adding headers

CMakeLists.txt

@@ -47,7 +47,7 @@ list(APPEND CMAKE_MODULE_PATH "${ECRC_CMAKE_MODULE_PATH}")
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
 include(EcrcInit)
 include(GenPkgConfig)
-include(FindPkgConfig)
+find_package(PkgConfig REQUIRED)
 
 # Create project and check C compiler
 cmake_policy(SET CMP0048 NEW)
@@ -173,6 +173,9 @@ if(STARPU)
     if(STARPU_FOUND)
         include_directories(${STARPU_INCLUDE_DIRS})
         link_directories(${STARPU_LIBRARY_DIRS})
+        link_directories(${STARPU_SHM_STATIC_LIBRARY_DIRS})
+        #message(STATUS "STARPU_SHM_STATIC_LIBRARY_DIRS=${STARPU_SHM_STATIC_LIBRARY_DIRS}")
+        #message(STATUS "STARPU_SHM_STATIC_FOUND=${STARPU_SHM_FOUND_STATIC}")
         add_definitions("-DSTARPU")
         list(APPEND DOXYGEN_ENABLED_SECTIONS STARPU)
     else()

COPYRIGHTS.txt

@@ -0,0 +1,2 @@
+2017-2022 King Abdullah University of Science and 
+ *                      Technology (KAUST). All rights reserved.

Jenkinsfile

@@ -30,12 +30,12 @@ pipeline {
                     # if any command exits with value other than 0 (zero)
 
                     # loads modules
-                    module load gcc/5.5.0
-                    module load mkl/2018-initial
-                    module load openmpi/3.0.0-gcc-5.5.0
-                    module load starpu/1.2.3-gcc-5.5.0-mkl-openmpi-3.0.0
-                    module load gsl/2.4-gcc-5.5.0
-                    module load cmake/3.9.6
+                    module load gcc/10.2.0
+                    module load mkl/2020.0.166
+                    module load openmpi/4.1.0-gcc-10.2.0
+                    module load starpu/1.2.10-gcc-10.2.0-mkl-openmpi-4.1.0
+                    module load gsl/2.6-gcc-10.2.0
+                    module load cmake/3.21.2
 
                     # variables
                     BUILDDIR="$WORKSPACE/build/"
@@ -63,12 +63,12 @@ pipeline {
                     # if any command exits with value other than 0 (zero)
 
                     # loads modules
-                    module load gcc/5.5.0
-                    module load mkl/2018-initial
-                    module load openmpi/3.0.0-gcc-5.5.0
-                    module load starpu/1.2.3-gcc-5.5.0-mkl-openmpi-3.0.0
-                    module load gsl/2.4-gcc-5.5.0
-                    module load cmake/3.9.6
+                    module load gcc/10.2.0
+                    module load mkl/2020.0.166
+                    module load openmpi/4.1.0-gcc-10.2.0
+                    module load starpu/1.2.10-gcc-10.2.0-mkl-openmpi-4.1.0
+                    module load gsl/2.6-gcc-10.2.0
+                    module load cmake/3.21.2
 
                     # variables
                     BUILDDIR="$WORKSPACE/build/"

VERSION.txt

@@ -1 +1 @@
-0.3.0
+0.3.1

examples/approximation/dense.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/dense.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/approximation/minimal.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/minimal.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/approximation/randtlr.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/randtlr.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/approximation/spatial.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/spatial.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/problem/CMakeLists.txt

@@ -13,6 +13,7 @@
 set(examples_files
     "spatial.c"
     "spatial_bivariate.c"
+    "spatial_non_gaussian.c"    
     "randtlr.c"
     "minimal.c"
     "dense.c"

examples/problem/acoustic.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2020 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/acoustic.c 
- * @version 0.3.0
+ * @version 0.3.1
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

examples/problem/dense.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/dense.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/problem/minimal.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/minimal.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/problem/particles.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/particles.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  */

examples/problem/randtlr.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/randtlr.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/problem/rbf_cube.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2020 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/rbf_cube.c
- * @version 0.3.0
+ * @version 0.3.1
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

examples/problem/rbf_virus.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2020 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/rbf_virus.c
- * @version 0.3.0
+ * @version 0.3.1
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

examples/problem/spatial.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/spatial.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

examples/problem/spatial_bivariate.c

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/spatial.c
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2020-06-09
  * */

