Unverified Commit 11f6da93 authored by Eisenhauer, Greg's avatar Eisenhauer, Greg Committed by GitHub
Browse files

Merge pull request #4971 from eisenhauer/backport-bp5-compress-fix 

Fix BP5 when compression is applied to memory selections (Release Branch)
parents 96885c7a 6d539cdf

source/adios2/engine/bp5/BP5Writer.cpp

+34 −12
Original line number Diff line number Diff line
@@ -2622,13 +2622,6 @@ void BP5Writer::PutCommon(VariableBase &variable, const void *values, bool sync) 


        int DimCount = (int)variable.m_Count.size();

        helper::DimsArray ZeroDims(DimCount, (size_t)0);

        // get a temporary span then fill with memselection now

        format::BufferV::BufferPos bp5span(0, 0, 0);



        m_BP5Serializer.Marshal((void *)&variable, variable.m_Name.c_str(), variable.m_Type,

                                variable.m_ElementSize, DimCount, Shape, Count, Start, nullptr,

                                false, &bp5span);

        void *ptr = m_BP5Serializer.GetPtr(bp5span.bufferIdx, bp5span.posInBuffer);



        if (!sourceRowMajor)

        {
@@ -2636,11 +2629,40 @@ void BP5Writer::PutCommon(VariableBase &variable, const void *values, bool sync) 
            std::reverse(MemoryCount.begin(), MemoryCount.end());

            std::reverse(varCount.begin(), varCount.end());

        }



        if (!variable.m_Operations.empty())

        {

            // Compression needs contiguous data upfront, so copy the

            // selected sub-region into a temp buffer first, then let

            // Marshal compress from it via the normal data path.

            size_t n = helper::GetTotalSize(variable.m_Count) * ObjSize;

            std::vector<char> tmpBuf(n);



            helper::NdCopy((const char *)values, helper::CoreDims(ZeroDims), MemoryCount,

                           sourceRowMajor, false, tmpBuf.data(), MemoryStart, varCount,

                           sourceRowMajor, false, (int)ObjSize, helper::CoreDims(),

                           helper::CoreDims(), helper::CoreDims(), helper::CoreDims(),

                           false /* safemode */, memSpace, /* duringWrite */ true);

            m_BP5Serializer.Marshal((void *)&variable, variable.m_Name.c_str(), variable.m_Type,

                                    variable.m_ElementSize, DimCount, Shape, Count, Start,

                                    tmpBuf.data(), sync, nullptr);

        }

        else

        {

            // No compression: allocate space in the output buffer via span,

            // then NdCopy directly into it (avoids an extra copy).

            format::BufferV::BufferPos bp5span(0, 0, 0);

            m_BP5Serializer.Marshal((void *)&variable, variable.m_Name.c_str(), variable.m_Type,

                                    variable.m_ElementSize, DimCount, Shape, Count, Start, nullptr,

                                    false, &bp5span);

            void *ptr = m_BP5Serializer.GetPtr(bp5span.bufferIdx, bp5span.posInBuffer);



            helper::NdCopy((const char *)values, helper::CoreDims(ZeroDims), MemoryCount,

                       sourceRowMajor, false, (char *)ptr, MemoryStart, varCount, sourceRowMajor,

                       false, (int)ObjSize, helper::CoreDims(), helper::CoreDims(),

                       helper::CoreDims(), helper::CoreDims(), false /* safemode */, memSpace,

                       /* duringWrite */ true);

                           sourceRowMajor, false, (char *)ptr, MemoryStart, varCount,

                           sourceRowMajor, false, (int)ObjSize, helper::CoreDims(),

                           helper::CoreDims(), helper::CoreDims(), helper::CoreDims(),

                           false /* safemode */, memSpace, /* duringWrite */ true);

        }

    }

    else

    {

source/adios2/toolkit/format/bp5/BP5Deserializer.cpp

+1 −1
Original line number Diff line number Diff line
@@ -2276,7 +2276,7 @@ void BP5Deserializer::FinalizeGet(const ReadRequest &Read, const bool freeAddr) 
        const Box<Dims> BlockBox = helper::StartEndBox(Dims(inStart.begin(), inStart.end()),

