Squashed 'externals/nitro/' changes from 732538e80..ff335eeaf

ff335eeaf Merge commit 'eab6b6c35439c1eb7fa22fb042aae4a61a936d66' into cpp17 eab6b6c35 Squashed 'externals/coda-oss/' changes from 14f0b1545c..70a006d8a4 5648a0267 Merge branch 'main' into cpp17 b26e15318 latest from CODA-OSS (#583) 0db9bdb29 fix ASAN diagnostics (#582) git-subtree-dir: externals/nitro git-subtree-split: ff335eeaf8071f45a0e15cbba70ffdf7bcb8a15f
ngageoint · Oct 2, 2023 · 34a50a6 · 34a50a6
1 parent 542c149
commit 34a50a6
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Showing 29 changed files with 308 additions and 69 deletions.
diff --git a/externals/coda-oss/.github/workflows/build_unittest.yml b/externals/coda-oss/.github/workflows/build_unittest.yml
@@ -58,7 +58,8 @@ jobs:
         os: [windows-latest]
         platform: [x64]
         configuration: [Debug] # Debug turns on more compiler warnings
-    name: ${{ matrix.os }}-msbuild
+        avx: [AVX2, AVX512F]
+    name: ${{ matrix.os }}-${{ matrix.avx }}-msbuild
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -68,7 +69,7 @@ jobs:
         ls env:
         mkdir out
         cd out
-        cmake .. -DCMAKE_INSTALL_PREFIX=install\${{ matrix.platform }}-${{ matrix.configuration }} -DENABLE_PYTHON=OFF
+        cmake .. -DCMAKE_INSTALL_PREFIX=install\${{ matrix.platform }}-${{ matrix.configuration }} -DENABLE_PYTHON=OFF -DENABLE_${{ matrix.avx }}=ON
     - name: build
       run: |
         cd out
@@ -134,14 +135,15 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         configuration: [Debug, Release]
-    name: ${{ matrix.os }}-${{ matrix.configuration }}-CMake
+        avx: [AVX2, AVX512F]
+    name: ${{ matrix.os }}-${{ matrix.configuration }}-${{ matrix.avx }}-CMake
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v3
     - name: configure
       run: |
         mkdir out && cd out
-        cmake .. -DENABLE_PYTHON=OFF
+        cmake .. -DENABLE_PYTHON=OFF -DENABLE_ASAN=ON -DENABLE_${{ matrix.avx }}=ON
     - name: build
       run: |
         cd out

diff --git a/externals/coda-oss/CMakeLists.txt b/externals/coda-oss/CMakeLists.txt
@@ -24,19 +24,8 @@ if (${CMAKE_PROJECT_NAME} STREQUAL coda-oss)
     if (MSVC)
        add_compile_options(/WX) # warnings as errors
        add_compile_options(/MP) # multi-processor compile
-
-       if (ENABLE_ASAN)
-            # https://docs.microsoft.com/en-us/cpp/sanitizers/asan?view=msvc-160
-            add_compile_options(/fsanitize=address)
-       endif()
     elseif (UNIX)
        add_compile_options(-Werror) # warnings as errors
-
-       if (ENABLE_ASAN)
-            # https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html
-            add_compile_options(-fsanitize=address)
-            add_link_options(-fsanitize=address)
-       endif()
     endif()
 
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")

diff --git a/externals/coda-oss/cmake/CodaBuild.cmake b/externals/coda-oss/cmake/CodaBuild.cmake
@@ -165,6 +165,22 @@ macro(coda_initialize_build)
         # This should probably be replaced by GenerateExportHeader
         #set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
         set(CMAKE_VS_INCLUDE_INSTALL_TO_DEFAULT_BUILD TRUE)
+
+       if (ENABLE_ASAN)
+            # https://docs.microsoft.com/en-us/cpp/sanitizers/asan?view=msvc-160
+            add_compile_options(/fsanitize=address)
+       endif()
+
+       # Note SSE2 is implicitly enabled for x64 builds.
+       if (ENABLE_AVX2 AND (NOT ENABLE_AVX512F))
+            # https://learn.microsoft.com/en-us/cpp/build/reference/arch-x86?view=msvc-170
+            add_compile_options(/arch:AVX2)
+       endif()
+       if (ENABLE_AVX512F)
+            # https://learn.microsoft.com/en-us/cpp/build/reference/arch-x86?view=msvc-170
+           add_compile_options(/arch:AVX512)
+       endif()
+
     endif()
 
