ginkgo-project · tcojean · Dec 2, 2019 · Oct 21, 2019 · Oct 29, 2019 · Oct 30, 2019
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -56,6 +56,8 @@ stages:
     - |
         (( $(ctest -N | tail -1 | sed 's/Total Tests: //') != 0 )) || exit 1
     - ctest -V
+    - make install
+    - make test_install
   dependencies: []
   except:
       - schedules

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,23 @@ commits. For a comprehensive list, use the following command:
 git log --first-parent
 ```
 
+## Version 1.1.1
+This version of Ginkgo provides a few fixes in Ginkgo's core routines. The
+supported systems and requirements are unchanged from version 1.1.0.
+
+### Fixes
++ Improve Ginkgo's installation and fix the `test_install` step ([#406](https://github.com/ginkgo-project/ginkgo/pull/406)),
++ Fix some documentation issues ([#406](https://github.com/ginkgo-project/ginkgo/pull/406)),
++ Fix multiple code issues reported by sonarqube ([#406](https://github.com/ginkgo-project/ginkgo/pull/406)),
++ Update the git-cmake-format repository ([#399](https://github.com/ginkgo-project/ginkgo/pull/399)),
++ Improve the global update header script ([#390](https://github.com/ginkgo-project/ginkgo/pull/390)),
++ Fix broken bounds checks ([#388](https://github.com/ginkgo-project/ginkgo/pull/388)),
++ Fix CSR strategies and improve performance ([#379](https://github.com/ginkgo-project/ginkgo/pull/379)),
++ Fix a small typo in the stencil examples ([#381](https://github.com/ginkgo-project/ginkgo/pull/381)),
++ Fix ELL error on small matrices ([#375](https://github.com/ginkgo-project/ginkgo/pull/375)),
++ Fix SellP read function ([#374](https://github.com/ginkgo-project/ginkgo/pull/374)),
++ Add factorization support in `create_new_algorithm.sh`  ([#371](https://github.com/ginkgo-project/ginkgo/pull/371))
+
 ## Version 1.1.0
 
 The Ginkgo team is proud to announce the new minor release of Ginkgo version

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.9)
 
-project(Ginkgo LANGUAGES C CXX VERSION 1.1.0 DESCRIPTION "A numerical linear algebra library targeting many-core architectures")
+project(Ginkgo LANGUAGES C CXX VERSION 1.1.1 DESCRIPTION "A numerical linear algebra library targeting many-core architectures")
 set(Ginkgo_VERSION_TAG "master")
 set(PROJECT_VERSION_TAG ${Ginkgo_VERSION_TAG})
 
@@ -160,8 +160,9 @@ if(GINKGO_DEVEL_TOOLS)
 endif()
 
 # Generate the global `ginkgo/ginkgo.hpp` header with every call of make
+# when bash is present and the developer tools are enabled
 find_program(BASH bash)
-if(NOT "${BASH}" STREQUAL "BASH-NOTFOUND")
+if(NOT "${BASH}" STREQUAL "BASH-NOTFOUND" AND GINKGO_DEVEL_TOOLS)
     add_custom_target(generate_ginkgo_header ALL
         COMMAND ${Ginkgo_SOURCE_DIR}/dev_tools/scripts/update_ginkgo_header.sh
         WORKING_DIRECTORY ${Ginkgo_SOURCE_DIR})
@@ -187,6 +188,7 @@ add_custom_target(test_install
     COMMAND ${CMAKE_COMMAND} -G${CMAKE_GENERATOR} -H${Ginkgo_SOURCE_DIR}/test_install
         -B${Ginkgo_BINARY_DIR}/test_install
         -DCMAKE_PREFIX_PATH=${CMAKE_INSTALL_PREFIX}/${GINKGO_INSTALL_CONFIG_DIR}
+        -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     COMMAND ${CMAKE_COMMAND} --build ${Ginkgo_BINARY_DIR}/test_install
     COMMAND ${Ginkgo_BINARY_DIR}/test_install/test_install
     COMMENT "Running a test on the installed binaries. This requires running `(sudo) make install` first.")

