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114
README.md
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@ -1,12 +1,16 @@
<!--
<<<<<<< HEAD
Time-stamp: "Last modified 2024-09-12 11:39:28 delucia"
=======
Time-stamp: "Last modified 2024-06-13 09:43:22 delucia"
>>>>>>> 9272556 (Fixes in README and poet.cpp)
-->
# POET
[POET](https://doi.org/10.5281/zenodo.4757913) is a coupled reactive transport
simulator implementing a parallel architecture and a fast, original MPI-based
Distributed Hash Table.
[POET](https://doi.org/10.5281/zenodo.4757913) is a coupled reactive
transport simulator implementing a parallel architecture and a fast,
original MPI-based Distributed Hash Table.
![POET's Coupling Scheme](./docs/Scheme_POET_en.svg)
@ -17,7 +21,7 @@ pages](https://naaice.git-pages.gfz-potsdam.de/poet).
## External Libraries
The following external header library is shipped with POET:
The following external libraries are shipped with POET:
- **argh** - https://github.com/adishavit/argh (BSD license)
- **IPhreeqc** with patches from GFZ -
@ -36,17 +40,32 @@ To compile POET you need following software to be installed:
- CMake 3.9+
- Eigen3 3.4+ (required by `tug`)
- *optional*: `doxygen` with `dot` bindings for documentation
- R language and environment (distro dependent)
- R language and environment including headers or `-dev` packages
(distro dependent)
The following R packages (and their dependencies) must also be installed:
The following R packages (and their dependencies) must also be
installed:
- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
- [RInside](https://cran.r-project.org/web/packages/RInside/index.html)
- [qs](https://cran.r-project.org/web/packages/qs/index.html)
This can be simply achieved by issuing the following commands:
```sh
# start R environment
$ R
# install R dependencies (case sensitive!)
> install.packages(c("Rcpp", "RInside","qs"))
> q(save="no")
```
### Compiling source code
POET is built with CMake. You can generate Makefiles by running the usual:
POET is built with CMake. You can generate Makefiles by running the
usual:
```sh
mkdir build && cd build
@ -58,22 +77,22 @@ and generate Makefiles from it. You're now able to run `make` to start
build process.
If everything went well you'll find the executables at
`build/app/poet`, but it is recommended to install the POET project
`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:
- **POET_DHT_Debug**=_boolean_ - toggles the output of detailed statistics about
DHT usage. Defaults to _OFF_.
- **POET_ENABLE_TESTING**=_boolean_ - enables small set of unit tests (more to
come). Defaults to _OFF_.
- **POET_PHT_ADDITIONAL_INFO**=_boolean_ - enabling the count of accesses to one
PHT bucket. Use with caution, as things will get slowed down significantly.
Defaults to _OFF_.
- **POET_PREPROCESS_BENCHS**=*boolean* - enables the preprocessing of predefined
models/benchmarks. Defaults to *ON*.
- **POET_DHT_Debug**=_boolean_ - toggles the output of detailed
statistics about DHT usage. Defaults to _OFF_.
- **POET_ENABLE_TESTING**=_boolean_ - enables small set of unit tests
(more to come). Defaults to _OFF_.
- **POET_PHT_ADDITIONAL_INFO**=_boolean_ - enabling the count of
accesses to one PHT bucket. Use with caution, as things will get
slowed down significantly. Defaults to _OFF_.
- **POET_PREPROCESS_BENCHS**=*boolean* - enables the preprocessing of
predefined models/benchmarks. Defaults to *ON*.
### Example: Build from scratch
@ -130,7 +149,8 @@ poet
With the installation of POET, two executables are provided:
- `poet` - the main executable to run simulations
- `poet_init` - a preprocessor to generate input files for POET from R scripts
- `poet_init` - a preprocessor to generate input files for POET from
R scripts
Preprocessed benchmarks can be found in the `share/poet` directory
with an according *runtime* setup. More on those files and how to
@ -142,28 +162,29 @@ Run POET by `mpirun ./poet [OPTIONS] <RUNFILE> <SIMFILE>
<OUTPUT_DIRECTORY>` where:
- **OPTIONS** - POET options (explained below)
- **RUNFILE** - Runtime parameters described as R script
- **RUNFILE** - Runtime parameters described as R script
- **SIMFILE** - Simulation input prepared by `poet_init`
- **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
- **OUTPUT_DIRECTORY** - path, where all output of POET should be
stored
### POET options
### POET command line arguments
The following parameters can be set:
| Option | Value | Description |
|-----------------------------|--------------|--------------------------------------------------------------------------------------------------------------------------|
| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
| **-P, --progress** | | show progress bar |
| **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) |
| **--dht** | | enabling DHT usage (defaults to _OFF_) |
| **--qs** | | store results using qs::qsave() (.qs extension) instead of default RDS (.rds) |
| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
| **--dht-size=** | _1-n_ | size of DHT per process involved in megabyte (defaults to _1000 MByte_) |
| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
| **--interp-size** | _1-n_ | size of PHT (interpolation) per process in megabyte |