examples/problem/spatial_non_gaussian.c

@@ -0,0 +1,88 @@
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
+ *                      Technology (KAUST). All rights reserved.
+ *
+ * STARS-H is a software package, provided by King Abdullah
+ *             University of Science and Technology (KAUST)
+ *
+ * @file examples/problem/spatial_non_gaussian.c
+ * @version 0.3.1
+ * @author Sameh Abdulah
+ * @date 2020-06-09
+ * */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <starsh.h>
+#include <starsh-spatial.h>
+
+int main(int argc, char **argv)
+{
+    int problem_ndim = 2;
+    // Possible values for kernel_type are:
+    int kernel_type = STARSH_SPATIAL_NON_GAUSSIAN_SIMD;
+    // Correlation length
+    double beta = 0.1;
+    // Smoothing parameter for Matern kernel
+    double nu = 0.5;
+    // Scaling factor
+    double sigma = 1.0;
+    // Set level of noise
+    double noise = 0;
+    // Bivariate correlation
+    double corr = 0.1;
+    // Size of desired matrix
+    int N = 5000;
+    // 'N' for nonsymmetric matrix and 'd' for double precision
+    char symm = 'N', dtype = 'd';
+    int ndim = 2;
+    STARSH_int shape[2] = {N, N};
+    // OBSOLETE3 for kernel PARSIMONIOUS and
+    // OBSOLETE4 for kernel PARSIMONIOUS2
+    enum STARSH_PARTICLES_PLACEMENT place = STARSH_PARTICLES_OBSOLETE1;
+    int info;
+    srand(0);
+    // Generate data for spatial statistics problem
+    STARSH_ssdata *data;
+    STARSH_kernel *kernel;
+    // STARSH_SPATIAL for spatial statistics problem
+    // kernel_type is enum type, for possible values look into starsh-spatial.h
+    // STARSH_SATIAL_NDIM to indicate next parameter shows dimensionality of
+    //   spatial statistics problem
+    // STARSH_SPATIAL_BETA to indicate next parameter is correlation length
+    // STARSH_SPATIAL_NU to indicate next parameter is smoothing parameter for
+    //   Matern kernel
+    // STARSH_SPATIAL_NOISE to indicate next parameter is a noise
+    // 0 at the end to indicate end of arguments
+	info = starsh_application((void **)&data, &kernel, N, dtype, 
+			STARSH_SPATIAL, kernel_type, STARSH_SPATIAL_NDIM, problem_ndim,
+			STARSH_SPATIAL_BETA, beta, STARSH_SPATIAL_NU, nu, 
+			STARSH_SPATIAL_NOISE, noise, STARSH_SPATIAL_PLACE, place,
+			STARSH_SPATIAL_SIGMA, 1.0,
+            0);
+    if(info != 0)
+    {
+        printf("wrong parameters for the non-gaussian spatial statistics problem\n");
+        return info;
+    }
+    // Init problem with given data and kernel and print short info
+    STARSH_problem *problem;
+    info = starsh_problem_new(&problem, ndim, shape, symm, dtype, data, data,
+            kernel, "Spatial Statistics example");
+    if(info != 0)
+    {
+        printf("Error in starsh problem\n");
+        exit(info);
+    }
+    printf("STARSH problem was succesfully generated\n");
+    starsh_problem_info(problem);
+    // Compute dense matrix
+    Array *array;
+    info = starsh_problem_to_array(problem, &array);
+    if(info != 0)
+    {
+        printf("Error when computing matrix elements\n");
+        exit(info);
+    }
+    printf("Matrix was successfully computed\n");
+    return 0;
+}

include/common.h

@@ -1,4 +1,4 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
@@ -9,7 +9,7 @@
  * @cond
  * This command in pair with endcond will prevent file from being documented.
  *
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2020-06-09
  * */

include/starsh-acoustic.h

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2020 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file include/starsh-acoustic.h
- * @version 0.3.0
+ * @version 0.3.1
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

include/starsh-cauchy.h

@@ -1,11 +1,11 @@
-/*! @copyright (c) 2017 King Abdullah University of Science and
+/*! @copyright (c) 2017-2022 King Abdullah University of Science and 
  *                      Technology (KAUST). All rights reserved.
  *
  * STARS-H is a software package, provided by King Abdullah
  *             University of Science and Technology (KAUST)
  *
  * @file include/starsh-minimal.h
- * @version 0.3.0
+ * @version 0.3.1
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */