perf: remove RRuntime as there is no need anymore

app/poet.cpp

@@ -18,11 +18,11 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
+#include <RInside.h>
 #include <Rcpp.h>
 #include <poet/ChemSim.hpp>
 #include <poet/DiffusionModule.hpp>
 #include <poet/Grid.hpp>
-#include <poet/RRuntime.hpp>
 #include <poet/SimParams.hpp>
 
 #include <cstring>
@@ -62,7 +62,7 @@ int main(int argc, char *argv[]) {
   }
 
   /* initialize R runtime */
-  RRuntime R(argc, argv);
+  RInside R(argc, argv);
 
   /*Loading Dependencies*/
   // TODO: kann raus
@@ -114,7 +114,8 @@ int main(int argc, char *argv[]) {
 
   // TODO: Grid anpassen
 
-  Grid grid(R, poet::GridParams(R));
+  GridParams grid_params = GridParams(R);
+  Grid grid(grid_params);
   // grid.init_from_R();
 
   params.initVectorParams(R, grid.getSpeciesCount());

include/poet/ChemSim.hpp

@@ -23,7 +23,7 @@
 
 #include "DHT_Wrapper.hpp"
 #include "Grid.hpp"
-#include "RRuntime.hpp"
+#include "RInside.h"
 #include "SimParams.hpp"
 #include <bits/stdint-uintn.h>
 #include <cstdint>
@@ -69,7 +69,7 @@ public:
    * @param R_ R runtime
    * @param grid_ Initialized grid
    */
-  ChemSim(SimParams &params, RRuntime &R_, Grid &grid_);
+  ChemSim(SimParams &params, RInside &R_, Grid &grid_);
 
   /**
    * @brief Run iteration of simulation in sequential mode
@@ -139,7 +139,7 @@ protected:
    * @brief Instance of RRuntime object
    *
    */
-  RRuntime &R;
+  RInside &R;
 
   /**
    * @brief Initialized grid object
@@ -224,7 +224,7 @@ public:
    * @param R_ R runtime
    * @param grid_ Grid object
    */
-  ChemMaster(SimParams &params, RRuntime &R_, Grid &grid_);
+  ChemMaster(SimParams &params, RInside &R_, Grid &grid_);
 
   /**
    * @brief Destroy the ChemMaster object
@@ -445,7 +445,7 @@ public:
    * @param grid_ Grid object
    * @param dht_comm Communicator addressing all processes marked as worker
    */
-  ChemWorker(SimParams &params, RRuntime &R_, Grid &grid_, MPI_Comm dht_comm);
+  ChemWorker(SimParams &params, RInside &R_, Grid &grid_, MPI_Comm dht_comm);
 
   /**
    * @brief Destroy the ChemWorker object

include/poet/Grid.hpp

@@ -21,7 +21,6 @@
 #ifndef GRID_H
 #define GRID_H
 
-#include "RRuntime.hpp"
 #include "poet/SimParams.hpp"
 #include <Rcpp.h>
 #include <array>
@@ -67,7 +66,7 @@ public:
    *
    * @param R
    */
-  Grid(RRuntime &R, poet::GridParams grid_args);
+  Grid(poet::GridParams grid_args);
 
   ~Grid();
   /**
@@ -97,78 +96,17 @@ public:
                         std::string module_name = poet::GRID_MODULE_NAME)
       -> std::vector<double>;
 
-  /**
-   * @brief Shuffle the grid and export it to C memory area
-   *
-   * This will call shuffle_field inside R runtime, set the resulting grid as
-   * buffered data frame in RRuntime object and write R grid to continous C
-   * memory area.
-   *
-   * @param[in,out] buffer Pointer to C memory area
-   */
-  void shuffleAndExport(double *buffer);
-
-  /**
-   * @brief Unshuffle the grid and import it from C memory area into R runtime
-   *
-   * Write C memory area into temporary R grid variable and unshuffle it.
-   *
-   * @param buffer Pointer to C memory area
-   */
-  void importAndUnshuffle(double *buffer);
-
-  /**
-   * @brief Import a C memory area as a work package into R runtime
-   *
-   * Get a skeleton from getSkeletonDataFrame inside R runtime and set this as
-   * buffer data frame of RRuntime object. Now convert C memory area to R data
-   * structure.
-   *
-   * @param buffer Pointer to C memory area
-   * @param wp_size Count of grid cells per work package
-   */
-  void importWP(double *buffer, unsigned int wp_size);
-
-  /**
-   * @brief Export a work package from R runtime into C memory area
-   *
-   * Set buffer data frame in RRuntime object to data frame holding the results
-   * and convert this to C memory area.
-   *
-   * @param buffer Pointer to C memory area
-   */
-  void exportWP(double *buffer);
-
 private:
-  /**
-   * @brief Instance of RRuntime
-   *
-   */
-  RRuntime R;
-
-  // uint32_t species_count;
 
