V1.1.3

CMakeLists.txt

@@ -98,6 +98,11 @@ list(APPEND LIBS ${LAPACKE_LIBRARIES})
 link_directories(${LAPACKE_LIBRARY_DIRS_DEP})
 include_directories(${LAPACKE_INCLUDE_DIRS})
 
+if (${BLA_VENDOR} MATCHES "Intel10_64lp" OR ${BLA_VENDOR} MATCHES "Intel" OR ${BLA_VENDOR} MATCHES "Intel10_64lp_seq")
+    message(STATUS "Linked to MKL")
+    add_compile_definitions(USE_MKL)
+endif()
+
 # Add all dependencies for ExaGeoStatCPP
 #-----------------------------
 
@@ -164,7 +169,7 @@ if (USE_R)
     if (${R_FOUND})
         message(STATUS "Using R technology")
         list(APPEND LIBS R)
-        add_definitions(-DUSING_R)
+        add_definitions(-DUSE_R)
     endif ()
 endif ()
 

README.md

@@ -55,10 +55,18 @@ statisticians with modest computational resources.
 
 ## Installation
 
-> Note: Installation requires at least **CMake of version 3.2**. to build ExaGeoStatCPP.
+### Requirements
+To build and run this software, you will need:
+
+1. [CMake](https://cmake.org/download/) (version 3.2 or higher)
+2. [wget](https://www.gnu.org/software/wget/)
+3. **gcc** and **g++** compilers
+4. **autoconf** and **automake**
+5. [libtool](https://www.gnu.org/software/libtool/)
+6. [R](https://cran.r-project.org/bin/windows/base/) (only if you plan on using the R functionality)
 
 ### C++ source code installation
-To install the `ExaGeoStat` project locally, run the following commands in your terminal:
+To install the `ExaGeoStatCPP` project locally (C++ version), run the following commands in your terminal:
 
 1. Clone the project from the remote gitHub repository into your local machine using the following command
    ```bash
@@ -70,14 +78,14 @@ To install the `ExaGeoStat` project locally, run the following commands in your
    cd ExaGeoStatCPP
    ```
 
-3. Run `configure` script with the flag `-h` for help, to know the supported options and their corresponding flags.
+3. Run `configure` script   (use the `-h` flag for help, to know the supported options and their corresponding flags). This step is **not required** when using R.
    ```bash
-   ./configure -h
+   ./configure -e 
    ```
 
-4. Run `clean_build.sh` script with the flag `-h` for help, to know the needed arguments to run with your specific options.
+4. Run `clean_build.sh` (use the `-h` flag for help, to know the needed arguments to run with your specific options). This step is **not required** when using R.
    ```bash
-   ./clean_build.sh -h
+   ./clean_build.sh
    ```
 
 5. Export the installation paths of the dependencies to your `.bashrc` file, e.g.
@@ -91,18 +99,56 @@ ExaGeoStatCPP.
 ### R package installation
 1. Open the R prompt window by simply running `R` command in the terminal, inside the prompt, we will install needed packages by running the following commands:
    ```R
-   install.packages(Rcpp)
-   install.packages("assert")
+   install.packages("Rcpp")
+   install.packages("assertthat")
    ```
 
-2. close the R prompt and return to the terminal. Run the following command, make sure your current path is the ExaGeoStat project directory
+2. close the R prompt and return to the terminal. Run the following command, make sure your current path is the ExaGeoStatCPP project directory
 
    ```commandline
    R CMD INSTALL . --configure-args="-r"
    ```
 
 > For more detailed information on installing ExaGeoStat with different configurations and enabling technologies such as CUDA, MPI, R, etc., please refer to the [User Manual](USER_MANUAL.md)
 
+## Common Installation Errors and Solutions
+
+### 1. Missing CMake
+The installation requires **CMake** version 3.2 or higher. Ensure it is installed on your system before proceeding with the installation of **ExaGeoStatCPP**.
+
+To install CMake, use:
+```sh
+sudo apt install cmake
+```
+
+### 2. Missing Libtool
+If you encounter the following error during installation:
+```
+./autogen.sh: line 17: libtool: command not found
+./autogen.sh: line 20: glibtool: command not found
+```
+This indicates that **Libtool** is missing. You can install it using:
+```sh
+sudo apt install libtool libtool-bin
+```
+
+Alternatively, you can install **Libtool** locally:
+```sh
+wget http://ftpmirror.gnu.org/libtool/libtool-2.4.7.tar.gz
+tar -xvzf libtool-2.4.7.tar.gz
+cd libtool-2.4.7
+./configure --prefix=$HOME/local
+make
+make install
+```
+Then, update your environment variables:
+```sh
+export PATH=$HOME/local/bin:$PATH
+export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
+export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig:$PKG_CONFIG_PATH
+```
+After this, restart your terminal or run `source ~/.bashrc` to apply the changes.
+
 
