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Marco De Lucia
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README.md
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README.md
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<!--
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<<<<<<< HEAD
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Time-stamp: "Last modified 2024-09-12 11:39:28 delucia"
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=======
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Time-stamp: "Last modified 2024-06-13 09:43:22 delucia"
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>>>>>>> 9272556 (Fixes in README and poet.cpp)
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-->
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# POET
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[POET](https://doi.org/10.5281/zenodo.4757913) is a coupled reactive transport
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simulator implementing a parallel architecture and a fast, original MPI-based
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Distributed Hash Table.
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[POET](https://doi.org/10.5281/zenodo.4757913) is a coupled reactive
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transport simulator implementing a parallel architecture and a fast,
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original MPI-based Distributed Hash Table.
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@ -17,7 +21,7 @@ pages](https://naaice.git-pages.gfz-potsdam.de/poet).
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## External Libraries
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The following external header library is shipped with POET:
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The following external libraries are shipped with POET:
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- **argh** - https://github.com/adishavit/argh (BSD license)
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- **IPhreeqc** with patches from GFZ -
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@ -36,17 +40,32 @@ To compile POET you need following software to be installed:
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- CMake 3.9+
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- Eigen3 3.4+ (required by `tug`)
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- *optional*: `doxygen` with `dot` bindings for documentation
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- R language and environment (distro dependent)
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- R language and environment including headers or `-dev` packages
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(distro dependent)
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The following R packages (and their dependencies) must also be installed:
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The following R packages (and their dependencies) must also be
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installed:
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- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
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- [RInside](https://cran.r-project.org/web/packages/RInside/index.html)
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- [qs](https://cran.r-project.org/web/packages/qs/index.html)
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This can be simply achieved by issuing the following commands:
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```sh
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# start R environment
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$ R
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# install R dependencies (case sensitive!)
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> install.packages(c("Rcpp", "RInside","qs"))
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> q(save="no")
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```
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### Compiling source code
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POET is built with CMake. You can generate Makefiles by running the usual:
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POET is built with CMake. You can generate Makefiles by running the
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usual:
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```sh
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mkdir build && cd build
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@ -58,22 +77,22 @@ and generate Makefiles from it. You're now able to run `make` to start
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build process.
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If everything went well you'll find the executables at
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`build/app/poet`, but it is recommended to install the POET project
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`build/src/poet`, but it is recommended to install the POET project
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structure to a desired `CMAKE_INSTALL_PREFIX` with `make install`.
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During the generation of Makefiles, various options can be specified
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via `cmake -D <option>=<value> [...]`. Currently, there are the
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following available options:
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- **POET_DHT_Debug**=_boolean_ - toggles the output of detailed statistics about
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DHT usage. Defaults to _OFF_.
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- **POET_ENABLE_TESTING**=_boolean_ - enables small set of unit tests (more to
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come). Defaults to _OFF_.
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- **POET_PHT_ADDITIONAL_INFO**=_boolean_ - enabling the count of accesses to one
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PHT bucket. Use with caution, as things will get slowed down significantly.
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Defaults to _OFF_.
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- **POET_PREPROCESS_BENCHS**=*boolean* - enables the preprocessing of predefined
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models/benchmarks. Defaults to *ON*.
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- **POET_DHT_Debug**=_boolean_ - toggles the output of detailed
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statistics about DHT usage. Defaults to _OFF_.
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- **POET_ENABLE_TESTING**=_boolean_ - enables small set of unit tests
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(more to come). Defaults to _OFF_.
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- **POET_PHT_ADDITIONAL_INFO**=_boolean_ - enabling the count of
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accesses to one PHT bucket. Use with caution, as things will get
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slowed down significantly. Defaults to _OFF_.
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- **POET_PREPROCESS_BENCHS**=*boolean* - enables the preprocessing of
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predefined models/benchmarks. Defaults to *ON*.