                                                       Dims(inCount.begin(), inCount.end()));

        const Box<Dims> IntersectionBox = helper::IntersectionBox(selectionBox, BlockBox);

        VirtualIncomingData = Read.DestinationAddr; //  Don't do the fake offset thing

        VirtualIncomingData = IncomingData; //  Don't do the fake offset thing

        helper::DimsArray intersectStart(IntersectionBox.first);

        helper::DimsArray intersectCount(IntersectionBox.second);

        helper::DimsArray blockStart(BlockBox.first);

testing/adios2/engine/bp/operations/TestBPWriteReadSZ.cpp

+120 −0
Original line number Diff line number Diff line
@@ -1020,6 +1020,125 @@ void SZAccuracy2DSmallSel(const std::string accuracy) 
#endif

}



void SZMemorySelection3D(const std::string accuracy)

{

    // BP3/BP4 don't support compression + MemorySelection

    if (engineName == "BP3" || engineName == "BP4")

        GTEST_SKIP();



    // Write a 3D sub-region from a larger in-memory buffer (with ghost cells)

    // using SetMemorySelection + compression. Verifies that compression

    // works correctly with strided memory layouts (GitHub issue #4965).



    const size_t Nx = 10, Ny = 12, Nz = 8;

    const size_t ghost = 1;

    const size_t Mx = Nx + 2 * ghost;

    const size_t My = Ny + 2 * ghost;

    const size_t Mz = Nz + 2 * ghost;



    // Fill the interior of a halo'd buffer with known values.

    // Buffer layout is row-major with dims {Mx, My, Mz}: index = (i*My + j)*Mz + k

    std::vector<double> full(Mx * My * Mz, -1.0);

    for (size_t i = ghost; i < Nx + ghost; ++i)

        for (size_t j = ghost; j < Ny + ghost; ++j)

            for (size_t k = ghost; k < Nz + ghost; ++k)

                full[(i * My + j) * Mz + k] = static_cast<double>(i + j * Nx + k * Nx * Ny);



#if ADIOS2_USE_MPI

    const std::string fname("BPWRSZ3DMemSel_" + accuracy + "_MPI.bp");

    adios2::ADIOS adios(MPI_COMM_WORLD);

#else

    const std::string fname("BPWRSZ3DMemSel_" + accuracy + ".bp");

    adios2::ADIOS adios;

#endif

    {

        adios2::IO io = adios.DeclareIO("TestIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        auto var = io.DefineVariable<double>("data", {Nx, Ny, Nz}, {0, 0, 0}, {Nx, Ny, Nz},

                                             adios2::ConstantDims);



        adios2::Operator szOp = adios.DefineOperator("szCompressor", adios2::ops::LossySZ);

        var.AddOperation(szOp, {{adios2::ops::sz::key::accuracy, accuracy}});



        var.SetMemorySelection({{ghost, ghost, ghost}, {Mx, My, Mz}});



        adios2::Engine writer = io.Open(fname, adios2::Mode::Write);

        writer.BeginStep();

        writer.Put(var, full.data(), adios2::Mode::Sync);

        writer.EndStep();

        writer.Close();

    }



    auto checkInterior = [&](const std::vector<double> &result, const double tol) {

        for (size_t i = 0; i < Nx; ++i)

            for (size_t j = 0; j < Ny; ++j)

                for (size_t k = 0; k < Nz; ++k)

                {

                    double expected =

                        static_cast<double>((i + ghost) + (j + ghost) * Nx + (k + ghost) * Nx * Ny);

                    size_t idx = (i * Ny + j) * Nz + k;

                    ASSERT_NEAR(result[idx], expected, tol)

                        << "Mismatch at (" << i << "," << j << "," << k << ")";

                }

    };



    // Read back into a contiguous buffer (verify write path)

    {

        adios2::IO io = adios.DeclareIO("ReadIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        adios2::Engine reader = io.Open(fname, adios2::Mode::Read);

        reader.BeginStep();

        auto var = io.InquireVariable<double>("data");

        ASSERT_TRUE(var);

        ASSERT_EQ(var.Shape().size(), 3);

        ASSERT_EQ(var.Shape()[0], Nx);

        ASSERT_EQ(var.Shape()[1], Ny);

