mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-16 12:54:50 +01:00
202 lines
7.5 KiB
Markdown
202 lines
7.5 KiB
Markdown
|
|
<!--
|
|
Time-stamp: "Last modified 2021-02-08 13:46:00 mluebke"
|
|
-->
|
|
|
|
# POET
|
|
|
|
POET is a coupled reactive transport simulator implementing a parallel
|
|
architecture and a fast, original MPI-based Distributed Hash Table.
|
|
|
|
## External Libraries
|
|
|
|
The following external header library is shipped with POET:
|
|
|
|
- **argh** - https://github.com/adishavit/argh (BSD license)
|
|
|
|
## Installation
|
|
|
|
### Requirements
|
|
|
|
To compile POET you need several software to be installed:
|
|
|
|
- C/C++ compiler (tested with GCC)
|
|
- MPI-Implementation (tested with OpenMPI and MVAPICH)
|
|
- R language and environment
|
|
- CMake 3.9+
|
|
|
|
If you want to build documentation during compilation, `doxygen`and `graphviz` must be provided too.
|
|
|
|
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://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 obtained POET from git, you should be able to generate Makefiles by running
|
|
|
|
```sh
|
|
mkdir build && cd build
|
|
cmake ..
|
|
```
|
|
|
|
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
|
|
process.
|
|
|
|
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
|
|
|
|
```sh
|
|
mkdir build && cd build
|
|
cmake -D POET_SET_BRANCH="<BRANCH>" ..
|
|
```
|
|
|
|
where currently available branches/tags are:
|
|
|
|
- dev
|
|
|
|
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`.
|
|
|
|
During the generation of Makefiles, various options can be specified via `cmake -D <option>=<value> [...]`. Currently there are the following available options:
|
|
|
|
- **DHT_Debug**=_boolean_ - toggles the output of detailed statistics about DHT
|
|
usage (`cmake -D DHT_Debug=ON`). Defaults to _OFF_.
|
|
- **BUILD_DOC**=_boolean_ - toggles the generation of documantiation during
|
|
compilation process. Defaults to _ON_.
|
|
- _only from svn version:_ **POET_SET_BRANCH**=_string_ - set branch or tag whose code is used
|
|
|
|
### Example: Build from scratch
|
|
|
|
Assuming that only the C/C++ compiler, MPI libraries, R runtime environment and
|
|
CMake have been installed, POET can be installed as follows:
|
|
|
|
```sh
|
|
# start R environment
|
|
$ R
|
|
|
|
# install R dependencies
|
|
> install.packages(c("devtools", "Rcpp", "RInside"))
|
|
> 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
|
|
$ cd <POET_dir>
|
|
|
|
# Build process
|
|
$ mkdir build && cd build
|
|
$ cmake -DCMAKE_INSTALL_PREFIX=/home/<user>/poet ..
|
|
$ make -j<max_numprocs>
|
|
$ make install
|
|
```
|
|
|
|
This will install a POET project structure into `/home/<user>/poet` which is
|
|
called hereinafter `<POET_INSTALL_DIR>`. 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:
|
|
|
|
```sh
|
|
.
|
|
└── poet/
|
|
├── bin/
|
|
│ └── poet
|
|
├── data/
|
|
│ └── SimDol2D.R
|
|
├── docs/
|
|
│ └── html/
|
|
│ ├── index.html
|
|
│ └── ...
|
|
└── R_lib/
|
|
├── kin_r_library.R
|
|
└── parallel_r_library.R
|
|
```
|
|
|
|
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 generated html documentation just open `docs/html/index.html`
|
|
with the browser of your choice.
|
|
|
|
## 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_INSTALL_DIR>/data/SimDol2D.R`)
|
|
- **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
|
|
|
|
### Runtime options
|
|
|
|
The following parameters can be set:
|
|
|
|
| Option | Value | Description |
|
|
| ------------------------ | ------------ | -------------------------------------------------------------- |
|
|
| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
|
|
| **--ignore-result** | | disables store of simulation resuls |
|
|
| **--dht** | | enabling DHT usage (defaults to _OFF_) |
|
|
| **--dht-nolog** | | disabling applying of logarithm before rounding |
|
|
| **--dht-signif=** | _1..n_ | set rounding to number of significant digits (defaults to _5_) |
|
|
| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
|
|
| **--dht-size=** | _1-n_ | size of DHT per process involved in byte (defaults to _1 GiB_) |
|
|
| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
|
|
| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
|
|
|
|
#### Additions to `dht-signif`
|
|
|
|
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`
|
|
|
|
Following values can be set:
|
|
|
|
- _0_ = snapshots are disabled
|
|
- _1_ = only stores snapshot at the end of the simulation with name
|
|
`<OUTPUT_DIRECTORY>.dht`
|
|
- _2_ = stores snapshot at the end and after each iteration iteration
|
|
snapshot files are stored in `<DIRECTORY>/iter<n>.dht`
|
|
|
|
### 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. 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 `<POET_INSTALL_DIR>/bin` and run:
|
|
|
|
```sh
|
|
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 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:
|
|
|
|
```sh
|
|
mpirun -n 4 ./poet --dht SimDol2D.R output
|
|
```
|
|
|
|
## About the usage of MPI_Wtime()
|
|
|
|
Implemented time measurement functions uses `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).
|