Release v0.3.0

Add GPU support via KBLAS+StarPU New application: acoustic wave scattering New application: mesh deformations
ecrc · Nov 21, 2020 · 27df2d4 · 27df2d4
1 parent 0714c92
commit 27df2d4
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -51,7 +51,7 @@ include(FindPkgConfig)
 
 # Create project and check C compiler
 cmake_policy(SET CMP0048 NEW)
-project(STARS-H VERSION 0.1.1 LANGUAGES C Fortran)
+project(STARS-H VERSION 0.3.0 LANGUAGES C Fortran)
 
 message(STATUS "Building ${PROJECT_NAME} ${PROJECT_VERSION}")
 
@@ -69,6 +69,12 @@ set(CMAKE_BUILD_TYPE Release CACHE STRING
 option(OPENMP "Use OpenMP" ON)
 option(MPI "Use MPI" ON)
 option(STARPU "Use StarPU" ON)
+# Since KBLAS does not support pkg-config, it is OFF by default, since user has
+# to provide path by means of
+# CFLAGS="-I/path/to/kblas/include -L/path/to/kblas/lib"
+option(KBLAS "Use KBLAS" ON)
+option(CUDA "Use CUDA" ON)
+#set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -gencode arch=compute_70,code=sm_70")
 
 # Option to force using parallel blas instead of sequential
 option(USE_PARALLEL_BLAS "Prefer parallel blas libraries" OFF)
@@ -109,7 +115,7 @@ endif()
 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 # the RPATH to be used when installing
 #set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 # Packaging (make package)
 #set(CPACK_PACKAGE_VERSION ${STARSH_VERSION})
 #set(CPACK_GENERATOR "TGZ")
@@ -174,6 +180,25 @@ if(STARPU)
     endif()
 endif()
 
+# KBLAS depends on CUDA
+if(KBLAS)
+    set(CUDA ON)
+endif()
+
+# Check CUDA option
+if(CUDA)
+    # If CUDA itself is available
+    if(CMAKE_CUDA_COMPILER)
+        enable_language(CUDA)
+        add_definitions("-DCUDA")
+    # If it is not available
+    else()
+        set(CUDA OFF)
+        # Also disable dependent KBLAS option
+        set(KBLAS OFF)
+    endif()
+endif(CUDA)
+
 # Check if GNU Scientific Library is available (for Matern kernel and
 # Bessel function)
 if(GSL)
@@ -306,6 +331,17 @@ if(BLA_VENDOR MATCHES "Intel")
     add_definitions("-DMKL")
 endif()
 
+if(STARPU AND KBLAS)
+    add_definitions("-DKBLAS")
+#    find_package(MAGMA)
+#    if(MAGMA_FOUND)
+#        include_directories(${MAGMA_INCLUDE_DIRS})
+#        link_directories(${MAGMA_LIBRARY_DIRS})
+#        add_definitions("-DKBLAS")
+#    else()
+#        set(KBLAS OFF)
+#    endif()
+endif()
 
 ###############################################################################
 ##                          PRINT CONFIGURATION                              ##

diff --git a/Data.md b/Data.md
@@ -0,0 +1,18 @@
+# Dataset
+
+## Mesh Deformation Application
+
+Dataset is available in KAUST repository: https://repository.kaust.edu.sa/handle/10754/664938. 
+
+DOI:10.25781/KAUST-V2EF2 
+
+## Acoustic Scattering Application
+
+Dataset is available in KAUST repository: https://repository.kaust.edu.sa/handle/10754/664400.
+
+
+DOI:10.25781/KAUST-I0634 
+
+For more information on the dataset please refer to the readme files in the data repositories.
+
+
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -117,5 +117,4 @@ pipeline {
             }
         }
     }
-
 }
diff --git a/README.md b/README.md
@@ -1,19 +1,16 @@
 What is STARS-H?
 ================
 
-STARS-H is a **high performance parallel open-source** package of **Software
-for Testing Accuracy, Reliability and Scalability of Hierarchical
-computations**. It
-provides a hierarchical matrix market in order to benchmark performance of
-various libraries for hierarchical matrix compressions and computations
-(including itself). **Why hierarchical matrices?** Because such matrices arise
-in many PDEs and use much less memory, while requiring fewer flops for
-computations. There are several hierarchical data formats, each one with its
-own performance and memory footprint. STARS-H intends to provide a standard for
-assessing accuracy and performance of hierarchical matrix libraries on a given
-hardware architecture environment. STARS-H currently supports the tile low-rank
-(TLR) data format for approximation on shared and distributed-memory systems,
-using MPI, OpenMP and task-based programming models.
+The Software for Testing Accuracy, Reliability and Scalability of Hierarchical (STARS-H)
+computations is a parallel  library that provides a high performance matrix market of
+rank structured matrix operators. STARS-H supports various matrix kernels that are
+proxies for many scientific applications, and optionally compresses them by exploiting
+their data sparsity. This translates into a lower arithmetic complexity and memory footprint.
+STARS-H intends to provide a standard software environment for assessing accuracy and performance
+of 𝓗-matrix libraries on a given hardware architecture. STARS-H currently supports
+the tile low-rank (TLR) data format for approximation on shared and distributed-memory systems,
+possibly equipped with GPUs, using MPI, OpenMP and task-based programming models.
+
 