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### Example: Build from scratch
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@ -130,7 +149,8 @@ poet
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With the installation of POET, two executables are provided:
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- `poet` - the main executable to run simulations
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- `poet_init` - a preprocessor to generate input files for POET from R scripts
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- `poet_init` - a preprocessor to generate input files for POET from
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R scripts
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Preprocessed benchmarks can be found in the `share/poet` directory
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with an according *runtime* setup. More on those files and how to
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@ -144,14 +164,15 @@ Run POET by `mpirun ./poet [OPTIONS] <RUNFILE> <SIMFILE>
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- **OPTIONS** - POET options (explained below)
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- **RUNFILE** - Runtime parameters described as R script
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- **SIMFILE** - Simulation input prepared by `poet_init`
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- **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
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- **OUTPUT_DIRECTORY** - path, where all output of POET should be
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stored
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### POET options
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### POET command line arguments
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The following parameters can be set:
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| Option | Value | Description |
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|-----------------------------|--------------|--------------------------------------------------------------------------------------------------------------------------|
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|-----------------------------|--------------|----------------------------------------------------------------------------------|
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| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
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| **-P, --progress** | | show progress bar |
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| **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) |
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@ -177,12 +198,13 @@ Following values can be set:
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### Example: Running from scratch
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We will continue the above example and start a simulation with *barite_het*,
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which simulation files can be found in
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`<INSTALL_DIR>/share/poet/barite/barite_het*`. As transport a heterogeneous
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diffusion is used. It's a small 2D grid, 2x5 grid, simulating 50 time steps with
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a time step size of 100 seconds. To start the simulation with 4 processes `cd`
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into your previously installed POET-dir `<POET_INSTALL_DIR>/bin` and run:
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We will continue the above example and start a simulation with
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*barite_het*, which simulation files can be found in
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`<INSTALL_DIR>/share/poet/barite/barite_het*`. As transport a
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heterogeneous diffusion is used. It's a small 2D grid, 2x5 grid,
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simulating 50 time steps with a time step size of 100 seconds. To
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start the simulation with 4 processes `cd` into your previously
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installed POET-dir `<POET_INSTALL_DIR>/bin` and run:
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```sh
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cp ../share/poet/barite/barite_het* .
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@ -192,11 +214,11 @@ mpirun -n 4 ./poet barite_het_rt.R barite_het.rds output
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After a finished simulation all data generated by POET will be found
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in the directory `output`.
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You might want to use the DHT to cache previously simulated data and reuse them
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in further time-steps. Just append `--dht` to the options of POET to activate
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the usage of the DHT. Also, after each iteration a DHT snapshot shall be
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produced. This is done by appending the `--dht-snaps=<value>` option. The
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resulting call would look like this:
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You might want to use the DHT to cache previously simulated data and
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reuse them in further time-steps. Just append `--dht` to the options
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of POET to activate the usage of the DHT. Also, after each iteration a
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DHT snapshot shall be produced. This is done by appending the
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`--dht-snaps=<value>` option. The resulting call would look like this:
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```sh
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mpirun -n 4 ./poet --dht --dht-snaps=2 barite_het_rt.R barite_het.rds output
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@ -1 +1 @@
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Subproject commit 48e65d87ad70f84aec01c27d9560cd3094a8129c
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Subproject commit e6e5e0d5156c093241a53e6ce074ef346d64ae26
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14
src/poet.cpp
14
src/poet.cpp
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// Time-stamp: "Last modified 2024-06-13 09:46:48 delucia"
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/*
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** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
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** Potsdam)
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@ -220,15 +222,11 @@ ParseRet parseInitValues(char **argv, RuntimeParameters ¶ms) {
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// R["dht_log"] = simparams.dht_log;
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try {
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// Rcpp::Function source("source");
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// Rcpp::Function ReadRObj("ReadRObj");
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// Rcpp::Function SaveRObj("SaveRObj");
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Rcpp::List init_params_(ReadRObj_R(init_file));
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params.init_params = init_params_;
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global_rt_setup = std::make_unique<Rcpp::List>(
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source_R(runtime_file, Rcpp::Named("local", true)));
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global_rt_setup = std::make_unique<Rcpp::List>(source_R(runtime_file, Rcpp::Named("local", true)));
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*global_rt_setup = (*global_rt_setup)["value"];
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// MDL add "out_ext" for output format to R setup
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@ -422,6 +420,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters ¶ms,
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return profiling;
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}
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<<<<<<< HEAD
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std::vector<std::string> getSpeciesNames(const Field &&field, int root,
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MPI_Comm comm) {
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std::uint32_t n_elements;
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@ -465,6 +464,11 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
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return species_names_out;
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}
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=======
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// MAIN
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>>>>>>> 9272556 (Fixes in README and poet.cpp)
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int main(int argc, char *argv[]) {
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int world_size;
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