Merge branch 'release/1.2'

emfomy · Sep 8, 2017 · f0b1835 · f0b1835
2 parents 7ce116f + d31a8b7
commit f0b1835
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,26 +1,31 @@
 # The main CMake setting
 
-# Set project
-project(ISVD)
 # cmake_minimum_required(VERSION 3.0)
 cmake_minimum_required(VERSION 2.8.12)
-set(ISVD_NAME "Integrated Singular Value Decomposition")
 
-# Set version number
+# Set project
+set(ISVD_NAME "Integrated Singular Value Decomposition")
 set(ISVD_MAJOR_VERSION 1)
-set(ISVD_MINOR_VERSION 1)
-set(ISVD_PATCH_VERSION 1)
+set(ISVD_MINOR_VERSION 2)
+set(ISVD_PATCH_VERSION 0)
 set(ISVD_VERSION "${ISVD_MAJOR_VERSION}.${ISVD_MINOR_VERSION}.${ISVD_PATCH_VERSION}")
 
+# Set cache options
+include(cmake/cache.cmake)
+
+# Initialize project
+cmake_policy(SET CMP0048 OLD)
+project(ISVD)
+
 # Set Makefile
 set(CMAKE_COLOR_MAKEFILE ON)
 # set(CMAKE_VERBOSE_MAKEFILE ON)
 
 # Set module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules")
 
-# Include utilities
-include(cmake/utilities.cmake)
+# Variables
+string(ASCII 27 Esc)
 
 # Set the options
 include(cmake/options.cmake)
@@ -43,8 +48,5 @@ add_subdirectory(share)
 add_subdirectory(check)
 add_subdirectory(doxygen)
 
-# Set flags
-include(cmake/flags.cmake)
-
 # Display message
 include(cmake/display.cmake)
diff --git a/README.md b/README.md
@@ -12,6 +12,9 @@ Integrated Singular Value Decomposition (iSVD)
 ### Author
 * Mu Yang <<emfomy@gmail.com>>
 
+### Tutorial
+* @ref tutorial_main
+
 ## Requirements
 * [CMake](https://cmake.org) 2.8+ (CMake 3+ recommended).
 * C/C++ compiler with C99/C++98 standard support ([GCC](https://gcc.gnu.org) 4.4+ recommended).
@@ -20,7 +23,7 @@ Integrated Singular Value Decomposition (iSVD)
 
 ### Optional
 * [Intel&reg; Math Kernel Library](https://software.intel.com/en-us/intel-mkl) (**Recommended** for better performance, used for BLAS & LAPACK).
-<!-- * [MAGMA](http://icl.cs.utk.edu/magma/) 2+ (Used for BLAS & LAPACK with GPU support). -->
+* [MAGMA](http://icl.cs.utk.edu/magma/) 2+ (Used for BLAS & LAPACK with GPU support).
 * [OpenMP](http://openmp.org) Library (**Recommended** for better performance, used for multi-thread parallelization).
 * [Google Test Library](https://github.com/google/googletest) (Used for code testing).
 * [DOxygen](http://www.stack.nl/~dimitri/doxygen/) (Used for documentation).
@@ -50,33 +53,57 @@ The following table are the main options
 | `ISVD_BLAS`            | the selection BLAS/LAPACK library. | Options: `BLAS/MKL`            |
 | `ISVD_BUILD_DEMO`      | build demo codes.                  |                                |
 | `ISVD_BUILD_DOC`       | build documentation.               |                                |
+| `ISVD_BUILD_LIB`       | build libraries.                   |                                |
 | `ISVD_BUILD_TEST`      | build unit tests.                  |                                |
 | `ISVD_INDEX_TYPE`      | the selection index type.          | Options: `32/64`               |
 | `ISVD_OMP`             | the selection OpenMP library.      | Options: `OFF/GOMP/IOMP`       |
+| `ISVD_USE_GPU`         | enable GPU support.                |                                |
+| `ISVD_VERBOSE_TEST`    | enable verbose unit tests.         |                                |
 | `GTEST_ROOT`           | the root path of Google Test.      | Require `ISVD_BUILD_TEST`      |
 | `INTEL_ROOT`           | the root path of Intel libraries.  | Require `ISVD_BLAS = MKL`      |
 | `MKL_ROOT`             | the root path of Intel MKL.        | Require `ISVD_BLAS = MKL`      |
 | `MPI_PROCS`            | the number of MPI processes.       | Only used in demo codes.       |
 | `OMP_THRDS`            | the number of OpenMP threads.      | Only used in demo/check codes. |
-<!-- | `ISVD_USE_GPU`         | enable GPU support.                |                                | -->
 
 ### Makefile
 
 The following table are the main make rules
 
 | Command        | Detail                         |
 |----------------|--------------------------------|
-| `make all`     | build all binaries             |
+| `make all`     | build all libraries            |
 | `make install` | install package                |
 | `make check`   | build and run unit tests       |
 | `make doc`     | build documentation            |
 | `make help`    | display make-rules             |
 
-### Definitions
+## Usage
+
+* Define `ISVD_USE_ILP64` before include `isvd.h` to use 64-bit integer.
+* All 64bit libraries and executables are named with suffix "`_64`".
+
+### Libraries
+
+Please link exact one library of each kind.
 