   std::uint8_t dim;
   std::array<std::uint32_t, MAX_DIM> d_spatial;
   std::array<std::uint32_t, MAX_DIM> n_cells;
 
   std::map<std::string, StateMemory *> state_register;
-  // std::map<std::string, std::vector<std::string>> prop_register;
 
   prop_vec prop_names;
 
   std::map<std::string, std::vector<double>> grid_init;
-
-  /**
-   * @brief Get a SkeletonDataFrame
-   *
-   * Return a skeleton with \e n rows of current grid
-   *
-   * @param rows number of rows to return skeleton
-   * @return Rcpp::DataFrame Can be seen as a skeleton. The content of the data
-   * frame might be irrelevant.
-   */
-  Rcpp::DataFrame getSkeletonDataFrame(unsigned int rows);
 };
 } // namespace poet
 #endif // GRID_H

include/poet/RRuntime.hpp

@@ -1,137 +0,0 @@
-/*
-** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
-** Potsdam)
-**
-** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
-**
-** POET is free software; you can redistribute it and/or modify it under the
-** terms of the GNU General Public License as published by the Free Software
-** Foundation; either version 2 of the License, or (at your option) any later
-** version.
-**
-** POET is distributed in the hope that it will be useful, but WITHOUT ANY
-** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License along with
-** this program; if not, write to the Free Software Foundation, Inc., 51
-** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-*/
-
-#ifndef RRUNTIME_H
-#define RRUNTIME_H
-
-#include <RInside.h>
-#include <Rcpp.h>
-
-#include <string>
-
-namespace poet {
-
-/**
- * @brief Provides an interface to a R runtime.
- *
- * RRuntime is a wrapper class around a RInside (R) runtime and provides several
- * simplified methods to use R commands inside POET.
- *
- */
-class RRuntime : public RInside {
- public:
-  /**
-   * @brief Construct a new RRuntime object
-   *
-   * Since this is an inherited class of RInside the constructor of the super
-   * class is just called.
-   *
-   * @param argc Argument counter of the program
-   * @param argv Argument values of the program
-   */
-  RRuntime(const int argc, const char *const argv[]) : RInside(argc, argv){};
-
-  /**
-   * Convert a R dataframe into a C continious memory area.
-   *
-   * @param buffer Name of the R internal variable name.
-   */
-
-  /**
-   * @brief Convert a R dataframe into a C continious memory area.
-   *
-   * A buffer data frame must be set beforehand with setBufferDataFrame. Then
-   * each value will be set into the continious memory area. This is done row
-   * wise.
-   *
-   * @todo: Might be more performant if all columns would be loaded at once and
-   * not for each column seperatly
-   *
-   * @param buffer Pointer to pre-allocated memory
-   */
-  void to_C_domain(double *buffer);
-
-  /**
-   * @brief Convert continious C memory area into R dataframe and puts it into R
-   * runtime.
-   *
-   * A buffer data frame must be set beforehand with setBufferDataFrame. Then
-   * each value will be set into buffered data frame of this object. This is
-   * done row wise.
-   *
-   * @todo: Might be more performant if all columns would be loaded at once and
-   * not for each column seperatly
-   *
-   * @param buffer Pointer to memory area which should be converted into R
-   * dataframe.
-   */
-  void from_C_domain(double *buffer);
-
-  /**
-   * @brief Set the Buffer Data Frame object
-   *
-   * Set the buffered data frame (will be mostly the grid) of this object.
-   *
-   * @param dfname Name of the data frame inside R runtime
-   */
-  void setBufferDataFrame(std::string dfname);
-
-  /**
-   * @brief Get the Buffer Data Frame object
-   *
-   * Returning the current buffered data frame as a Rcpp data frame.
-   *
-   * @return Rcpp::DataFrame Current buffered data frame
-   */
-  Rcpp::DataFrame getBufferDataFrame();
-
-  /**
-   * @brief Get the Buffer N Col object
-   *
-   * Get the numbers of columns of the buffered data frame.
-   *
-   * @return size_t Count of columns of buffered data frame
-   */
-  size_t getBufferNCol();
-
-  /**
-   * @brief Get the Buffer N Row object
-   *
-   * Get the numbers of rows of the buffered data frame.
-   *
-   * @return size_t Count of rows of buffered data frame
-   */
-  size_t getBufferNRow();
-
- private:
-  /**
-   * @brief Buffered data frame
-   *
-   * This is used to convert a R data frame into continious memory used by C/C++
-   * runtime and vice versa. Must be set with setBufferDataFrame and can be
-   * manipulated with from_C_domain.
-   * 
-   * @todo: Find a cleaner solution. Maybe abstraction via another class.
-   *
-   */
-  Rcpp::DataFrame dfbuff;
-};
-}  // namespace poet
-#endif  // RRUNTIME_H

include/poet/SimParams.hpp

@@ -25,9 +25,8 @@
 #include <string>
 #include <vector>
 
-#include "RRuntime.hpp"
-#include "Rcpp/DataFrame.h"
 #include "argh.hpp" // Argument handler https://github.com/adishavit/argh
+#include <RInside.h>
 #include <Rcpp.h>
 // BSD-licenced
 
