Fix posix transport offset (#4603)

* ignore build.*/

* Fix wrong offset in POSIX transport when reading a block of >2147381248 bytes.

* fix

Author: pnorbert

.gitignore

@@ -47,8 +47,9 @@ CMakeSettings.json
 
 # CMake generated files
 build/
+build.*/
 .idea/
 .vscode/
 
 # redis dump files
-*.rdb
+*.rdb

source/adios2/toolkit/transport/file/FilePOSIX.cpp

@@ -514,7 +514,7 @@ void FilePOSIX::Read(char *buffer, size_t size, size_t start)
             position += DefaultMaxFileBatchSize;
             start += DefaultMaxFileBatchSize;
         }
-        lf_PRead(&buffer[position], remainder, position);
+        lf_PRead(&buffer[position], remainder, start);
     }
     else
     {

testing/adios2/engine/bp/CMakeLists.txt

@@ -104,6 +104,7 @@ bp_gtest_add_tests_helper(WriteReadADIOS2 MPI_ALLOW)
 async_gtest_add_tests_helper(WriteReadADIOS2 MPI_ALLOW)
 
 gtest_add_tests_helper(WriteReadFlatten MPI_ONLY BP Engine.BP. .BP5 WORKING_DIRECTORY ${BP5_DIR} EXTRA_ARGS "BP5" )
+gtest_add_tests_helper(LargeBlocks MPI_NONE BP Engine.BP. .BP5 WORKING_DIRECTORY ${BP5_DIR} EXTRA_ARGS "BP5" )
 
 bp_gtest_add_tests_helper(WriteReadADIOS2fstream MPI_ALLOW)
 bp_gtest_add_tests_helper(WriteReadADIOS2stdio MPI_ALLOW)

testing/adios2/engine/bp/TestBPLargeBlocks.cpp

@@ -0,0 +1,137 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * TestLargeBlocks.cpp :
+ *
+ *  Created on: Aug 5, 2025
+ *      Author: Norbert Podhorszki
+ */
+
+#include <cstdint>
+#include <cstring>
+
+#include <iostream>
+#include <stdexcept>
+
+#include <adios2.h>
+
+#include <gtest/gtest.h>
+
+std::string engineName; // comes from command line
+
+class LargeBlocks : public ::testing::Test
+{
+public:
+    LargeBlocks() = default;
+};
+
+constexpr size_t DefaultMaxFileBatchSize = 2147381248;
+
+TEST_F(LargeBlocks, MultiBlock)
+{
+    // Write a small variable
+    // Write a large (>2147381248 bytes) so that it's offset is >0 in the file.
+    // Read the large variable back and confirm that the data on the
+    // chunk boundary of 2147381248 bytes is correct.
+    // Testing if the POSIX reader transport is reading in chunks of 2147381248
+    // bytes correctly (from the correct offsets)
+
+    adios2::ADIOS adios;
+
+    const std::string fname = "LargeBlocks.bp";
+    size_t NX = DefaultMaxFileBatchSize / 4 +
+                1024; // data must be > 2147381248 bytes to test chunked writing/reading
+
+    std::vector<uint32_t> LargeData(NX);
+    uint32_t myvalue = 0;
+    for (size_t n = 0; n < NX; ++n)
+    {
+        LargeData[n] = myvalue++;
+    }
+
+    // Writer
+    {
+        adios2::IO outIO = adios.DeclareIO("Output");
+        if (!engineName.empty())
+        {
+            outIO.SetEngine(engineName);
+        }
+        adios2::Engine writer = outIO.Open(fname, adios2::Mode::Write);
+        auto varSmall = outIO.DefineVariable<uint32_t>("small", {2000}, {0}, {2000});
+        auto varLarge = outIO.DefineVariable<uint32_t>("large", {NX}, {0}, {NX});
+
+        std::cout << "Writing to " << fname << std::endl;
+        writer.BeginStep();
+        writer.Put(varSmall, LargeData.data(), adios2::Mode::Deferred);
+        writer.Put(varLarge, LargeData.data(), adios2::Mode::Deferred);
+        writer.EndStep();
+        writer.Close();
+    }
+
+    // Reader with streaming
+    {
+        adios2::IO inIO = adios.DeclareIO("Input");
+        if (!engineName.empty())
+        {
+            inIO.SetEngine(engineName);
+        }
+        adios2::Engine reader = inIO.Open(fname, adios2::Mode::ReadRandomAccess);
+        std::cout << "Reading as stream with BeginStep/EndStep:" << std::endl;
+
+        auto varLarge = inIO.InquireVariable<uint32_t>("large");
+        EXPECT_TRUE(varLarge);
+        std::cout << " large data shape " << varLarge.Shape()[0] << std::endl;
+
+        varLarge.SetSelection({{0}, {NX}});
+        std::vector<uint32_t> data(NX);
+        reader.Get(varLarge, data.data());
+        reader.PerformGets();
+
+        size_t TestOffset = DefaultMaxFileBatchSize / 4;
+        std::cout << "large data from " << TestOffset - 10 << ":" << std::endl;
+        std::cout << "  written: " << std::endl;
+        for (size_t i = TestOffset - 10; i < TestOffset + 10; ++i)
+        {
+            std::cout << static_cast<int>(LargeData[i]) << " ";
+        }
+        std::cout << std::endl;
+        std::cout << "  read: " << std::endl;
+        for (size_t i = TestOffset - 10; i < TestOffset + 10; ++i)
+        {
+            std::cout << static_cast<int>(data[i]) << " ";
+        }
+        std::cout << std::endl;
+        for (size_t i = TestOffset - 10; i < TestOffset + 10; ++i)
+        {
+            EXPECT_EQ(data[i], LargeData[i]);
+        }
+        reader.Close();
+    }
+}
+
+int main(int argc, char **argv)
+{
+#if ADIOS2_USE_MPI
+    int provided;
+
+    // MPI_THREAD_MULTIPLE is only required if you enable the SST MPI_DP
+    MPI_Init_thread(nullptr, nullptr, MPI_THREAD_MULTIPLE, &provided);
+#endif
+
+    int result;
+    ::testing::InitGoogleTest(&argc, argv);
+
+    if (argc > 1)
+    {
+        engineName = std::string(argv[1]);
+    }
+
+    result = RUN_ALL_TESTS();
+
+#if ADIOS2_USE_MPI
+    MPI_Finalize();
+#endif
+
+    return result;
+}