-* Define `ISVD_USE_ILP64` to use 64-bit integer.
-* Define `ISVD_USE_MKL`   to enable Intel MKL.
-<!-- * Define `ISVD_USE_GPU`   to enable GPU support. -->
+* Correct
+  * `gcc test.c -I<include-path> -L<library-path> -Wl,-rpath <library-path> -lisvd_core -lisvd_la_mkl_iomp -lisvd_gpu_magma`
+  * `gcc test.c -I<include-path> -L<library-path> -Wl,-rpath <library-path> -lisvd_core -lisvd_la_blas -lisvd_gpu_none`
+* Wrong
+  * `gcc test.c -I<include-path> -L<library-path> -Wl,-rpath <library-path> -lisvd_core`
+    * (Some kind of libraries are not linked)
+  * `gcc test.c -I<include-path> -L<library-path> -Wl,-rpath <library-path> -lisvd_core -lisvd_la_blas -lisvd_gpu_magma -lisvd_gpu_none`
+    * (Some kind of libraries are linked multiple times)
+
+| Name                   | Kind           | Detail                                 |
+|------------------------|----------------|----------------------------------------|
+| `isvd_core`            | Core           | Core routines                          |
+| `isvd_la_blas`         | Linear Algebra | Sequential Plain BLAS                  |
+| `isvd_la_mkl`          | Linear Algebra | Sequential Intel MKL                   |
+| `isvd_la_mkl_gomp`     | Linear Algebra | Parallel Intel MKL using GNU OpenMP    |
+| `isvd_la_mkl_iomp`     | Linear Algebra | Parallel Intel MKL using Intel OpenMP  |
+| `isvd_gpu_none`        | GPU            | No GPU                                 |
+| `isvd_gpu_magma`       | GPU            | MAGMA GPU                              |
 
 ## Q&amp;A
 
@@ -95,11 +122,16 @@ The following table are the main make rules
 
 * Set `GTEST_ROOT` to a folder containing `include` and `lib` of Google Test.
 
+### How to enable multithread support?
+
+* Set `ISVD_OMP` with `ccmake` before building libraries.
+* Make sure your LAPACK&amp;BLAS / Intel MKL uses supports multithreading.
+
 ### How to use 64-bit integer?
 
-* Set `ISVD_USE_ILP64` with `ccmake`.
-* If you want to compile directly, add `-DISVD_USE_ILP64` to compiler flag.
-* Make sure your LAPACK&amp;BLAS / Intel MKL uses 64bit integer. Make sure you uses the correct library and flags of Intel MKL.
+* Set `ISVD_USE_ILP64` with `ccmake` before building libraries.
+* Add `-DISVD_USE_ILP64` to compile flag.
+* Make sure your LAPACK&amp;BLAS / Intel MKL uses 64bit integer.
 
 ## Reference
 * [Ting-Li Chen, Dawei D. Chang, Su-Yun Huang, Hung Chen, Chienyao Lin, Weichung Wang, “Integrating Multiple Random Sketches for Singular Value Decomposition”](https://arxiv.org/abs/1608.08285)

diff --git a/check/CMakeLists.txt b/check/CMakeLists.txt
@@ -15,32 +15,39 @@ if(NOT ISVD_BUILD_TEST)
   return()
 endif()
 
-# GTest
-if(GTEST_FOUND)
-  list(APPEND INCS "${GTEST_INCLUDE_DIRS}")
-  list(APPEND LIBS "${GTEST_BOTH_LIBRARIES}")
-  list(APPEND DEFS "ISVD_USE_GTEST")
-endif()
+# Target rule
+function(ISVD_SET_TARGET_CHECK_CPU target)
+  isvd_set_target_omp(${target} CXX)
+  isvd_set_target_mpi(${target})
+  isvd_set_target_blas(${target})
+  isvd_set_target_gtest(${target})
+  target_link_libraries(${target} checkisvd extmmio)
+  target_compile_definitions(${target} PUBLIC "-DISVD_DATA_PATH=\"${PROJECT_SOURCE_DIR}/data\"")
+endfunction()
+
+function(ISVD_SET_TARGET_CHECK_GPU target)
+  isvd_set_target_omp(${target} CXX)
+  isvd_set_target_mpi(${target})
+  isvd_set_target_blas(${target})
+  isvd_set_target_gtest(${target})
+  isvd_set_target_gpu(${target})
+  target_link_libraries(${target} checkisvd_gpu extmmio)
+  target_compile_definitions(${target} PUBLIC "-DISVD_DATA_PATH=\"${PROJECT_SOURCE_DIR}/data\"")
+endfunction()
 