diff --git a/cmake/GinkgoConfig.cmake.in b/cmake/GinkgoConfig.cmake.in
@@ -61,6 +61,8 @@ set(GINKGO_JACOBI_FULL_OPTIMIZATIONS @GINKGO_JACOBI_FULL_OPTIMIZATIONS@)
 set(GINKGO_CUDA_ARCHITECTURES @GINKGO_CUDA_ARCHITECTURES@)
 set(GINKGO_CUDA_HOST_COMPILER @CMAKE_CUDA_HOST_COMPILER@)
 
+set(GINKGO_HAVE_PAPI_SDE @GINKGO_HAVE_PAPI_SDE@)
+
 # Ginkgo external package variables
 set(GINKGO_USE_EXTERNAL_CAS "@GINKGO_USE_EXTERNAL_CAS@")
 set(GINKGO_USE_EXTERNAL_GTEST "@GINKGO_USE_EXTERNAL_GTEST@")
@@ -80,10 +82,13 @@ set(TPL_RAPIDJSON_INCLUDE_DIRS "@TPL_RAPIDJSON_INCLUDE_DIRS@")
 # Ginkgo installation configuration
 set(GINKGO_CONFIG_FILE_PATH "${CMAKE_CURRENT_LIST_DIR}")
 string(REPLACE "@GINKGO_INSTALL_CONFIG_DIR@" "" GINKGO_INSTALL_PREFIX "${GINKGO_CONFIG_FILE_PATH}")
-set(GINKGO_INSTALL_INCLUDE_DIR "@GINKGO_INSTALL_INCLUDE_DIR@")
-set(GINKGO_INSTALL_LIBRARY_DIR "@GINKGO_INSTALL_LIBRARY_DIR@")
-set(GINKGO_INSTALL_PKGCONFIG_DIR "@GINKGO_INSTALL_PKGCONFIG_DIR@")
-set(GINKGO_INSTALL_CONFIG_DIR "@GINKGO_INSTALL_CONFIG_DIR@")
+set(GINKGO_INSTALL_INCLUDE_DIR "${GINKGO_INSTALL_PREFIX}/@GINKGO_INSTALL_INCLUDE_DIR@")
+set(GINKGO_INSTALL_LIBRARY_DIR "${GINKGO_INSTALL_PREFIX}/@GINKGO_INSTALL_LIBRARY_DIR@")
+set(GINKGO_INSTALL_PKGCONFIG_DIR "${GINKGO_INSTALL_PREFIX}/@GINKGO_INSTALL_PKGCONFIG_DIR@")
+set(GINKGO_INSTALL_CONFIG_DIR "${GINKGO_INSTALL_PREFIX}/@GINKGO_INSTALL_CONFIG_DIR@")
+set(GINKGO_INSTALL_MODULE_DIR "${GINKGO_INSTALL_PREFIX}/@GINKGO_INSTALL_MODULE_DIR@")
+set(CMAKE_MODULE_PATH "${GINKGO_INSTALL_MODULE_DIR}")
+
 
 set(GINKGO_INTERFACE_LINK_LIBRARIES "@GINKGO_INTERFACE_LINK_LIBRARIES@")
 set(GINKGO_INTERFACE_LINK_FLAGS "@GINKGO_INTERFACE_LINK_FLAGS@")
@@ -111,6 +116,8 @@ set(GINKGO_OPENMP_LIBRARIES @OpenMP_CXX_LIBRARIES@)
 
 set(GINKGO_OPENMP_FLAGS "@OpenMP_CXX_FLAGS@")
 
