Testing writing null blocks without affecting the read

testing/adios2/engine/bp/TestBPWriteReadMultiblock.cpp

@@ -2093,6 +2093,139 @@ TEST_F(BPWriteReadMultiblockTest, MultiblockPerformDataWrite)
     }
 }
 
+//******************************************************************************
+// Test reading data where some processes do not contribute to the data
+// and some blocks are null
+//******************************************************************************
+
+TEST_F(BPWriteReadMultiblockTest, MultiblockNullBlocks)
+{
+    // Each process would write a 2x8 array and all processes would
+    // form a mpiSize * Nx 1D array
+    const std::string fname("MultiblockNullBlocks.bp");
+
+    int mpiRank = 0, mpiSize = 1;
+    // Number of elements per blocks (blocksize)
+    const size_t Nx = 8;
+    // Number of blocks per process (= number of flushes)
+    const size_t Nblocks = 3;
+    // Number of steps
+    const size_t NSteps = 3;
+
+#if ADIOS2_USE_MPI
+    MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+    MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+#endif
+
+#if ADIOS2_USE_MPI
+    adios2::ADIOS adios(MPI_COMM_WORLD);
+#else
+    adios2::ADIOS adios;
+#endif
+    /* Write */
+    {
+        adios2::IO io = adios.DeclareIO("TestIO");
+        adios2::Dims shape{static_cast<size_t>(mpiSize), static_cast<size_t>(Nx * (Nblocks - 1))};
+        adios2::Dims start{static_cast<size_t>(mpiRank), 0};
+        adios2::Dims count{1, Nx};
+
+        auto var_i32 = io.DefineVariable<int32_t>("i32", shape, start, count);
+
+        if (!engineName.empty())
+        {
+            io.SetEngine(engineName);
+        }
+
+        adios2::Engine bpWriter = io.Open(fname, adios2::Mode::Write);
+
+        for (size_t step = 0; step < NSteps; ++step)
+        {
+            bpWriter.BeginStep();
+
+            size_t nb = 0;
+            for (size_t b = 0; b < Nblocks; ++b)
+            {
+                // Generate test data for each process / block uniquely
+                int t = static_cast<int>(step * Nblocks + b);
+                SmallTestData currentTestData =
+                    generateNewSmallTestData(m_TestData, t, mpiRank, mpiSize);
+
+                // the first block does not contribute to the variable's data
+                if (b == 0)
+                {
+                    std::array<int32_t, Nx> I32_empty;
+                    var_i32.SetSelection(
+                        adios2::Box<adios2::Dims>({(size_t)mpiRank, b * Nx}, {0, 0}));
+                    bpWriter.Put(var_i32, I32_empty.data());
+                }
+                else
+                {
+                    ++nb;
+                    start = {static_cast<size_t>(mpiRank), static_cast<size_t>(Nx * (nb - 1))};
+                    count = {1, Nx};
+                    var_i32.SetSelection({start, count});
+                    bpWriter.Put(var_i32, currentTestData.I32.data(), adios2::Mode::Sync);
+                }
+
+                bpWriter.PerformDataWrite();
+            }
+            bpWriter.EndStep();
+        }
+        bpWriter.Close();
+    }
+    // Read and check correctness
+    {
+        adios2::IO io = adios.DeclareIO("ReadIO");
+
+        if (!engineName.empty())
+        {
+            io.SetEngine(engineName);
+        }
+
+        adios2::Engine bpReader = io.Open(fname, adios2::Mode::ReadRandomAccess);
+
+        auto var_i32 = io.InquireVariable<int32_t>("i32");
+        EXPECT_TRUE(var_i32);
+        EXPECT_EQ(var_i32.ShapeID(), adios2::ShapeID::GlobalArray);
+        EXPECT_EQ(var_i32.Steps(), NSteps);
+        EXPECT_EQ(var_i32.Shape()[0], mpiSize);
+        EXPECT_EQ(var_i32.Shape()[1], Nx * (Nblocks - 1));
+
+        SmallTestData testData;
+        std::array<int32_t, Nx> I32;
+
+        const auto i32AllInfo = bpReader.AllStepsBlocksInfo(var_i32);
+        EXPECT_EQ(i32AllInfo.size(), NSteps);
+
+        for (size_t step = 0; step < NSteps; step++)
+        {
+            var_i32.SetStepSelection({step, 1});
+            for (size_t b = 1; b < Nblocks; ++b)
+            {
+                std::cout << "Read step " << step << " block=" << b << std::endl;
+                // Generate test data for each process / block uniquely
+                int t = static_cast<int>(step * Nblocks + b);
+                SmallTestData currentTestData =
+                    generateNewSmallTestData(m_TestData, t, mpiRank, mpiSize);
+
+                // Block 0 was not written so all blocks are shifted back
+                const adios2::Box<adios2::Dims> sel({(size_t)mpiRank, (b - 1) * Nx}, {1, Nx});
+                var_i32.SetSelection(sel);
+                bpReader.Get(var_i32, I32.data(), adios2::Mode::Sync);
+
+                for (size_t i = 0; i < Nx; ++i)
+                {
+                    std::stringstream ss;
+                    ss << "step=" << step << " block=" << b << " i=" << i << " rank=" << mpiRank;
+                    std::string msg = ss.str();
+                    EXPECT_EQ(I32[i], currentTestData.I32[i]) << msg;
+                }
+            }
+        }
+        bpReader.Close();
+    }
+}
+
 //******************************************************************************
 // main
 //******************************************************************************

testing/adios2/engine/bp/operations/TestBPWriteReadBlosc2.cpp

@@ -858,6 +858,119 @@ void Blosc2Accuracy3DSel(const std::string accuracy, const std::string threshold
     }
 }
 