 ## Usage
 #### C++ Example
@@ -127,14 +173,66 @@ int main(int argc, char **argv) {
     return 0;
 }
 ```
-### R Example:
-```R
+## R Example
+Here is an example demonstrating how to use **ExaGeoStatCPP** in R:
+
+```r
+# Load the ExaGeoStatCPP library
+library(ExaGeoStatCPP)
+
+# Set parameters for the simulation
+ncores <- 30
+ngpus <- 0
+problem_size <- 1600
+dts <- 320
+lts <- 0
+computation <- "exact"
+dimension <- "2D"
+kernel <- "univariate_matern_stationary"
+initial_theta <- c(1,0.1,0.5)
+lower_bound <- c(0.1,0.1,0.1)
+upper_bound <- c(5,5,5)
+p <- 1
+q <- 1
+opt_itrs <- 100
+
+# Initialize hardware configuration
 hardware <- new(Hardware, computation, ncores, ngpus, p, q)
-exageostat_data <- simulate_data(kernel=kernel, initial_theta=initial_theta, problem_size=problem_size, dts=dts, dimension=dimension)
-estimated_theta <- model_data(data=exageostat_data, kernel=kernel, dts=dts, dimension=dimension,lb=lower_bound, ub=upper_bound, mle_itr=10)
-predict_data(train_data=list(x, y, z_measurement), test_data=list(test_x, test_y), kernel=kernel, dts=dts, estimated_theta=estimated_theta)
+
+# Simulate spatial data based on the specified kernel and parameters
+exageostat_data <- simulate_data(
+  kernel = kernel,
+  initial_theta = initial_theta,
+  problem_size = problem_size,
+  dts = dts,
+  dimension = dimension
+)
+
+# Estimate model parameters using MLE
+estimated_theta <- model_data(
+  matrix=exageostat_data$m,
+  x=exageostat_data$x,
+  y=exageostat_data$y,
+  kernel=kernel, dts=dts,
+  dimension=dimension,
+  lb=lower_bound,
+  ub=upper_bound,
+  mle_itr=opt_itrs)
+
+# Perform spatial prediction using the estimated parameters
+test_x <- c(0.2, 0.330)
+test_y <- c(0.104, 0.14)
+predict_data(
+  train_data=list(x=exageostat_data$x, y=exageostat_data$y, exageostat_data$m),
+  test_data=list(test_x, test_y),
+  kernel=kernel,
+  dts=dts,
+  estimated_theta=estimated_theta)
+
 ```
 
+This example walks through initializing hardware, simulating spatial data, estimating model parameters, and making predictions using **ExaGeoStatCPP** in R.
+
 > Please take a look at the end-to-end examples as a reference for using all the operations.
 
 ## Contributing
@@ -188,4 +286,4 @@ Find detailed information on how to contribute to ExaGeoStatCPP [here](CONTRIBUT
 [BSD 3-Clause](LICENSE)
 
 ## Handout
-![ExaGeoStatCPP-handout.png](docs/ExaGeoStatCPP-handout.png)
+![ExaGeoStatCPP-handout.png](docs/ExaGeoStatCPP-handout.png)

configure

@@ -17,6 +17,7 @@ BLUE='\033[0;34m'
 NC='\033[0m'
 
 INSTALL_PREFIX=$PWD/installdir/_deps
+BASE_DIR=$PWD
 
 # Function to install CMake from source
 install_cmake() {
@@ -36,12 +37,11 @@ install_cmake() {
   cd cmake-3.28.1 || exit 1
 
   # Configure, build, and install CMake to the specified location
-  ./bootstrap --prefix="$INSTALL_PREFIX" --parallel=2 -- -DCMAKE_USE_OPENSSL=OFF
+  ./bootstrap --prefix="$INSTALL_PREFIX/CMAKE" --parallel=2 -- -DCMAKE_USE_OPENSSL=OFF
   make -j 2
-  sudo make install
-
+  make install
   # Clean up
-  cd "$temp_dir" || exit 1
+  cd "$BASE_DIR" || exit 1
   rm -rf "$temp_dir"
 }
 