+# Modulepath configuration
+
 # NOTE: we do not export benchmarks, examples, tests or devel tools
 #     so `third_party` libraries are currently unneeded.
 

diff --git a/cmake/Modules/FindPAPI.cmake b/cmake/Modules/FindPAPI.cmake
@@ -68,30 +68,31 @@ if(PAPI_INCLUDE_DIR)
 
     if (PAPI_LIBRARY)
         # find the components
-       foreach(component IN LISTS PAPI_FIND_COMPONENTS)
-           file(WRITE "${CMAKE_BINARY_DIR}/papi_${component}_detect.c"
-             "
-             #include <papi.h>
-             int main() {
-              int retval;
-              retval = PAPI_library_init(PAPI_VER_CURRENT);
-                if (retval != PAPI_VER_CURRENT && retval > 0)
-                 return -1;
-                if (PAPI_get_component_index(\"${component}\") < 0)
-                 return 0;
-                return 1;
-             }
-            ")
-        try_run(PAPI_${component}_FOUND
-            gko_result_unused
-            "${CMAKE_BINARY_DIR}"
-            "${CMAKE_BINARY_DIR}/papi_${component}_detect.c"
-            LINK_LIBRARIES ${PAPI_LIBRARY}
-            )
+        enable_language(C)
+        foreach(component IN LISTS PAPI_FIND_COMPONENTS)
+            file(WRITE "${CMAKE_BINARY_DIR}/papi_${component}_detect.c"
+                "
+                #include <papi.h>
+                int main() {
+                 int retval;
+                 retval = PAPI_library_init(PAPI_VER_CURRENT);
+                   if (retval != PAPI_VER_CURRENT && retval > 0)
+                    return -1;
+                   if (PAPI_get_component_index(\"${component}\") < 0)
+                    return 0;
+                   return 1;
+                }"
+                )
+            try_run(PAPI_${component}_FOUND
+                gko_result_unused
+                "${CMAKE_BINARY_DIR}"
+                "${CMAKE_BINARY_DIR}/papi_${component}_detect.c"
+                LINK_LIBRARIES ${PAPI_LIBRARY}
+                )
 
-        if (NOT PAPI_${component}_FOUND EQUAL 1)
-            unset(PAPI_${component}_FOUND)
-        endif()
+            if (NOT PAPI_${component}_FOUND EQUAL 1)
+                unset(PAPI_${component}_FOUND)
+            endif()
         endforeach()
     endif()
 endif()

diff --git a/cmake/build_helpers.cmake b/cmake/build_helpers.cmake
@@ -94,4 +94,4 @@ endmacro()
 
 macro(ginkgo_switch_to_windows_dynamic lang)
     ginkgo_switch_windows_link(${lang} "MT" "MD")
-endmacro()
+endmacro()
diff --git a/cmake/install_helpers.cmake b/cmake/install_helpers.cmake
@@ -6,6 +6,7 @@ set(GINKGO_INSTALL_INCLUDE_DIR "include")
 set(GINKGO_INSTALL_LIBRARY_DIR "lib")
 set(GINKGO_INSTALL_PKGCONFIG_DIR "lib/pkgconfig")
 set(GINKGO_INSTALL_CONFIG_DIR "lib/cmake/Ginkgo")
+set(GINKGO_INSTALL_MODULE_DIR "lib/cmake/Ginkgo/Modules")
 
 function(ginkgo_install_library name subdir)
     # install .so and .a files
@@ -33,6 +34,9 @@ function(ginkgo_install)
         install(FILES "${Ginkgo_SOURCE_DIR}/third_party/papi_sde/papi_sde_interface.h"
             DESTINATION "${GINKGO_INSTALL_INCLUDE_DIR}/third_party/papi_sde"
             )
+        install(FILES "${Ginkgo_SOURCE_DIR}/cmake/Modules/FindPAPI.cmake"
+            DESTINATION "${GINKGO_INSTALL_MODULE_DIR}/"
+            )
     endif()
 
     # export targets

diff --git a/core/device_hooks/cuda_hooks.cpp b/core/device_hooks/cuda_hooks.cpp
@@ -43,9 +43,9 @@ namespace gko {
 
 version version_info::get_cuda_version() noexcept
 {
-    // We just return 1.1.0 with a special "not compiled" tag in placeholder
-    // modules.
-    return {1, 1, 0, "not compiled"};
+    // We just return the version with a special "not compiled" tag in
+    // placeholder modules.
+    return {GKO_VERSION_STR, "not compiled"};
 }
 
 

diff --git a/core/device_hooks/omp_hooks.cpp b/core/device_hooks/omp_hooks.cpp
@@ -38,9 +38,9 @@ namespace gko {
 
 version version_info::get_omp_version() noexcept
 {
-    // We just return 1.1.0 with a special "not compiled" tag in placeholder
-    // modules.
-    return {1, 1, 0, "not compiled"};
+    // We just return the version with a special "not compiled" tag in
+    // placeholder modules.
+    return {GKO_VERSION_STR, "not compiled"};
 }
 
 

diff --git a/core/device_hooks/reference_hooks.cpp b/core/device_hooks/reference_hooks.cpp
@@ -39,9 +39,9 @@ namespace gko {
 
 version version_info::get_reference_version() noexcept
 {
-    // We just return 1.1.0 with a special "not compiled" tag in placeholder
-    // modules.
