Merge branch 'hotfix/1.2'

emfomy · Sep 14, 2017 · e4127b3 · e4127b3
2 parents cb2b9eb + de22bdd
commit e4127b3
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -45,7 +45,6 @@ include(cmake/vars.cmake)
 
 # Add subdirectories
 add_subdirectory(ext)
-add_subdirectory(include)
 add_subdirectory(src)
 add_subdirectory(demo)
 add_subdirectory(share)

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@ Integrated Singular Value Decomposition (iSVD)
 * https://github.com/emfomy/isvd
 
 ### Documentation
-* http://emfomy.github.io/isvd
+* Please download from https://github.com/emfomy/isvd/releases or build using **make doc** (see below) on your own computer.
 
 ### Author
 * Mu Yang <<emfomy@gmail.com>>
@@ -33,17 +33,18 @@ Integrated Singular Value Decomposition (iSVD)
 Please use the following commands to create Makefiles
 
 ```
+cd <isvd-source-folder>
 mkdir build
 cd build
-cmake <path-to-source>
+cmake ..
 ```
 
 ### Options
 
 Use the following command to set options
 
 ```
-ccmake <path-to-source>
+ccmake ..
 ```
 
 The following table are the main options
@@ -67,20 +68,28 @@ The following table are the main options
 
 ### Makefile
 
-The following table are the main make rules
+The following table are the main Makefile rules
 
-| Command        | Detail                         |
-|----------------|--------------------------------|
-| `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             |
+| Command        | Detail                         | Options                        |
+|----------------|--------------------------------|--------------------------------|
+| `make all`     | build all libraries            |                                |
+| `make install` | install package                |                                |
+| `make check`   | build and run unit tests       | Require `ISVD_BUILD_TEST`      |
+| `make doc`     | build documentation            | Require `ISVD_BUILD_DOC`       |
+| `make help`    | display make-rules             |                                |
+
+### Test installation
+
+* Set `ISVD_BUILD_TEST` using **ccmake**. (Also recommended to unset `ISVD_VERBOSE_TEST` if GPU is enabled).
+* Run **make check**
+  * Known issue: RealSingle_WenYinIntegration.Test.#/s_integrate_wen_yin_# always fail the test.
 
 ## Usage
 
 * Define `ISVD_USE_ILP64` before include `isvd.h` to use 64-bit integer.
 * All 64bit libraries and executables are named with suffix "`_64`".
+* The header files are located in `build/include`
+* The libraries are located in `build/lib`
 
 ### Libraries
 

diff --git a/check/CMakeLists.txt b/check/CMakeLists.txt
@@ -35,7 +35,7 @@ function(ISVD_SET_TARGET_CHECK_CPU target)
   isvd_set_target_mpi(${target} CXX)
   isvd_set_target_blas(${target})
   isvd_set_target_gtest(${target})
-  target_link_libraries(${target} checkisvd extmmio)
+  target_link_libraries(${target} checkisvd_gpu_none checkisvd_core_la extmmio)
   target_compile_definitions(${target} PUBLIC "-DISVD_DATA_PATH=\"${PROJECT_SOURCE_DIR}/data\"")
 endfunction()
 
@@ -45,18 +45,18 @@ function(ISVD_SET_TARGET_CHECK_GPU target)
   isvd_set_target_blas(${target})
   isvd_set_target_gtest(${target})
   isvd_set_target_gpu(${target})
-  target_link_libraries(${target} checkisvd_gpu extmmio)
+  target_link_libraries(${target} checkisvd_gpu_magma checkisvd_core_la extmmio)
   target_compile_definitions(${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")
+include_directories("${CMAKE_CURRENT_CONFIG_DIR}/lib"
+                    "${PROJECT_BINARY_DIR}/include/c"
+                    "${PROJECT_BINARY_DIR}/lib"
+             SYSTEM "${PROJECT_SOURCE_DIR}/ext/mmio")
 