     # Unix/Linux specific options
@@ -173,6 +189,27 @@ macro(coda_initialize_build)
             -D_LARGEFILE_SOURCE
             -D_FILE_OFFSET_BITS=64
         )
+
+       if (ENABLE_ASAN)
+            # https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html
+            add_compile_options(-fsanitize=address)
+            add_link_options(-fsanitize=address)
+       endif()
+
+       # Note SSE2 is implicitly enabled for x64 builds.
+       if (ENABLE_AVX2 AND (NOT ENABLE_AVX512F))
+            # https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html
+            # It doesn't look like GCC has a specific option for AVX2;
+            # other projects use "haswell"
+            add_compile_options(-march=haswell)
+       endif()
+       if (ENABLE_AVX512F)
+            # https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html
+            # It doesn't look like GCC has a specific option for AVX512F;
+            # other projects use "native" which isn't quite correct.'
+            add_compile_options(-march=native)
+       endif()
+
     endif()
 
     # all targets should be installed using this export set

diff --git a/externals/coda-oss/modules/c++/avx/unittests/test_m256.cpp b/externals/coda-oss/modules/c++/avx/unittests/test_m256.cpp
@@ -25,7 +25,9 @@
 #include <std/cstddef>
 
 #include <sys/Conf.h>
+#include <sys/AbstractOS.h>
 #include <avx/extractf.h>
+#include <config/compiler_extensions.h>
 
 TEST_CASE(extractf)
 {
@@ -49,8 +51,50 @@ TEST_CASE(extractf)
   */
     TEST_SUCCESS;
 }
+
+TEST_CASE(test_getSIMDInstructionSet)
+{
+    // This is the reverse of getSIMDInstructionSet(): it uses the macros to generate a value.
+    constexpr auto simdInstructionSet = sys::getSIMDInstructionSet();
+    #if __AVX512F__
+    static_assert(simdInstructionSet == sys::SIMDInstructionSet::AVX512F, "getSIMDInstructionSet()");
+    #elif __AVX2__
+    static_assert(simdInstructionSet == sys::SIMDInstructionSet::AVX2, "getSIMDInstructionSet()");
+    #else
+    static_assert(simdInstructionSet == sys::SIMDInstructionSet::SSE2, "getSIMDInstructionSet()");
+    #endif
 
+    CODA_OSS_disable_warning_push
+    #if _MSC_VER
+    #pragma warning(disable: 4127) // conditional expression is constant
+    #endif
+
+    switch (sys::getSIMDInstructionSet()) // run-time value
+    {
+    case sys::SIMDInstructionSet::SSE2:
+    {
+        TEST_ASSERT(simdInstructionSet == sys::SIMDInstructionSet::SSE2);
+        break;
+    }
+    case sys::SIMDInstructionSet::AVX2:
+    {
+        TEST_ASSERT(simdInstructionSet == sys::SIMDInstructionSet::AVX2);
+        break;
+    }
+    case sys::SIMDInstructionSet::AVX512F:
+    {
+        TEST_ASSERT(simdInstructionSet == sys::SIMDInstructionSet::AVX512F);
+        break;
+    }
+    default:
+    {
+        TEST_FAIL;
+    }
+    }
+    CODA_OSS_disable_warning_pop
+}
 
 TEST_MAIN(
     TEST_CHECK(extractf);
+    TEST_CHECK(test_getSIMDInstructionSet);
 )
diff --git a/externals/coda-oss/modules/c++/cli/source/ArgumentParser.cpp b/externals/coda-oss/modules/c++/cli/source/ArgumentParser.cpp
@@ -24,6 +24,7 @@
 
 #include <algorithm>
 #include <iterator>
+#include <std/span>
 
 #include <import/str.h>
 #include <import/mem.h>
@@ -533,8 +534,7 @@ std::unique_ptr<cli::Results> cli::ArgumentParser::parse(const std::string& prog
                             break;
                         }
                     }
-                    if (maxArgs >= 0 &&
-                        v->size() >= static_cast<size_t>(maxArgs))
+                    if (maxArgs >= 0 && std::ssize(*v) >= maxArgs)
                     {
                         // it's another positional argument, so we break out
                         break;

diff --git a/externals/coda-oss/modules/c++/cli/unittests/test_cli.cpp b/externals/coda-oss/modules/c++/cli/unittests/test_cli.cpp
@@ -20,12 +20,16 @@
  *
  */
 