-    return {1, 1, 0, "not compiled"};
+    // We just return the version with a special "not compiled" tag in
+    // placeholder modules.
+    return {GKO_VERSION_STR, "not compiled"};
 }
 
 

diff --git a/core/devices/cuda/executor.cpp b/core/devices/cuda/executor.cpp
@@ -48,7 +48,7 @@ std::shared_ptr<const Executor> CudaExecutor::get_master() const noexcept
 }
 
 
-int CudaExecutor::num_execs[max_devices];
+unsigned CudaExecutor::num_execs[max_devices];
 
 
 std::mutex CudaExecutor::mutex[max_devices];

diff --git a/core/matrix/coo.cpp b/core/matrix/coo.cpp
@@ -108,10 +108,13 @@ void Coo<ValueType, IndexType>::convert_to(
     Csr<ValueType, IndexType> *result) const
 {
     auto exec = this->get_executor();
-    auto tmp = Csr<ValueType, IndexType>::create(exec, this->get_size());
+    auto tmp = Csr<ValueType, IndexType>::create(
+        exec, this->get_size(), this->get_num_stored_elements(),
+        result->get_strategy());
     tmp->values_ = this->values_;
     tmp->col_idxs_ = this->col_idxs_;
     exec->run(coo::make_convert_to_csr(tmp.get(), this));
+    tmp->make_srow();
     tmp->move_to(result);
 }
 
@@ -120,10 +123,13 @@ template <typename ValueType, typename IndexType>
 void Coo<ValueType, IndexType>::move_to(Csr<ValueType, IndexType> *result)
 {
     auto exec = this->get_executor();
-    auto tmp = Csr<ValueType, IndexType>::create(exec, this->get_size());
+    auto tmp = Csr<ValueType, IndexType>::create(
+        exec, this->get_size(), this->get_num_stored_elements(),
+        result->get_strategy());
     tmp->values_ = std::move(this->values_);
     tmp->col_idxs_ = std::move(this->col_idxs_);
     exec->run(coo::make_convert_to_csr(tmp.get(), this));
+    tmp->make_srow();
     tmp->move_to(result);
 }
 

diff --git a/core/matrix/dense.cpp b/core/matrix/dense.cpp
@@ -108,12 +108,21 @@ inline void conversion_helper(Csr<ValueType, IndexType> *result,
 {
     auto exec = source->get_executor();
 
-    size_type num_stored_nonzeros = 0;
-    exec->run(dense::make_count_nonzeros(source, &num_stored_nonzeros));
-    auto tmp = Csr<ValueType, IndexType>::create(
-        exec, source->get_size(), num_stored_nonzeros, result->get_strategy());
-    exec->run(op(tmp.get(), source));
-    tmp->move_to(result);
+    if (source->get_size()) {
+        size_type num_stored_nonzeros = 0;
+        exec->run(dense::make_count_nonzeros(source, &num_stored_nonzeros));
+        auto tmp = Csr<ValueType, IndexType>::create(exec, source->get_size(),
+                                                     num_stored_nonzeros,
+                                                     result->get_strategy());
+        exec->run(op(tmp.get(), source));
+        tmp->move_to(result);
+    }
+    // If source is empty, there is no need to copy data or to call kernels
+    else {
+        auto tmp =
+            Csr<ValueType, IndexType>::create(exec, result->get_strategy());
+        tmp->move_to(result);
+    }
 }
 
 

diff --git a/core/matrix/ell.cpp b/core/matrix/ell.cpp
@@ -134,10 +134,11 @@ void Ell<ValueType, IndexType>::convert_to(
     size_type num_stored_elements = 0;
     exec->run(ell::make_count_nonzeros(this, &num_stored_elements));
 
-    auto tmp = Csr<ValueType, IndexType>::create(exec, this->get_size(),
-                                                 num_stored_elements);
+    auto tmp = Csr<ValueType, IndexType>::create(
+        exec, this->get_size(), num_stored_elements, result->get_strategy());
     exec->run(ell::make_convert_to_csr(tmp.get(), this));
 
+    tmp->make_srow();
     tmp->move_to(result);
 }
 

diff --git a/core/matrix/hybrid.cpp b/core/matrix/hybrid.cpp
@@ -135,10 +135,11 @@ void Hybrid<ValueType, IndexType>::convert_to(
     size_type num_stored_elements = 0;
     exec->run(hybrid::make_count_nonzeros(this, &num_stored_elements));
 
-    auto tmp = Csr<ValueType, IndexType>::create(exec, this->get_size(),
-                                                 num_stored_elements);
+    auto tmp = Csr<ValueType, IndexType>::create(
+        exec, this->get_size(), num_stored_elements, result->get_strategy());
     exec->run(hybrid::make_convert_to_csr(tmp.get(), this));
 
+    tmp->make_srow();
     tmp->move_to(result);
 }
 
@@ -161,8 +162,9 @@ void Hybrid<ValueType, IndexType>::read(const mat_data &data)
     get_each_row_nnz(data, row_nnz);
     strategy_->compute_hybrid_config(row_nnz, &ell_lim, &coo_lim);
 
-    auto tmp = Hybrid::create(this->get_executor()->get_master(), data.size,
-                              ell_lim, data.size[0], coo_lim);
+    auto tmp =
+        Hybrid::create(this->get_executor()->get_master(), data.size, ell_lim,
+                       data.size[0], coo_lim, this->get_strategy());
 
     // Get values and column indexes.
