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Minor Release v1.1.1
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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](#406)),
+ Fix some documentation issues ([#406](#406)),
+ Fix multiple code issues reported by sonarqube ([#406](#406)),
+ Update the git-cmake-format repository ([#399](#399)),
+ Improve the global update header script ([#390](#390)),
+ Fix broken bounds checks ([#388](#388)),
+ Fix CSR strategies and improve performance ([#379](#379)),
+ Fix a small typo in the stencil examples ([#381](#381)),
+ Fix ELL error on small matrices ([#375](#375)),
+ Fix SellP read function ([#374](#374)),
+ Add factorization support in `create_new_algorithm.sh`  ([#371](#371)).
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tcojean authored Dec 2, 2019
2 parents b9bec82 + c8ec186 commit 08d2c52
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2 changes: 2 additions & 0 deletions .gitlab-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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17 changes: 17 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
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6 changes: 4 additions & 2 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -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})

Expand Down Expand Up @@ -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})
Expand All @@ -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.")
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15 changes: 11 additions & 4 deletions cmake/GinkgoConfig.cmake.in
Original file line number Diff line number Diff line change
Expand Up @@ -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@")
Expand All @@ -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@")
Expand Down Expand Up @@ -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.

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47 changes: 24 additions & 23 deletions cmake/Modules/FindPAPI.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -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()
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2 changes: 1 addition & 1 deletion cmake/build_helpers.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -94,4 +94,4 @@ endmacro()

macro(ginkgo_switch_to_windows_dynamic lang)
ginkgo_switch_windows_link(${lang} "MT" "MD")
endmacro()
endmacro()
4 changes: 4 additions & 0 deletions cmake/install_helpers.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
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6 changes: 3 additions & 3 deletions core/device_hooks/cuda_hooks.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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"};
}


Expand Down
6 changes: 3 additions & 3 deletions core/device_hooks/omp_hooks.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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"};
}


Expand Down
6 changes: 3 additions & 3 deletions core/device_hooks/reference_hooks.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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"};
}


Expand Down
2 changes: 1 addition & 1 deletion core/devices/cuda/executor.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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];
Expand Down
10 changes: 8 additions & 2 deletions core/matrix/coo.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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);
}

Expand All @@ -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);
}

Expand Down
21 changes: 15 additions & 6 deletions core/matrix/dense.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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);
}
}


Expand Down
5 changes: 3 additions & 2 deletions core/matrix/ell.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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);
}

Expand Down
10 changes: 6 additions & 4 deletions core/matrix/hybrid.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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);
}

Expand All @@ -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;
Expand Down
17 changes: 9 additions & 8 deletions core/matrix/sellp.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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] =
Expand Down Expand Up @@ -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);
}

Expand Down
14 changes: 13 additions & 1 deletion core/test/base/exception_helpers.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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)
{
Expand Down Expand Up @@ -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(
Expand Down
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