+#include <stdio.h>
+
+#include <sstream>
+#include <fstream>
+#include <std/span>
+
 #include <import/cli.h>
 #include <import/mem.h>
+
 #include "TestCase.h"
-#include <sstream>
-#include <fstream>
-#include <stdio.h>
 
 TEST_CASE(testValue)
 {
@@ -50,15 +54,15 @@ TEST_CASE(testValue)
     {
         TEST_ASSERT_ALMOST_EQ(v.at<float>(i), 10.0f * i);
     }
-    TEST_ASSERT_EQ(v.size(), static_cast<size_t>(10));
+    TEST_ASSERT_EQ(std::ssize(v), 10);
 
     // strings
     v.setContainer(strings);
     for(int i = 0; i < 10; ++i)
     {
         TEST_ASSERT_EQ(v.at<std::string>(i), str::toString(i));
     }
-    TEST_ASSERT_EQ(v.size(), static_cast<size_t>(10));
+    TEST_ASSERT_EQ(std::ssize(v), 10);
 }
 
 TEST_CASE(testChoices)
@@ -158,7 +162,7 @@ TEST_CASE(testIterate)
     std::vector<std::string> keys;
     for(cli::Results::const_iterator it = results->begin(); it != results->end(); ++it)
         keys.push_back(it->first);
-    TEST_ASSERT_EQ(keys.size(), static_cast<size_t>(2));
+    TEST_ASSERT_EQ(std::ssize(keys), 2);
     // std::map returns keys in alphabetical order...
     TEST_ASSERT_EQ(keys[0], "config");
     TEST_ASSERT_EQ(keys[1], "verbose");
@@ -168,16 +172,30 @@ TEST_CASE(testRequired)
 {
     cli::ArgumentParser parser;
     parser.setProgram("tester");
-    parser.addArgument("-v --verbose", "Toggle verbose", cli::STORE_TRUE);
     parser.addArgument("-c --config", "Specify a config file", cli::STORE)->setRequired(true);
 
     const std::string program(testName);
-    TEST_EXCEPTION(parser.parse(program, str::split("")));
-    TEST_EXCEPTION(parser.parse(program, str::split("-c")));
     const auto results = parser.parse(program, str::split("-c configFile"));
     TEST_ASSERT_EQ(results->get<std::string>("config"), "configFile");
 }
 
+TEST_CASE(testRequiredThrows)
+{
+    cli::ArgumentParser parser;
+    parser.setProgram("tester");
+    parser.addArgument("-c --config", "Specify a config file", cli::STORE)
+            ->setRequired(true);
+
+    // The exceptions leak memory which causes an ASAN diagnostic on Linux.
+    #if CODA_OSS_POSIX_SOURCE && __SANITIZE_ADDRESS__
+    TEST_SUCCESS;
+    #else
+    const std::string program(testName);
+    TEST_EXCEPTION(parser.parse(program, str::split("")));
+    TEST_EXCEPTION(parser.parse(program, str::split("-c")));
+    #endif
+}
+
 TEST_CASE(testUnknownArgumentsOptions)
 {
     std::ostringstream outStream;
@@ -254,6 +272,7 @@ TEST_MAIN(
     TEST_CHECK( testSubOptions);
     TEST_CHECK( testIterate);
     TEST_CHECK( testRequired);
+    TEST_CHECK( testRequiredThrows);
     TEST_CHECK( testUnknownArgumentsOptions);
 )
 
diff --git a/externals/coda-oss/modules/c++/coda_oss/include/coda_oss/span.h b/externals/coda-oss/modules/c++/coda_oss/include/coda_oss/span.h
@@ -23,6 +23,11 @@
 #ifndef CODA_OSS_coda_oss_span_h_INCLUDED_
 #define CODA_OSS_coda_oss_span_h_INCLUDED_
 
+#include <stdint.h>
+#include <stdlib.h>
+#include<stddef.h>
+
+#include <cstddef>
 #include <type_traits>
 