 # Set include paths
 include_directories("${PROJECT_CONFIG_DIR}/include/c"
                     "${CMAKE_CURRENT_CONFIG_DIR}/src"
+                    "${PROJECT_CONFIG_DIR}/src"
              SYSTEM "${PROJECT_SOURCE_DIR}/ext")
 
 # Add subdirectories
 add_subdirectory(src)
 
-# Set libraries
-list(APPEND LIBS checkisvd)
-list(APPEND LIBS extmmio)
-
-# Set definitions
-list(APPEND DEFS "-DISVD_DATA_PATH=\"${PROJECT_SOURCE_DIR}/data\"")
-
 # Configure files
 isvd_configure_x_fn("${CMAKE_CURRENT_SOURCE_DIR}/check" "${CMAKE_CURRENT_CONFIG_DIR}/check" "${ISVD_S_TYPES}")
 isvd_configure_x_fn("${CMAKE_CURRENT_SOURCE_DIR}/check" "${CMAKE_CURRENT_CONFIG_DIR}/check" "${ISVD_D_TYPES}")
-isvd_configure_in_fn("${CMAKE_CURRENT_SOURCE_DIR}/check" "${CMAKE_CURRENT_CONFIG_DIR}/check")
+isvd_configure_fn("${CMAKE_CURRENT_SOURCE_DIR}/check" "${CMAKE_CURRENT_CONFIG_DIR}/check")
 
 # Include macros
 include(check.cmake)
@@ -50,30 +57,30 @@ macro(ISVD_CHECK_FN xtypes)
 
   isvd_set_types(${xtypes})
 
-  # CPU unit tests
-  set(DEFS_TMP "${DEFS}")
-  list(REMOVE_ITEM DEFS "ISVD_USE_GPU")
-
   # Sketching
-  add_mpi_check(libisvd/core/stage/${x}_sketch_gaussian_projection "${XName} Precision Gaussian Projection Sketching check" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_sketch_gaussian_projection "${XName} Precision Gaussian Projection Sketching" "1;2;3;4;6;12")
 
   # Orthogonalization
-  add_mpi_check(libisvd/core/stage/${x}_orthogonalize_gramian "${XName} Precision Gramian Orthogonalization check" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_orthogonalize_gramian "${XName} Precision Gramian Orthogonalization" "1;2;3;4;6;12")
 
   # Integration
-  add_mpi_check(libisvd/core/stage/${x}_integrate_kolmogorov_nagumo "${XName} Precision Kolmogorov Nagumo Integration check" "1;2;3;4;6;12")
-  add_mpi_check(libisvd/core/stage/${x}_integrate_wen_yin "${XName} Precision Wen Yin Integration check" "1;2;3;4;6;12")
-  add_mpi_check(libisvd/core/stage/${x}_integrate_hierarchical_reduction "${XName} Precision Hierarchical Reduction Integration check" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_integrate_kolmogorov_nagumo "${XName} Precision Kolmogorov Nagumo Integration" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_integrate_wen_yin "${XName} Precision Wen Yin Integration" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_integrate_hierarchical_reduction "${XName} Precision Hierarchical Reduction Integration" "1;2;3;4;6;12")
 
   # Postprocessing
-  add_mpi_check(libisvd/core/stage/${x}_postprocess_gramian "${XName} Precision Gramian Postprocessing check" "1;2;3;4;6;12")
-  add_mpi_check(libisvd/core/stage/${x}_postprocess_symmetric "${XName} Precision Symmetric Postprocessing check" "1;2;3;4;6;12")
-
-  set(DEFS "${DEFS_TMP}")
-  unset(DEFS_TMP)
+  add_mpi_check_cpu(libisvd/core/stage/${x}_postprocess_gramian "${XName} Precision Gramian Postprocessing" "1;2;3;4;6;12")
+  add_mpi_check_cpu(libisvd/core/stage/${x}_postprocess_symmetric "${XName} Precision Symmetric Postprocessing" "1;2;3;4;6;12")
 