 # Add subdirectories
-add_subdirectory(src)
+add_subdirectory(lib)
 
 # Configure files
 isvd_configure_x_fn("${CMAKE_CURRENT_SOURCE_DIR}/check" "${CMAKE_CURRENT_CONFIG_DIR}/check" "${ISVD_S_TYPES}")

diff --git a/check/check/libisvd/core/stage/@x@_integrate_hierarchical_reduction.cxx b/check/check/libisvd/core/stage/@x@_integrate_hierarchical_reduction.cxx
@@ -1,6 +1,6 @@
 #include <gtest/gtest.h>
 #include <mpi.h>
-#include <mmio/mmio.h>
+#include <mmio.h>
 #include <isvd.h>
 #include <libisvd.h>
 
@@ -10,7 +10,7 @@
 #define serr 1e-3
 #define derr 1e-8
 
-typedef @xtype@ isvd_val_t;
+typedef @xtype_____@ isvd_val_t;
 
 TEST(@XStr@_HierarchicalReductionIntegration, Test) {
 
@@ -26,7 +26,7 @@ TEST(@XStr@_HierarchicalReductionIntegration, Test) {
 
   // Read Qs
   file = fopen(QS_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -47,7 +47,7 @@ TEST(@XStr@_HierarchicalReductionIntegration, Test) {
 
   // Read Qbar
   file = fopen(Q_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -92,12 +92,12 @@ TEST(@XStr@_HierarchicalReductionIntegration, Test) {
   isvd_int_t ldqt = l;
 
   // Run stage
-  isvd_@x@IntegrateHierarchicalReduction(param, nullptr, 0, nullptr, 0, qst, ldqst, qt, ldqt);
+  isvd_@x@IntegrateHierarchicalReduction(param, NULL, 0, NULL, 0, qst, ldqst, qt, ldqt);
 
   // Gather results
   isvd_val_t *qt_ = isvd_@x@malloc(l * Pmb);
   isvd_int_t ldqt_ = l;
-  MPI_Gather(qt, mb*ldqt, MPI_@X_TYPE@, qt_, mb*ldqt, MPI_@X_TYPE@, mpi_root, MPI_COMM_WORLD);
+  MPI_Gather(qt, mb*ldqt, MPI_@XTYPE@, qt_, mb*ldqt, MPI_@XTYPE@, mpi_root, MPI_COMM_WORLD);
 
   if ( mpi_rank == mpi_root ) {
     // Compute space

diff --git a/check/check/libisvd/core/stage/@x@_integrate_kolmogorov_nagumo.cxx b/check/check/libisvd/core/stage/@x@_integrate_kolmogorov_nagumo.cxx
@@ -1,6 +1,6 @@
 #include <gtest/gtest.h>
 #include <mpi.h>
-#include <mmio/mmio.h>
+#include <mmio.h>
 #include <isvd.h>
 #include <libisvd.h>
 
@@ -15,7 +15,7 @@
 #define serr 1e-3
 #define derr 1e-8
 
-typedef @xtype@ isvd_val_t;
+typedef @xtype_____@ isvd_val_t;
 
 TEST(@XStr@_KolmogorovNagumoIntegration, Test) {
 
@@ -31,7 +31,7 @@ TEST(@XStr@_KolmogorovNagumoIntegration, Test) {
 
   // Read Qs
   file = fopen(QS_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -52,7 +52,7 @@ TEST(@XStr@_KolmogorovNagumoIntegration, Test) {
 
   // Read Qbar
   file = fopen(Q_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -107,7 +107,7 @@ TEST(@XStr@_KolmogorovNagumoIntegration, Test) {
   // Gather results
   isvd_val_t *qt_ = isvd_@x@malloc(l * Pmb);
   isvd_int_t ldqt_ = l;
-  MPI_Gather(qt, mb*ldqt, MPI_@X_TYPE@, qt_, mb*ldqt, MPI_@X_TYPE@, mpi_root, MPI_COMM_WORLD);
+  MPI_Gather(qt, mb*ldqt, MPI_@XTYPE@, qt_, mb*ldqt, MPI_@XTYPE@, mpi_root, MPI_COMM_WORLD);
 
