poet/README.md

POET

POET is a coupled reactive transport simulator implementing a parallel architecture and a fast distributed hash table.

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:

• devtools
• Rcpp
• RInside
• RedModRphree
• Rmufits

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
$ cmake . -B build
$ cd build
$ make

# move poet executable into POET project root
$ mv src/poet ..
$ cd ..

The executable can now be found in the POET project root.

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)
• 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

To continue the above example and start a simulation with SimDol2D.R:

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

The correspondending directory tree would be look like this:

.
└── 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.

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 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).

External Libraries

We use external libraries:

• argh - https://github.com/adishavit/argh (BSD license)