        ASSERT_EQ(var.Shape()[2], Nz);



        std::vector<double> result(Nx * Ny * Nz);

        reader.Get(var, result.data(), adios2::Mode::Sync);

        reader.EndStep();

        reader.Close();



        checkInterior(result, std::stod(accuracy));

    }



    // Read back with MemorySelection into a halo'd buffer (verify read path)

    {

        adios2::IO io = adios.DeclareIO("ReadMemSelIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        adios2::Engine reader = io.Open(fname, adios2::Mode::Read);

        reader.BeginStep();

        auto var = io.InquireVariable<double>("data");

        ASSERT_TRUE(var);



        const size_t Rx = Nx + 2 * ghost;

        const size_t Ry = Ny + 2 * ghost;

        const size_t Rz = Nz + 2 * ghost;

        std::vector<double> readBuf(Rx * Ry * Rz, -1.0);

        var.SetMemorySelection({{ghost, ghost, ghost}, {Rx, Ry, Rz}});

        reader.Get(var, readBuf.data(), adios2::Mode::Sync);

        reader.EndStep();

        reader.Close();



        // Extract interior from the halo'd read buffer into a contiguous buffer

        std::vector<double> result(Nx * Ny * Nz);

        for (size_t i = 0; i < Nx; ++i)

            for (size_t j = 0; j < Ny; ++j)

                for (size_t k = 0; k < Nz; ++k)

                    result[(i * Ny + j) * Nz + k] =

                        readBuf[((i + ghost) * Ry + (j + ghost)) * Rz + (k + ghost)];



        checkInterior(result, std::stod(accuracy));

    }

}



class BPWriteReadSZ : public ::testing::TestWithParam<std::string>

{

public:
@@ -1035,6 +1154,7 @@ TEST_P(BPWriteReadSZ, BPWRSZ1DSel) { SZAccuracy1DSel(GetParam()); } 
TEST_P(BPWriteReadSZ, BPWRSZ2DSel) { SZAccuracy2DSel(GetParam()); }

TEST_P(BPWriteReadSZ, BPWRSZ3DSel) { SZAccuracy3DSel(GetParam()); }

TEST_F(BPWriteReadSZ, BPWRSZ2DSmallSel) { SZAccuracy2DSmallSel("0.01"); }

TEST_F(BPWriteReadSZ, BPWRSZ3DMemSel) { SZMemorySelection3D("0.01"); }



INSTANTIATE_TEST_SUITE_P(SZAccuracy, BPWriteReadSZ,

                         ::testing::Values("0.01", "0.001", "0.0001", "0.00001"));

testing/adios2/engine/bp/operations/TestBPWriteReadSZ3.cpp

+116 −0
Original line number Diff line number Diff line
@@ -388,6 +388,121 @@ void SZ3Accuracy2D(const std::string accuracy) 
#endif

}



void SZ3MemorySelection3D(const std::string accuracy)

{

    // BP3/BP4 don't support compression + MemorySelection

    if (engineName == "BP3" || engineName == "BP4")

        GTEST_SKIP();



    // Write a 3D sub-region from a larger in-memory buffer (with ghost cells)

    // using SetMemorySelection + compression. Then read back both with and

    // without MemorySelection. (GitHub issue #4965)



    const size_t Nx = 10, Ny = 12, Nz = 8;

    const size_t ghost = 1;

    const size_t Mx = Nx + 2 * ghost;

    const size_t My = Ny + 2 * ghost;

    const size_t Mz = Nz + 2 * ghost;



    // Fill the interior of a halo'd buffer with known values.

    // Buffer layout is row-major with dims {Mx, My, Mz}: index = (i*My + j)*Mz + k

    std::vector<double> full(Mx * My * Mz, -1.0);

    for (size_t i = ghost; i < Nx + ghost; ++i)

        for (size_t j = ghost; j < Ny + ghost; ++j)

            for (size_t k = ghost; k < Nz + ghost; ++k)

                full[(i * My + j) * Mz + k] = static_cast<double>(i + j * Nx + k * Nx * Ny);



#if ADIOS2_USE_MPI

    const std::string fname("BPWRSZ3_3DMemSel_" + accuracy + "_MPI.bp");

    adios2::ADIOS adios(MPI_COMM_WORLD);