| **--interp-bucket-entries** | _1-n_ | number of entries to store at maximum in one PHT bucket |
| **--interp-min** | _1-n_ | number of entries in PHT bucket needed to start interpolation |
| Option | Value | Description |
|-----------------------------|--------------|----------------------------------------------------------------------------------|
| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
| **-P, --progress** | | show progress bar |
| **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) |
| **--dht** | | enabling DHT usage (defaults to _OFF_) |
| **--qs** | | store results using qs::qsave() (.qs extension) instead of default RDS (.rds) |
| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
| **--dht-size=** | _1-n_ | size of DHT per process involved in megabyte (defaults to _1000 MByte_) |
| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
| **--interp-size** | _1-n_ | size of PHT (interpolation) per process in megabyte |
| **--interp-bucket-entries** | _1-n_ | number of entries to store at maximum in one PHT bucket |
| **--interp-min** | _1-n_ | number of entries in PHT bucket needed to start interpolation |
#### Additions to `dht-snaps`
@ -177,12 +198,13 @@ Following values can be set:
### Example: Running from scratch
We will continue the above example and start a simulation with *barite_het*,
which simulation files can be found in
`<INSTALL_DIR>/share/poet/barite/barite_het*`. As transport a heterogeneous
diffusion is used. It's a small 2D grid, 2x5 grid, simulating 50 time steps with
a time step size of 100 seconds. To start the simulation with 4 processes `cd`
into your previously installed POET-dir `<POET_INSTALL_DIR>/bin` and run:
We will continue the above example and start a simulation with
*barite_het*, which simulation files can be found in
`<INSTALL_DIR>/share/poet/barite/barite_het*`. As transport a
heterogeneous diffusion is used. It's a small 2D grid, 2x5 grid,
simulating 50 time steps with a time step size of 100 seconds. To
start the simulation with 4 processes `cd` into your previously
installed POET-dir `<POET_INSTALL_DIR>/bin` and run:
```sh
cp ../share/poet/barite/barite_het* .
@ -192,11 +214,11 @@ mpirun -n 4 ./poet barite_het_rt.R barite_het.rds 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. Also, after each iteration a DHT snapshot shall be
produced. This is done by appending the `--dht-snaps=<value>` option. The
resulting call would look like this:
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. Also, after each iteration a
DHT snapshot shall be produced. This is done by appending the
`--dht-snaps=<value>` option. The resulting call would look like this:
```sh
mpirun -n 4 ./poet --dht --dht-snaps=2 barite_het_rt.R barite_het.rds output

2
ext/iphreeqc

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Subproject commit 48e65d87ad70f84aec01c27d9560cd3094a8129c
Subproject commit e6e5e0d5156c093241a53e6ce074ef346d64ae26

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src/poet.cpp
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// Time-stamp: "Last modified 2024-06-13 09:46:48 delucia"
/*
** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
** Potsdam)
@ -220,23 +222,19 @@ ParseRet parseInitValues(char **argv, RuntimeParameters &params) {
// R["dht_log"] = simparams.dht_log;
try {
// Rcpp::Function source("source");
// Rcpp::Function ReadRObj("ReadRObj");
// Rcpp::Function SaveRObj("SaveRObj");
Rcpp::List init_params_(ReadRObj_R(init_file));
params.init_params = init_params_;
global_rt_setup = std::make_unique<Rcpp::List>(
source_R(runtime_file, Rcpp::Named("local", true)));
global_rt_setup = std::make_unique<Rcpp::List>(source_R(runtime_file, Rcpp::Named("local", true)));
*global_rt_setup = (*global_rt_setup)["value"];
// MDL add "out_ext" for output format to R setup
(*global_rt_setup)["out_ext"] = params.out_ext;
params.timesteps =
Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
} catch (const std::exception &e) {
ERRMSG("Error while parsing R scripts: " + std::string(e.what()));
return ParseRet::PARSER_ERROR;
@ -253,7 +251,7 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
R.parseEval(std::string("state_T <- setNames(data.frame(matrix(TMP, nrow=" +
std::to_string(trans.GetRequestedVecSize()) +
")), TMP_PROPS)"));
R["TMP"] = Rcpp::wrap(chem.AsVector());
R["TMP_PROPS"] = Rcpp::wrap(chem.GetProps());
R.parseEval(std::string("state_C <- setNames(data.frame(matrix(TMP, nrow=" +
@ -267,11 +265,11 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
DiffusionModule &diffusion,
ChemistryModule &chem) {
/* Iteration Count is dynamic, retrieving value from R (is only needed by
* master for the following loop) */
uint32_t maxiter = params.timesteps.size();
if (params.print_progressbar) {
chem.setProgressBarPrintout(true);
}
@ -422,6 +420,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
return profiling;
}
<<<<<<< HEAD
std::vector<std::string> getSpeciesNames(const Field &&field, int root,
MPI_Comm comm) {
std::uint32_t n_elements;
@ -465,6 +464,11 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
return species_names_out;
}
=======
// MAIN
>>>>>>> 9272556 (Fixes in README and poet.cpp)
int main(int argc, char *argv[]) {
int world_size;