   // Check results
   if ( mpi_rank == mpi_root ) {

diff --git a/check/check/libisvd/core/stage/@x@_integrate_wen_yin.cxx b/check/check/libisvd/core/stage/@x@_integrate_wen_yin.cxx
@@ -1,6 +1,6 @@
 #include <gtest/gtest.h>
 #include <mpi.h>
-#include <mmio/mmio.h>
+#include <mmio.h>
 #include <isvd.h>
 #include <libisvd.h>
 
@@ -15,7 +15,7 @@
 #define serr 1e-3
 #define derr 1e-8
 
-typedef @xtype@ isvd_val_t;
+typedef @xtype_____@ isvd_val_t;
 
 TEST(@XStr@_WenYinIntegration, Test) {
 
@@ -31,7 +31,7 @@ TEST(@XStr@_WenYinIntegration, Test) {
 
   // Read Qs
   file = fopen(QS_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -52,7 +52,7 @@ TEST(@XStr@_WenYinIntegration, Test) {
 
   // Read Qbar
   file = fopen(Q_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -107,7 +107,7 @@ TEST(@XStr@_WenYinIntegration, Test) {
   // Gather results
   isvd_val_t *qt_ = isvd_@x@malloc(l * Pmb);
   isvd_int_t ldqt_ = l;
-  MPI_Gather(qt, mb*ldqt, MPI_@X_TYPE@, qt_, mb*ldqt, MPI_@X_TYPE@, mpi_root, MPI_COMM_WORLD);
+  MPI_Gather(qt, mb*ldqt, MPI_@XTYPE@, qt_, mb*ldqt, MPI_@XTYPE@, mpi_root, MPI_COMM_WORLD);
 
   // Check results
   if ( mpi_rank == mpi_root ) {

diff --git a/check/check/libisvd/core/stage/@x@_orthogonalize_gramian.cxx b/check/check/libisvd/core/stage/@x@_orthogonalize_gramian.cxx
@@ -1,6 +1,6 @@
 #include <gtest/gtest.h>
 #include <mpi.h>
-#include <mmio/mmio.h>
+#include <mmio.h>
 #include <isvd.h>
 #include <libisvd.h>
 
@@ -10,7 +10,7 @@
 #define serr 1e-3
 #define derr 1e-8
 
-typedef @xtype@ isvd_val_t;
+typedef @xtype_____@ isvd_val_t;
 
 TEST(@XStr@_GramianOrthogonalization, Test) {
 
@@ -25,7 +25,7 @@ TEST(@XStr@_GramianOrthogonalization, Test) {
 
   // Read Ys
   file = fopen(YS_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -46,7 +46,7 @@ TEST(@XStr@_GramianOrthogonalization, Test) {
 
   // Read Qs
   file = fopen(QS_PATH, "r");
-  ASSERT_NE(file, (void*)(nullptr));
+  ASSERT_NE(file, nullptr);
   ASSERT_EQ(mm_read_banner(file, &matcode), 0);
   EXPECT_TRUE(mm_is_array(matcode))   << mm_typecode_to_str(matcode);
   EXPECT_TRUE(mm_is_real(matcode))    << mm_typecode_to_str(matcode);
@@ -90,12 +90,12 @@ TEST(@XStr@_GramianOrthogonalization, Test) {
   isvd_@x@Omatcopy('N', Nl, mj, 1.0, yst0 + param.rowidxbegin * ldyst0, ldyst0, yst, ldyst);
 
   // Run
-  isvd_@x@OrthogonalizeGramian(param, nullptr, 0, nullptr, 0, yst, ldyst);
+  isvd_@x@OrthogonalizeGramian(param, NULL, 0, NULL, 0, yst, ldyst);
 
   // Gather results
   isvd_val_t *qst_ = isvd_@x@malloc(Pmb * ldyst);
   isvd_int_t ldqst_ = ldyst;
-  MPI_Gather(yst, mb*ldyst, MPI_@X_TYPE@, qst_, mb*ldyst, MPI_@X_TYPE@, mpi_root, MPI_COMM_WORLD);
+  MPI_Gather(yst, mb*ldyst, MPI_@XTYPE@, qst_, mb*ldyst, MPI_@XTYPE@, mpi_root, MPI_COMM_WORLD);
 
   if ( mpi_rank == mpi_root ) {
     // Compute space