     size_type ind = 0;

diff --git a/core/matrix/sellp.cpp b/core/matrix/sellp.cpp
@@ -76,19 +76,19 @@ size_type calculate_total_cols(const matrix_data<ValueType, IndexType> &data,
     IndexType current_slice = 0;
     size_type total_cols = 0;
     for (const auto &elem : data.nonzeros) {
+        if (elem.row != current_row) {
+            current_row = elem.row;
+            slice_lengths[current_slice] =
+                max(slice_lengths[current_slice], nonzeros_per_row);
+            nonzeros_per_row = 0;
+        }
         if (elem.row / slice_size != current_slice) {
             slice_lengths[current_slice] =
                 stride_factor *
                 ceildiv(slice_lengths[current_slice], stride_factor);
             total_cols += slice_lengths[current_slice];
             current_slice = elem.row / slice_size;
         }
-        if (elem.row != current_row) {
-            current_row = elem.row;
-            slice_lengths[current_slice] =
-                max(slice_lengths[current_slice], nonzeros_per_row);
-            nonzeros_per_row = 0;
-        }
         nonzeros_per_row += (elem.value != zero<ValueType>());
     }
     slice_lengths[current_slice] =
@@ -147,9 +147,10 @@ void Sellp<ValueType, IndexType>::convert_to(
 
     size_type num_stored_nonzeros = 0;
     exec->run(sellp::make_count_nonzeros(this, &num_stored_nonzeros));
-    auto tmp = Csr<ValueType, IndexType>::create(exec, this->get_size(),
-                                                 num_stored_nonzeros);
+    auto tmp = Csr<ValueType, IndexType>::create(
+        exec, this->get_size(), num_stored_nonzeros, result->get_strategy());
     exec->run(sellp::make_convert_to_csr(tmp.get(), this));
+    tmp->make_srow();
     tmp->move_to(result);
 }
 

diff --git a/core/test/base/exception_helpers.cpp b/core/test/base/exception_helpers.cpp
@@ -55,7 +55,7 @@ TEST(NotCompiled, ThrowsWhenUsed)
 }
 
 
-void does_not_support_int() { throw GKO_NOT_SUPPORTED(int); }
+void does_not_support_int() { GKO_NOT_SUPPORTED(int); }
 
 TEST(NotSupported, ReturnsNotSupportedException)
 {
@@ -131,6 +131,18 @@ TEST(AssertConformant, ThrowsWhenNotConformant)
 }
 
 
+TEST(AssertEqual, DoesNotThrowWhenEqual)
+{
+    ASSERT_NO_THROW(GKO_ASSERT_EQ(1, 1));
+}
+
+
+TEST(AssertEqual, ThrowsWhenNotEqual)
+{
+    ASSERT_THROW(GKO_ASSERT_EQ(0, 1), gko::ValueMismatch);
+}
+
+
 TEST(AssertEqualRows, DoesNotThrowWhenEqualRowSize)
 {
     ASSERT_NO_THROW(
-Original file line number
+Diff line change
@@ Expand Up @@
     }
-    int CudaExecutor::num_execs[max_devices];
+    unsigned CudaExecutor::num_execs[max_devices];
     std::mutex CudaExecutor::mutex[max_devices];
@@ Expand Down @@