@@ -85,7 +84,7 @@ using GridParams = struct s_GridParams {
 
   std::vector<std::string> props;
 
-  s_GridParams(poet::RRuntime &R);
+  s_GridParams(RInside &R);
 };
 
 using DiffusionParams = struct s_DiffusionParams {
@@ -97,7 +96,7 @@ using DiffusionParams = struct s_DiffusionParams {
   Rcpp::DataFrame vecinj;
   Rcpp::DataFrame vecinj_index;
 
-  s_DiffusionParams(poet::RRuntime &R);
+  s_DiffusionParams(RInside &R);
 };
 
 /**
@@ -149,7 +148,7 @@ public:
    * @return int Returns with 0 if no error occured, otherwise value less than 0
    * is returned.
    */
-  int parseFromCmdl(char *argv[], RRuntime &R);
+  int parseFromCmdl(char *argv[], RInside &R);
 
   /**
    * @brief Init std::vector values
@@ -162,7 +161,7 @@ public:
    * @param col_count Count of variables per grid cell (typically the count of
    * columns of each grid cell)
    */
-  void initVectorParams(RRuntime &R, int col_count);
+  void initVectorParams(RInside &R, int col_count);
 
   /**
    * @brief Set if dt differs

src/ChemMaster.cpp

@@ -33,7 +33,7 @@ using namespace poet;
 using namespace std;
 using namespace Rcpp;
 
-ChemMaster::ChemMaster(SimParams &params, RRuntime &R_, Grid &grid_)
+ChemMaster::ChemMaster(SimParams &params, RInside &R_, Grid &grid_)
     : ChemSim(params, R_, grid_) {
   t_simparams tmp = params.getNumParams();
 

src/ChemSim.cpp

@@ -33,7 +33,7 @@
 using namespace Rcpp;
 using namespace poet;
 
-ChemSim::ChemSim(SimParams &params, RRuntime &R_, Grid &grid_)
+ChemSim::ChemSim(SimParams &params, RInside &R_, Grid &grid_)
     : R(R_), grid(grid_) {
   t_simparams tmp = params.getNumParams();
   this->world_rank = tmp.world_rank;

src/ChemWorker.cpp

@@ -32,7 +32,7 @@ using namespace poet;
 using namespace std;
 using namespace Rcpp;
 
-ChemWorker::ChemWorker(SimParams &params, RRuntime &R_, Grid &grid_,
+ChemWorker::ChemWorker(SimParams &params, RInside &R_, Grid &grid_,
                        MPI_Comm dht_comm)
     : ChemSim(params, R_, grid_) {
   t_simparams tmp = params.getNumParams();

src/Grid.cpp

@@ -49,9 +49,8 @@ static inline int8_t get_type_id(std::string type) {
   return -1;
 }
 
-Grid::Grid(RRuntime &R, poet::GridParams grid_args) : R(R) {
+Grid::Grid(poet::GridParams grid_args) {
   // get dimension of grid
-  // this->dim = R.parseEval("length(mysetup$grid$n_cells)");
   this->dim = grid_args.n_cells.size();
 
   // assert that dim is 1 or 2
@@ -205,34 +204,3 @@ auto poet::Grid::getSpeciesByName(std::string name, std::string module_name)
   return std::vector<double>(module_memory->mem.begin() + begin_vec,
                              module_memory->mem.begin() + end_vec);
 }
-
-void Grid::shuffleAndExport(double *buffer) {
-  R.parseEval("tmp <- shuffle_field(mysetup$state_T, ordered_ids)");
-  R.setBufferDataFrame("tmp");
-  R.to_C_domain(buffer);
-}
-
-void Grid::importAndUnshuffle(double *buffer) {
-  R.setBufferDataFrame("GRID_TMP");
-  R.from_C_domain(buffer);
-  R["GRID_CHEM_DATA"] = R.getBufferDataFrame();
-  R.parseEval("result <- unshuffle_field(GRID_CHEM_DATA, ordered_ids)");
-}
-
-void Grid::importWP(double *buffer, unsigned int wp_size) {
-  R["GRID_WP_SKELETON"] = getSkeletonDataFrame(wp_size);
-  R.setBufferDataFrame("GRID_WP_SKELETON");
-  R.from_C_domain(buffer);
-  R["work_package_full"] = R.getBufferDataFrame();
-}
-void Grid::exportWP(double *buffer) {
-  R.setBufferDataFrame("result_full");
-  R.to_C_domain(buffer);
-}
-
-Rcpp::DataFrame Grid::getSkeletonDataFrame(unsigned int rows) {
-  R["GRID_ROWS"] = rows;
-
-  Rcpp::DataFrame tmp = R.parseEval("head(GRID_TMP,GRID_ROWS)");
-  return tmp;
-}

