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@ -5,11 +5,11 @@
# POET # POET
POET is a coupled reactive transport simulator implementing a parallel 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 ## External Libraries
We use external libraries: The following external header library is shipped with POET:
- **argh** - https://github.com/adishavit/argh (BSD license) - **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 - R language and environment
- CMake 3.9+ - CMake 3.9+
If documantiation should be build during compilation `doxygen`and `graphviz` If you want to build documentation during compilation, `doxygen`and `graphviz` must be provided too.
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) - [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html)
- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html) - [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
- [RInside](https://cran.r-project.org/web/packages/RInside/index.html) - [RInside](https://cran.r-project.org/web/packages/RInside/index.html)
- [RedModRphree](https://gitext.gfz-potsdam.de/delucia/RedModRphree) - [RedModRphree](https://git.gfz-potsdam.de/delucia/RedModRphree)
- [Rmufits](https://gitext.gfz-potsdam.de/delucia/Rmufits) - [Rmufits](https://git.gfz-potsdam.de/delucia/Rmufits)
### Compiling source code ### 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 ```sh
mkdir build && cd build mkdir build && cd build
@ -79,8 +78,8 @@ $ R
# install R dependencies # install R dependencies
> install.packages(c("devtools", "Rcpp", "RInside")) > install.packages(c("devtools", "Rcpp", "RInside"))
> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git") > devtools::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de")
> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/Rmufits.git") > devtools::install_gitlab("delucia/Rmufits", host="https://git.gfz-potsdam.de")
> q(save="no") > q(save="no")
# cd into POET project root # cd into POET project root
@ -94,8 +93,8 @@ $ make install
``` ```
This will install a POET project structure into `/home/<user>/poet` which is 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 called hereinafter `<POET_INSTALL_DIR>`. With this version of POET we **do not
recommend to install to hierarchies like `/usr/local/` etc. recommend** to install to hierarchies like `/usr/local/` etc.
The correspondending directory tree would look like this: The correspondending directory tree would look like this:
@ -115,12 +114,12 @@ The correspondending directory tree would look like this:
└── parallel_r_library.R └── 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 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/*` change paths of the R source files and recompile POET or also move `R_lib/*`
according to the binary. 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. with the browser of your choice.
## Running ## Running
@ -155,7 +154,7 @@ The following parameters can be set:
#### Additions to `dht-signif` #### 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`. use R vector `signif_vector` in `SIMFILE`.
#### Additions to `dht-snaps` #### Additions to `dht-snaps`
@ -171,9 +170,10 @@ Following values can be set:
### Example: Running from scratch ### Example: Running from scratch
We will 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 which is the only simulation supported at this moment. The required flow velocities
with 4 processes `cd` into your previously installed POET-dir snapshots are included in the R package Rmufits. It's a 2D, 50x50 grid, with 20 time
`<POET_INSTALL_DIR>/bin` and run: steps. To start the simulation with 4 processes `cd` into your previously installed
POET-dir `<POET_INSTALL_DIR>/bin` and run:
```sh ```sh
mpirun -n 4 ./poet ../data/SimDol2D.R output 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 After a finished simulation all data generated by POET will be found in the
directory `output`. 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 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: 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 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() ## About the usage of MPI_Wtime()
Implemented time measurement functions uses `MPI_Wtime()`. Some important Implemented time measurement functions uses `MPI_Wtime()`. Some important