diff --git a/README.md b/README.md index 079a6bad0..4b80d4f56 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,11 @@ # POET POET is a coupled reactive transport simulator implementing a parallel -architecture and a fast distributed hash table. +architecture and a fast, original MPI-based Distributed Hash Table. ## External Libraries -We use external libraries: +The following external header library is shipped with POET: - **argh** - https://github.com/adishavit/argh (BSD license) @@ -24,20 +24,19 @@ To compile POET you need several software to be installed: - R language and environment - CMake 3.9+ -If documantiation should be build during compilation `doxygen`and `graphviz` -must be provided too. +If you want to build documentation during compilation, `doxygen`and `graphviz` must be provided too. -The following R libraries must then be installed: +The following R libraries must then be installed, which will get the needed dependencies automatically: - [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html) - [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html) - [RInside](https://cran.r-project.org/web/packages/RInside/index.html) -- [RedModRphree](https://gitext.gfz-potsdam.de/delucia/RedModRphree) -- [Rmufits](https://gitext.gfz-potsdam.de/delucia/Rmufits) +- [RedModRphree](https://git.gfz-potsdam.de/delucia/RedModRphree) +- [Rmufits](https://git.gfz-potsdam.de/delucia/Rmufits) ### Compiling source code -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 +The generation of makefiles is done with CMake. If you obtained POET from git, you should be able to generate Makefiles by running ```sh mkdir build && cd build @@ -79,8 +78,8 @@ $ R # install R dependencies > install.packages(c("devtools", "Rcpp", "RInside")) -> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git") -> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/Rmufits.git") +> devtools::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de") +> devtools::install_gitlab("delucia/Rmufits", host="https://git.gfz-potsdam.de") > q(save="no") # cd into POET project root @@ -94,8 +93,8 @@ $ make install ``` This will install a POET project structure into `/home//poet` which is -called hereinafter ``. With this version of POET I would not -recommend to install to hierarchies like `/usr/local/` etc. +called hereinafter ``. With this version of POET we **do not +recommend** to install to hierarchies like `/usr/local/` etc. The correspondending directory tree would look like this: @@ -115,12 +114,12 @@ The correspondending directory tree would look like this: └── parallel_r_library.R ``` -The R libraries will be read in during runtime and the paths are hardcoded +The R libraries will be loaded at 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. -To display the generetated html documentation just open `docs/html/index.html` +To display the generated html documentation just open `docs/html/index.html` with the browser of your choice. ## Running @@ -155,7 +154,7 @@ The following parameters can be set: #### Additions to `dht-signif` -Only used if no vector is given in setup file. For individual valuies per column +Only used if no vector is given in setup file. For individual values per column use R vector `signif_vector` in `SIMFILE`. #### Additions to `dht-snaps` @@ -171,9 +170,10 @@ Following values can be set: ### Example: Running from scratch 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 -`/bin` and run: +which is the only simulation supported at this moment. The required flow velocities +snapshots are included in the R package Rmufits. It's a 2D, 50x50 grid, with 20 time +steps. To start the simulation with 4 processes `cd` into your previously installed +POET-dir `/bin` and run: ```sh mpirun -n 4 ./poet ../data/SimDol2D.R output @@ -182,7 +182,7 @@ mpirun -n 4 ./poet ../data/SimDol2D.R output After a finished simulation all data generated by POET will be found in the directory `output`. -You might want to use the DHT to cache previously simulated data points and +You might want to use the DHT to cache previously simulated data 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: @@ -190,15 +190,6 @@ activate the usage of the DHT. The resulting call would look like this: 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 - elements), 20 time steps The flow snapshots are **NOT INCLUDED** in project - directory but must be provided separately.~~ At this moment **SimDolKtz.R** is - not supported. - ## About the usage of MPI_Wtime() Implemented time measurement functions uses `MPI_Wtime()`. Some important