@@ -59,7 +59,7 @@ fi
 BUILDING_TESTS="OFF"
 BUILDING_HEAVY_TESTS="OFF"
 BUILDING_EXAMPLES="OFF"
-USING_HiCMA="OFF"
+USE_HiCMA="OFF"
 VERBOSE="OFF"
 USE_CUDA="OFF"
 USE_MPI="OFF"
@@ -112,7 +112,7 @@ while getopts ":tevhHi:cmpTwr" opt; do
     ;;
   H) ##### Using HiCMA #####
     echo "${GREEN}Using HiCMA.${NC}"
-    USING_HiCMA="ON"
+    USE_HiCMA="ON"
     ;;
   c) ##### Using cuda enabled #####
     echo "${GREEN}Cuda enabled ${NC}"
@@ -179,7 +179,7 @@ if [ -z "$BUILDING_EXAMPLES" ]; then
   echo "${RED}Building examples disabled.${NC}"
 fi
 
-if [ -z "$USING_HiCMA" ]; then
+if [ -z "$USE_HiCMA" ]; then
   echo "${RED}Using HiCMA is disabled.${NC}"
 fi
 
@@ -226,10 +226,8 @@ elif [ -x "/Applications/CMake.app/Contents/bin/cmake" ]; then
   cmake_command_bin="${cmake_install_dir}/cmake"
 else
   echo "Installing CMake from source"
-  mkdir "${ABSOLUTE_PATH}/inst/_deps/"
-  install_dir="${ABSOLUTE_PATH}/inst/_deps/"
-  install_cmake "$install_dir"
-  cmake_command_bin="${ABSOLUTE_PATH}/inst/_deps/bin/cmake"
+  install_cmake
+  cmake_command_bin="${INSTALL_PREFIX}/CMAKE/bin/cmake"
 fi
 
 "$cmake_command_bin" "$DEVELOPER_WARNINGS" -DCMAKE_EXPORT_COMPILE_COMMANDS=ON \
@@ -238,7 +236,7 @@ fi
   -DBUILD_TESTS="${BUILDING_TESTS}" \
   -DBUILD_HEAVY_TESTS="${BUILDING_HEAVY_TESTS}" \
   -DBUILD_EXAMPLES="${BUILDING_EXAMPLES}" \
-  -DUSE_HICMA="${USING_HiCMA}" \
+  -DUSE_HICMA="${USE_HiCMA}" \
   -DCMAKE_VERBOSE_MAKEFILE:BOOL=${VERBOSE} \
   -DUSE_CUDA="${USE_CUDA}" \
   -DUSE_MPI="${USE_MPI}" \

inst/include/Rcpp-adapters/FunctionsAdapter.hpp

@@ -65,6 +65,7 @@ namespace exageostat::adapters {
      * @param[in] aDimension Dimensionality of the problem ("2D" or "3D").
      * @param[in] aBand Bandwidth for band matrices, applicable in certain computational kernels.
      * @param[in] aMaxRank Maximum rank for low-rank approximations.
+     * @param[in] aAccuracy Accuracy value for low-rank approximations, The final value is computed as 10^(-1.0 * aAccuracy)
      * @param[in] apData Pointer to ExaGeoStatData object to be modeled.
      * @param[in] aMeasurementsVector Optional vector of measurements to enhance modeling, can be nullable.
      * @param[in] aLocationsX Optional vector of X coordinates for locations, can be nullable.
@@ -79,7 +80,7 @@ namespace exageostat::adapters {
                                               const std::vector<double> &aUpperBound, const int &aTolerance,
                                               const int &aMleIterations, const int &aDenseTileSize,
                                               const int &aLowTileSize, const std::string &aDimension, const int &aBand,
-                                              const int &aMaxRank, SEXP apData,
+                                              const int &aMaxRank, const int &aAccuracy, SEXP apData,
                                               Rcpp::Nullable<Rcpp::NumericVector> aMeasurementsVector = R_NilValue,
                                               Rcpp::Nullable<Rcpp::NumericVector> aLocationsX = R_NilValue,
                                               Rcpp::Nullable<Rcpp::NumericVector> aLocationsY = R_NilValue,