6.2 KiB
POET
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
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+
The following R libraries must then be installed:
Compiling source code
The generation of makefiles is done with CMake. So, running
cmake . -B build
will create the directory build. cd into it and run make to start build
process.
If everything went well you'll find the executable at build/src/poet.
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.
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:
# start R environment
$ 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")
> 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 I would not
recommend to install to hierarchies like /usr/local/ etc.
The correspondending directory tree would be look like this:
.
└── 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
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 valuies 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 /iter.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. To start the simulation
with 4 processes cd into your previously installed POET-dir
<POET_INSTALL_DIR>/bin and run:
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
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
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.~
About the usage of MPI_Wtime()
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).