 Vision of STARS-H
 =================
@@ -49,7 +46,7 @@ Applications in matrix-free form:
 3. Electrodynamics (sin(kr)/r and cos(kr)/r)
 4. Random synthetic TLR matrix
 5. Spatial statistics (exponential, square exponential and matern kernels)
-6. Mesh deformation using radial basis function (gaussian, exponential, inverse quadratic, inverse multi-quadratic, CPTS, and Wendland kernels)
+6. Mesh deformation using radial basis functions, i.e., Gaussian, exponential, inverse quadratic, inverse multi-quadratic, CPTS, and Wendland kernels.
 7. Acoustic scattering
 
 
@@ -138,5 +135,11 @@ and have additional steps on approximation of corresponding matrices.
 *Important notice: the approximation phase does not require the entire dense matrix 
 to be stored, since matrix elements are computed on the fly.*
 
+Dataset
+========
+
+Please see Data.md for information about dataset.
+
+
 
 ![Handout](docs/STARS-H-final.png)
diff --git a/SARS-CoV-2-meshes/GeneratePopulation.py b/SARS-CoV-2-meshes/GeneratePopulation.py
@@ -1,4 +1,4 @@
-# @version 1.3.0
+# @version 0.3.0
 
 import pandas as pd
 import numpy as np

diff --git a/SARS-CoV-2-meshes/HierarchicalPopulationCluster.py b/SARS-CoV-2-meshes/HierarchicalPopulationCluster.py
@@ -1,4 +1,4 @@
-# @version 1.3.0
+# @version 0.3.0
 
 import pandas as pd
 import numpy as np

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-1.3.0
+0.3.0
diff --git a/docs/STARS-H-final.png b/docs/STARS-H-final.png
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -5,7 +5,7 @@
 #             University of Science and Technology (KAUST)
 #
 # @file examples/CMakeLists.txt
-# @version 1.3.0
+# @version 0.3.0
 # @author Aleksandr Mikhalev
 # @date 2017-11-07
 

diff --git a/examples/approximation/CMakeLists.txt b/examples/approximation/CMakeLists.txt
@@ -5,7 +5,7 @@
 #             University of Science and Technology (KAUST)
 #
 # @file examples/approximation/CMakeLists.txt
-# @version 1.3.0
+# @version 0.3.0
 # @author Aleksandr Mikhalev
 # @date 2017-11-07
 

diff --git a/examples/approximation/dense.c b/examples/approximation/dense.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/dense.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/approximation/minimal.c b/examples/approximation/minimal.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/minimal.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/approximation/randtlr.c b/examples/approximation/randtlr.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/randtlr.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/approximation/spatial.c b/examples/approximation/spatial.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/approximation/spatial.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/problem/CMakeLists.txt b/examples/problem/CMakeLists.txt
@@ -5,7 +5,7 @@
 #             University of Science and Technology (KAUST)
 #
 # @file examples/problem/CMakeLists.txt
-# @version 1.3.0
+# @version 0.3.0
 # @author Aleksandr Mikhalev
 # @date 2020-06-09
 

diff --git a/examples/problem/acoustic.c b/examples/problem/acoustic.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/acoustic.c 
- * @version 1.3.0
+ * @version 0.3.0
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

diff --git a/examples/problem/dense.c b/examples/problem/dense.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/dense.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/problem/minimal.c b/examples/problem/minimal.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/minimal.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/problem/particles.c b/examples/problem/particles.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/particles.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  */

diff --git a/examples/problem/randtlr.c b/examples/problem/randtlr.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/randtlr.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/problem/rbf_cube.c b/examples/problem/rbf_cube.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/rbf_cube.c
- * @version 1.3.0
+ * @version 0.3.0
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

diff --git a/examples/problem/rbf_virus.c b/examples/problem/rbf_virus.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/rbf_virus.c
- * @version 1.3.0
+ * @version 0.3.0
  * @auther Rabab Alomairy
  * @author Aleksandr Mikhalev
  * @date 2020-06-09

diff --git a/examples/problem/spatial.c b/examples/problem/spatial.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/spatial.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2017-11-07
  * */

diff --git a/examples/problem/spatial_bivariate.c b/examples/problem/spatial_bivariate.c
@@ -5,7 +5,7 @@
  *             University of Science and Technology (KAUST)
  *
  * @file examples/problem/spatial.c
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2020-06-09
  * */

diff --git a/include/CMakeLists.txt b/include/CMakeLists.txt
@@ -5,7 +5,7 @@
 #             University of Science and Technology (KAUST)
 #
 # @file CMakeLists.txt
-# @version 1.3.0
+# @version 0.3.0
 # @author Eduardo Gonzalez Fisher
 # @author Aleksandr Mikhalev
 # @date 2020-06-09

diff --git a/include/common.h b/include/common.h
@@ -9,7 +9,7 @@
  * @cond
  * This command in pair with endcond will prevent file from being documented.
  *
- * @version 1.3.0
+ * @version 0.3.0
  * @author Aleksandr Mikhalev
  * @date 2020-06-09
  * */
-Original file line number
+Diff line change
@@ Expand Up / @@ -117,5 +117,4 @@ pipeline { @@
                 }
             }
         }
     }