   # GPU unit tests
   if(ISVD_USE_GPU)
+
+    # Sketching
+    add_mpi_check_gpu(libisvd/gpu/stage/${x}_sketch_gaussian_projection_gpu "${XName} Precision GPU Gaussian Projection Sketching" "1;2")
+
+    # Postprocessing
+    add_mpi_check_gpu(libisvd/gpu/stage/${x}_postprocess_gramian_gpu "${XName} Precision GPU Gramian Postprocessing" "1;2")
+    add_mpi_check_gpu(libisvd/gpu/stage/${x}_postprocess_symmetric_gpu "${XName} Precision GPU Symmetric Postprocessing" "1;2")
   endif()
 endmacro()
 

diff --git a/check/check.cmake b/check/check.cmake
@@ -15,7 +15,7 @@ macro(_ADD_CHECK_PREDO checktype)
   list(SORT files)
   list(REVERSE files)
   add_executable(${checktarget} EXCLUDE_FROM_ALL ${checkmain} ${files})
-  isvd_set_target(${checktarget} "")
+  isvd_set_target(${checktarget})
   target_compile_definitions(${checktarget} PUBLIC "ISVD_CHECK_NAME=\"${checkcomment}\"")
   set(CMAKE_CHECK_TARGETS ${CMAKE_CHECK_TARGETS} ${checktarget} PARENT_SCOPE)
   list(REVERSE files)
@@ -26,7 +26,13 @@ endmacro()
 macro(_ADD_CHECK checktype)
   set(checkmain check.cxx)
   _add_check_predo("${checktype}" "")
-  gtest_add_tests($<TARGET_FILE:${checktarget}> "" ${checkmain} ${files})
+
+  # Add test
+  if(ISVD_VERBOSE_TEST)
+    gtest_add_tests($<TARGET_FILE:${checktarget}> "" ${checkmain} ${files})
+  else()
+    add_test(NAME ${checkname} COMMAND $<TARGET_FILE:${checktarget}>)
+  endif()
 
   # Add rule
   add_custom_target(
@@ -42,13 +48,20 @@ macro(_ADD_MPI_CHECK checktype listprocs)
   set(checkmain check_mpi.cxx)
   _add_check_predo("${checktype}")
 
-  gtest_add_mpi_tests($<TARGET_FILE:${checktarget}> "${listprocs}" "" ${checkmain} ${files})
+  # Add test
+  if(ISVD_VERBOSE_TEST)
+    gtest_add_mpi_tests($<TARGET_FILE:${checktarget}> "${listprocs}" "" ${checkmain} ${files})
+  else()
+    foreach(procs ${listprocs})
+      add_test(NAME ${checkname}_${procs} COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${procs} ${CMAKE_COMMAND} -E env ${ENVS} $<TARGET_FILE:${checktarget}>)
+    endforeach()
+  endif()
 
   # Add rule
   foreach(procs ${listprocs})
     add_custom_target(
       check_${checkname}_${procs}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${procs} ${CMAKE_ENV} OMP_NUM_THREADS=${OMP_THRDS} $<TARGET_FILE:${checktarget}>
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${procs} ${CMAKE_COMMAND} -E env ${ENVS} $<TARGET_FILE:${checktarget}>
       DEPENDS ${checktarget}
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
       COMMENT "Run check ${checkpath}"
@@ -58,21 +71,24 @@ endmacro()
 
 ################################################################################
 
-function(ADD_CHECK checkpath checkcomment)
+function(ADD_CHECK_CPU checkpath checkcomment)
   _add_check("")
+  isvd_set_target_check_cpu(${checktarget})
 endfunction()
 
-function(ADD_CHECK_TEST checkpath checkcomment)
-  _add_check("test")
-endfunction()
-
-function(ADD_CHECK_DEATH checkpath checkcomment)
-  list(REMOVE_ITEM DEFS "ISVD_USE_GTEST")
-  _add_check("death_test")
+function(ADD_CHECK_GPU checkpath checkcomment)
+  _add_check("")
+  isvd_set_target_check_gpu(${checktarget})
 endfunction()
 
 ################################################################################
 
-function(ADD_MPI_CHECK checkpath checkcomment listprocs)
+function(ADD_MPI_CHECK_CPU checkpath checkcomment listprocs)
+  _add_mpi_check("" "${listprocs}")
+  isvd_set_target_check_cpu(${checktarget})
+endfunction()
+
+function(ADD_MPI_CHECK_GPU checkpath checkcomment listprocs)
   _add_mpi_check("" "${listprocs}")
+  isvd_set_target_check_gpu(${checktarget})
 endfunction()
diff --git a/check/check.cxx b/check/check.cxx
@@ -1,14 +1,11 @@
 #include <iostream>
 #include <gtest/gtest.h>
 #include <isvd.h>
-#include <libisvd.h>
 
 int main( int argc, char **argv ) {
 
-  mpi_int_t mpi_size = 1;
-  omp_int_t omp_size = isvd_getOmpSize();
-  printf("iSVD " ISVD_VERSION " " ISVD_CHECK_NAME " test\n");
-  printf("%d nodes, %d threads per node\n\n", mpi_size, omp_size);
+  printf("iSVD " ISVD_CHECK_NAME " unit test\n");
+  isvd_printEnvironment(MPI_COMM_WORLD);
 
   testing::InitGoogleTest(&argc, argv);
   int retval = RUN_ALL_TESTS();