src/RRuntime.cpp

@@ -1,64 +0,0 @@
-/*
-** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
-** Potsdam)
-**
-** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
-**
-** POET is free software; you can redistribute it and/or modify it under the
-** terms of the GNU General Public License as published by the Free Software
-** Foundation; either version 2 of the License, or (at your option) any later
-** version.
-**
-** POET is distributed in the hope that it will be useful, but WITHOUT ANY
-** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License along with
-** this program; if not, write to the Free Software Foundation, Inc., 51
-** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-*/
-
-#include <poet/RRuntime.hpp>
-
-#include <RInside.h>
-#include <Rcpp.h>
-
-#include <string>
-
-using namespace poet;
-
-void RRuntime::to_C_domain(double *buffer) {
-  size_t rowCount = dfbuff.nrow();
-  size_t colCount = dfbuff.ncol();
-
-  for (size_t i = 0; i < rowCount; i++) {
-    for (size_t j = 0; j < colCount; j++) {
-      /* Access column vector j and extract value of line i */
-      Rcpp::DoubleVector col = dfbuff[j];
-      buffer[i * colCount + j] = col[i];
-    }
-  }
-}
-
-void RRuntime::from_C_domain(double *buffer) {
-  size_t rowCount = dfbuff.nrow();
-  size_t colCount = dfbuff.ncol();
-
-  for (size_t i = 0; i < rowCount; i++) {
-    for (size_t j = 0; j < colCount; j++) {
-      /* Access column vector j and extract value of line i */
-      Rcpp::DoubleVector col = dfbuff[j];
-      col[i] = buffer[i * colCount + j];
-    }
-  }
-}
-
-void RRuntime::setBufferDataFrame(std::string dfname) {
-  this->dfbuff = parseEval(dfname);
-}
-
-Rcpp::DataFrame RRuntime::getBufferDataFrame() { return this->dfbuff; }
-
-size_t RRuntime::getBufferNCol() { return (this->dfbuff).ncol(); }
-
-size_t RRuntime::getBufferNRow() { return (this->dfbuff).nrow(); }

src/SimParams.cpp

@@ -18,10 +18,10 @@
 ** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include "poet/RRuntime.hpp"
 #include <bits/stdint-uintn.h>
 #include <poet/SimParams.hpp>
 
+#include <RInside.h>
 #include <Rcpp.h>
 
 #include <iostream>
@@ -32,7 +32,7 @@ using namespace poet;
 using namespace std;
 using namespace Rcpp;
 
-poet::GridParams::s_GridParams(poet::RRuntime &R) {
+poet::GridParams::s_GridParams(RInside &R) {
   this->n_cells =
       Rcpp::as<std::vector<uint32_t>>(R.parseEval("mysetup$grid$n_cells"));
   this->s_cells =
@@ -46,7 +46,7 @@ poet::GridParams::s_GridParams(poet::RRuntime &R) {
   // Rcpp::as<std::string>(R.parseEval("mysetup$grid$init_sim"));
 }
 
-poet::DiffusionParams::s_DiffusionParams(poet::RRuntime &R) {
+poet::DiffusionParams::s_DiffusionParams(RInside &R) {
   this->prop_names = Rcpp::as<std::vector<std::string>>(
       R.parseEval("names(mysetup$diffusion$init)"));
   this->alpha =
@@ -66,7 +66,7 @@ SimParams::SimParams(int world_rank_, int world_size_) {
   this->simparams.world_size = world_size_;
 }
 
-int SimParams::parseFromCmdl(char *argv[], RRuntime &R) {
+int SimParams::parseFromCmdl(char *argv[], RInside &R) {
   // initialize argh object
   argh::parser cmdl(argv);
 
@@ -180,7 +180,7 @@ int SimParams::parseFromCmdl(char *argv[], RRuntime &R) {
   return PARSER_OK;
 }
 
-void SimParams::initVectorParams(RRuntime &R, int col_count) {
+void SimParams::initVectorParams(RInside &R, int col_count) {
   if (simparams.dht_enabled) {
     /*Load significance vector from R setup file (or set default)*/
     bool signif_vector_exists = R.parseEval("exists('signif_vector')");