Before POET is ready to run, a working directory must be created. In this
-directory you should find the executable file, the R scripts
-`<POET_ROOT>/R_lib/kin_r_library.R` and `<POET_ROOT>/R_lib/parallel_r_library.R`
-and the simulation description e.g. `<POET_ROOT>/data/chem_problems/SimDol2D.R`.
-
 Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>` where:
 
 - **OPTIONS** - runtime parameters (explained below)
 - **SIMFILE** - simulation described as R script (currently supported:
-  `<POET_ROOT>/data/chem_problems/SimDol2D.R`)
+  `<POET_INSTALL_DIR>/data/SimDol2D.R`)
 - **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
 
 ### Runtime options
@@ -123,29 +142,15 @@ Following values can be set:
 ### Example: Running from scratch
 
 
-To continue the above example and start a simulation with `SimDol2D.R`:
+We will continue the above example and start a simulation with `SimDol2D.R`,
+which is the only simulation supported at this moment. To start the simulation
+with 4 processes `cd` into your previously installed POET-dir
+`<POET_INSTALL_DIR>/bin` and run:
 
 ``` sh
-mkdir WORK_DIR
-cp data/chem_problems/SimDol2D.R WORK_DIR
-cp R_lib/kin_r_library.R R_lib/parallel_r_library.R WORK_DIR
-mv poet WORK_DIR
+mpirun -n 4 ./poet ../data/SimDol2D.R output
 ```
 
-The correspondending directory tree would be look like this:
-
-``` sh
-.
-└── WORK_DIR/
-    ├── poet
-    ├── kin_r_library.R
-    ├── parallel_r_library.R
-    └── SimDol2D.R
-```
-
-Now, to start the simulation with 4 processes `cd` into `WORK_DIR` and run `mpirun -n 4 ./poet
-SimDol2D.R output`. 
-
 After a finished simulation all data generated by POET will be found in the
 directory `output`.
 
@@ -153,27 +158,22 @@ You might want to use the DHT to cache previously simulated data points and
 reuse them in further time-steps. Just append `-dht` to the options of POET to
 activate the usage of the DHT. The resulting call would look like this:
 
-`mpirun -n 4 ./poet -dht SimDol2D.R output`
+``` sh
+mpirun -n 4 ./poet -dht SimDol2D.R output
+```
 
 ## Examples included (more to come)
 
 - **SimDol2D.R** - simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20
 time steps 2)
-- **SimDolKtz.R** - simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k
+- ~~ **SimDolKtz.R** - simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k
 elements), 20 time steps The flow snapshots are **NOT INCLUDED** in project
-directory but must be provided separately
-
+directory but must be provided separately.~~
 
 ## About the usage of MPI_Wtime()
-Implemented time measurement functions uses `MPI_Wtime()`. Some important
+Implemented time measurement functions use `MPI_Wtime()`. Some important
 informations from the OpenMPI Man Page:
 
 For example, on platforms that support it, the clock_gettime() function will be
 used to obtain a monotonic clock value with whatever precision is supported on
 that platform (e.g., nanoseconds).
-
-## External Libraries
-
-We use external libraries:
-
-- **argh** - https://github.com/adishavit/argh (BSD license)

R_lib/CMakeLists.txt

@@ -0,0 +1 @@
+install(FILES kin_r_library.R parallel_r_library.R DESTINATION R_lib)

data/CMakeLists.txt

@@ -0,0 +1 @@
+install(FILES SimDol2D.R DESTINATION data)

src/CMakeLists.txt

@@ -2,9 +2,11 @@ configure_file(poet.h.in poet.h)
 
 add_executable(poet poet.cpp)
 target_include_directories(poet PUBLIC "${PROJECT_BINARY_DIR}/src")
-target_link_libraries(poet PRIVATE POET_Model POET_Util MPI::MPI_C)
+target_link_libraries(poet PUBLIC POET_Model POET_Util MPI::MPI_C)
 target_compile_definitions(poet PRIVATE OMPI_SKIP_MPICXX)
 
+install(TARGETS poet DESTINATION bin)
+
 add_subdirectory(DHT)
 add_subdirectory(model)
 add_subdirectory(util)

src/poet.cpp

@@ -69,8 +69,8 @@ int main(int argc, char *argv[]) {
   /*Loading Dependencies*/
   std::string r_load_dependencies = "suppressMessages(library(Rmufits));"
                                     "suppressMessages(library(RedModRphree));"
-                                    "source('kin_r_library.R');"
-                                    "source('parallel_r_library.R');";
+                                    "source('../R_lib/kin_r_library.R');"
+                                    "source('../R_lib/parallel_r_library.R');";
   R.parseEvalQ(r_load_dependencies);
 
   SimParams params(world_rank, world_size);

src/util/CMakeLists.txt

@@ -1,4 +1,4 @@
 add_library(POET_Util RRuntime.cpp SimParams.cpp)
 target_include_directories(POET_Util PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${R_INCLUDE_DIRS})
-target_link_libraries(POET_Util ${R_LIBRARIES})
-target_compile_definitions(POET_Util PUBLIC STRICT_R_HEADERS)
+target_link_libraries(POET_Util PUBLIC ${R_LIBRARIES})
+target_compile_definitions(POET_Util PUBLIC STRICT_R_HEADERS)