#else

    const std::string fname("BPWRSZ3_3DMemSel_" + accuracy + ".bp");

    adios2::ADIOS adios;

#endif

    {

        adios2::IO io = adios.DeclareIO("TestIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        auto var = io.DefineVariable<double>("data", {Nx, Ny, Nz}, {0, 0, 0}, {Nx, Ny, Nz},

                                             adios2::ConstantDims);



        adios2::Operator sz3Op = adios.DefineOperator("sz3Compressor", "sz3");

        var.AddOperation(sz3Op, {{"accuracy", accuracy}});



        var.SetMemorySelection({{ghost, ghost, ghost}, {Mx, My, Mz}});



        adios2::Engine writer = io.Open(fname, adios2::Mode::Write);

        writer.BeginStep();

        writer.Put(var, full.data(), adios2::Mode::Sync);

        writer.EndStep();

        writer.Close();

    }



    auto checkInterior = [&](const std::vector<double> &result, const double tol) {

        for (size_t i = 0; i < Nx; ++i)

            for (size_t j = 0; j < Ny; ++j)

                for (size_t k = 0; k < Nz; ++k)

                {

                    double expected =

                        static_cast<double>((i + ghost) + (j + ghost) * Nx + (k + ghost) * Nx * Ny);

                    size_t idx = (i * Ny + j) * Nz + k;

                    ASSERT_NEAR(result[idx], expected, tol)

                        << "Mismatch at (" << i << "," << j << "," << k << ")";

                }

    };



    // Read back into a contiguous buffer (verify write path)

    {

        adios2::IO io = adios.DeclareIO("ReadIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        adios2::Engine reader = io.Open(fname, adios2::Mode::Read);

        reader.BeginStep();

        auto var = io.InquireVariable<double>("data");

        ASSERT_TRUE(var);



        std::vector<double> result(Nx * Ny * Nz);

        reader.Get(var, result.data(), adios2::Mode::Sync);

        reader.EndStep();

        reader.Close();



        checkInterior(result, std::stod(accuracy));

    }



    // Read back with MemorySelection into a halo'd buffer (verify read path)

    {

        adios2::IO io = adios.DeclareIO("ReadMemSelIO");

        if (!engineName.empty())

            io.SetEngine(engineName);



        adios2::Engine reader = io.Open(fname, adios2::Mode::Read);

        reader.BeginStep();

        auto var = io.InquireVariable<double>("data");

        ASSERT_TRUE(var);



        const size_t Rx = Nx + 2 * ghost;

        const size_t Ry = Ny + 2 * ghost;

        const size_t Rz = Nz + 2 * ghost;

        std::vector<double> readBuf(Rx * Ry * Rz, -1.0);

        var.SetMemorySelection({{ghost, ghost, ghost}, {Rx, Ry, Rz}});

        reader.Get(var, readBuf.data(), adios2::Mode::Sync);

        reader.EndStep();

        reader.Close();



        // Extract interior from the halo'd read buffer into a contiguous buffer

        std::vector<double> result(Nx * Ny * Nz);

        for (size_t i = 0; i < Nx; ++i)

            for (size_t j = 0; j < Ny; ++j)

                for (size_t k = 0; k < Nz; ++k)

                    result[(i * Ny + j) * Nz + k] =

                        readBuf[((i + ghost) * Ry + (j + ghost)) * Rz + (k + ghost)];



        checkInterior(result, std::stod(accuracy));

    }

}



class BPWriteReadSZ3 : public ::testing::TestWithParam<std::string>

{

public:
@@ -398,6 +513,7 @@ public: 


TEST_P(BPWriteReadSZ3, BPWRSZ3_1D) { SZ3Accuracy1D(GetParam()); }

TEST_P(BPWriteReadSZ3, BPWRSZ3_2D) { SZ3Accuracy2D(GetParam()); }

TEST_F(BPWriteReadSZ3, BPWRSZ3_3DMemSel) { SZ3MemorySelection3D("0.01"); }



INSTANTIATE_TEST_SUITE_P(SZ3Accuracy, BPWriteReadSZ3, ::testing::Values("0.01", "0.001", "0.0001"));