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Fixes in README and poet.cpp

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This commit is contained in:
Marco De Lucia 2024-06-13 09:47:32 +02:00
parent 25937ec5fd
commit fc7a78be54
2 changed files with 19 additions and 20 deletions
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31
README.md
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@ -32,7 +32,8 @@ To compile POET you need following software to be installed:
- CMake 3.9+ - CMake 3.9+
- Eigen3 3.4+ (required by `tug`) - Eigen3 3.4+ (required by `tug`)
- *optional*: `doxygen` with `dot` bindings for documentation - *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 The following R packages (and their dependencies) must also be
installed: installed:
@ -162,20 +163,20 @@ Run POET by `mpirun ./poet [OPTIONS] <RUNFILE> <SIMFILE>
The following parameters can be set: The following parameters can be set:
| Option | Value | Description | | Option | Value | Description |
|-----------------------------|--------------|--------------------------------------------------------------------------------------------------------------------------| |-----------------------------|--------------|----------------------------------------------------------------------------------|
| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) | | **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
| **-P, --progress** | | show progress bar | | **-P, --progress** | | show progress bar |
| **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) | | **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) |
| **--dht** | | enabling DHT usage (defaults to _OFF_) | | **--dht** | | enabling DHT usage (defaults to _OFF_) |
| **--qs** | | store results using qs::qsave() (.qs extension) instead of default RDS (.rds) | | **--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-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-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-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file | | **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
| **--interp-size** | _1-n_ | size of PHT (interpolation) per process in megabyte | | **--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-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 | | **--interp-min** | _1-n_ | number of entries in PHT bucket needed to start interpolation |
#### Additions to `dht-snaps` #### Additions to `dht-snaps`

8
src/poet.cpp
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@ -1,3 +1,5 @@
// Time-stamp: "Last modified 2024-09-12 14:53:17 delucia"
/* /*
** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of ** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
** Potsdam) ** Potsdam)
@ -220,9 +222,6 @@ ParseRet parseInitValues(char **argv, RuntimeParameters &params) {
// R["dht_log"] = simparams.dht_log; // R["dht_log"] = simparams.dht_log;
try { try {
// Rcpp::Function source("source");
// Rcpp::Function ReadRObj("ReadRObj");
// Rcpp::Function SaveRObj("SaveRObj");
Rcpp::List init_params_(ReadRObj_R(init_file)); Rcpp::List init_params_(ReadRObj_R(init_file));
params.init_params = init_params_; params.init_params = init_params_;
@ -236,7 +235,7 @@ ParseRet parseInitValues(char **argv, RuntimeParameters &params) {
params.timesteps = params.timesteps =
Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps")); Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
} catch (const std::exception &e) { } catch (const std::exception &e) {
ERRMSG("Error while parsing R scripts: " + std::string(e.what())); ERRMSG("Error while parsing R scripts: " + std::string(e.what()));
return ParseRet::PARSER_ERROR; return ParseRet::PARSER_ERROR;
@ -466,7 +465,6 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
} }
int main(int argc, char *argv[]) { int main(int argc, char *argv[]) {
int world_size; int world_size;