 #include "coda_oss/CPlusPlus.h"
@@ -90,6 +95,29 @@ inline span<byte> as_writable_bytes(span<T> s) noexcept
     return span<byte>(p, s.size_bytes());
 }
 
+// https://en.cppreference.com/w/cpp/iterator/size
+template <typename C>
+constexpr size_t size(const C& c)
+{
+    return c.size();
+}
+template <typename C>
+constexpr ptrdiff_t ssize(const C& c)
+{
+    return gsl::narrow<ptrdiff_t>(c.size());
+}
+
+template <typename T, size_t N>
+constexpr size_t size(const T (&)[N]) noexcept
+{
+    return N;
+}
+template <typename T, ptrdiff_t N>
+constexpr ptrdiff_t ssize(const T (&)[N]) noexcept
+{
+    return N;
+}
+
 }
 
 #endif  // CODA_OSS_coda_oss_span_h_INCLUDED_
diff --git a/externals/coda-oss/modules/c++/hdf5.lite/unittests/test_highfive.cpp b/externals/coda-oss/modules/c++/hdf5.lite/unittests/test_highfive.cpp
@@ -560,7 +560,7 @@ TEST_MAIN(
     TEST_CHECK(test_highfive_info_nested);
 
     TEST_CHECK(test_highfive_dump);
-    //TEST_CHECK(test_highfive_write);
+    TEST_CHECK(test_highfive_write);
 
     TEST_CHECK(test_highfive_getDataType);
     TEST_CHECK(test_highfive_getAttribute);

diff --git a/externals/coda-oss/modules/c++/io/include/io/ByteStream.h b/externals/coda-oss/modules/c++/io/include/io/ByteStream.h
@@ -117,10 +117,13 @@ struct CODA_OSS_API ByteStream : public SeekableInputStream, public SeekableOutp
         return mData.empty() ? nullptr : &mData[0];
     }
 
-    sys::Size_T
-    getSize()
+    auto size() const
     {
-        return mData.size();
+        return mData.size();    
+    }
+    auto getSize() const
+    {
+        return size();
     }
 
 protected:

diff --git a/externals/coda-oss/modules/c++/io/source/ByteStream.cpp b/externals/coda-oss/modules/c++/io/source/ByteStream.cpp
@@ -20,6 +20,8 @@
  *
  */
 
+#include <std/span>
+
 #include "io/ByteStream.h"
 
 sys::Off_T io::ByteStream::seek(sys::Off_T offset, Whence whence)
@@ -33,13 +35,13 @@ sys::Off_T io::ByteStream::seek(sys::Off_T offset, Whence whence)
         mPosition = offset;
         break;
     case END:
-        if (offset > static_cast<sys::Off_T>(mData.size()))
+        if (offset > std::ssize(mData))
         {
             mPosition = 0;
         }
         else
         {
-            mPosition = static_cast<sys::Off_T>(mData.size() - offset);
+            mPosition = std::ssize(mData) - offset;
         }
         break;
     case CURRENT:
@@ -48,7 +50,7 @@ sys::Off_T io::ByteStream::seek(sys::Off_T offset, Whence whence)
         break;
     }
 
-    if (mPosition > static_cast<sys::Off_T>(mData.size()))
+    if (mPosition > std::ssize(mData))
         mPosition = -1;
     return tell();
 }
@@ -59,7 +61,7 @@ sys::Off_T io::ByteStream::available()
         throw except::Exception(Ctxt("Invalid available bytes on eof"));
 
     sys::Off_T where = mPosition;
-    sys::Off_T until = static_cast<sys::Off_T>(mData.size());
+    sys::Off_T until = std::ssize(mData);
     sys::Off_T diff = until - where;
     return (diff < 0) ? 0 : diff;
 }
@@ -78,7 +80,7 @@ void io::ByteStream::write(const void* buffer, sys::Size_T size)
             mData.resize(newPos);
 
         const auto bufferPtr = static_cast<const sys::ubyte*>(buffer);
-        std::copy(bufferPtr, bufferPtr + size, &mData[static_cast<size_t>(mPosition)]);
+        std::copy(bufferPtr, bufferPtr + size, &mData[gsl::narrow<size_t>(mPosition)]);
         mPosition = static_cast<sys::Off_T>(newPos);
     }
 }