+void Blosc2NullBlocks(const std::string accuracy, const std::string threshold,
+                      const std::string doshuffle)
+{
+    // Null blocks only work for BP4 and BP5
+    if (engineName == "BP3")
+        return;
+
+    // Each process would write a 1x8 array and all processes would
+    // form a mpiSize * Nx 1D array
+    const std::string fname("BPWRBlosc2NullBlock_" + accuracy + "_" + threshold + threshold + "_" +
+                            doshuffle + ".bp");
+
+    int mpiRank = 0, mpiSize = 1;
+    // Number of rows
+    const size_t Nx = 1000;
+    // Number of steps
+    const size_t NSteps = 1;
+
+    std::vector<float> r32s(Nx);
+    // range 0 to 999
+    std::iota(r32s.begin(), r32s.end(), 0.f);
+
+#if ADIOS2_USE_MPI
+    MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+    MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+#endif
+
+#if ADIOS2_USE_MPI
+    adios2::ADIOS adios(MPI_COMM_WORLD);
+#else
+    adios2::ADIOS adios;
+#endif
+    {
+        adios2::IO io = adios.DeclareIO("TestIO");
+
+        if (!engineName.empty())
+        {
+            io.SetEngine(engineName);
+        }
+
+        const adios2::Dims shape{static_cast<size_t>(Nx * mpiSize)};
+        const adios2::Dims start{static_cast<size_t>(Nx * mpiRank)};
+        const adios2::Dims count{Nx};
+
+        auto var_r32 = io.DefineVariable<float>("r32", shape, start, count);
+
+        // add operations
+        adios2::Operator Blosc2Op =
+            adios.DefineOperator("Blosc2Compressor", adios2::ops::LosslessBlosc);
+
+        var_r32.AddOperation(Blosc2Op, {{adios2::ops::blosc::key::clevel, accuracy},
+                                        {adios2::ops::blosc::key::threshold, threshold},
+                                        {adios2::ops::blosc::key::doshuffle, doshuffle}});
+        adios2::Engine bpWriter = io.Open(fname, adios2::Mode::Write);
+
+        for (size_t step = 0; step < NSteps; ++step)
+        {
+            bpWriter.BeginStep();
+            var_r32.SetSelection(adios2::Box<adios2::Dims>({mpiRank * Nx}, {Nx}));
+            bpWriter.Put<float>("r32", r32s.data());
+            var_r32.SetSelection(adios2::Box<adios2::Dims>({mpiRank * Nx}, {0}));
+            std::vector<float> r32_empty;
+            bpWriter.Put<float>("r32", r32_empty.data());
+            bpWriter.EndStep();
+        }
+
+        bpWriter.Close();
+    }
+
+    {
+        adios2::IO io = adios.DeclareIO("ReadIO");
+
+        if (!engineName.empty())
+        {
+            io.SetEngine(engineName);
+        }
+
+        adios2::Engine bpReader = io.Open(fname, adios2::Mode::Read);
+
+        unsigned int t = 0;
+        std::vector<float> decompressedR32s;
+
+        while (bpReader.BeginStep() == adios2::StepStatus::OK)
+        {
+            auto var_r32 = io.InquireVariable<float>("r32");
+            EXPECT_TRUE(var_r32);
+            ASSERT_EQ(var_r32.ShapeID(), adios2::ShapeID::GlobalArray);
+            ASSERT_EQ(var_r32.Steps(), NSteps);
+            ASSERT_EQ(var_r32.Shape()[0], mpiSize * Nx);
+
+            const adios2::Dims start{mpiRank * Nx + Nx / 2};
+            const adios2::Dims count{Nx / 2};
+            const adios2::Box<adios2::Dims> sel(start, count);
+            var_r32.SetSelection(sel);
+            bpReader.Get(var_r32, decompressedR32s);
+            bpReader.EndStep();
+
+            for (size_t i = 0; i < Nx / 2; ++i)
+            {
+                std::stringstream ss;
+                ss << "t=" << t << " i=" << i << " rank=" << mpiRank;
+                std::string msg = ss.str();
+
+                ASSERT_EQ(decompressedR32s[i], r32s[Nx / 2 + i]) << msg;
+            }
+            ++t;
+        }
+
+        EXPECT_EQ(t, NSteps);
+
+        bpReader.Close();
+    }
+}
 class BPWriteReadBlosc2
 : public ::testing::TestWithParam<std::tuple<std::string, std::string, std::string>>
 {
@@ -891,6 +1004,10 @@ TEST_P(BPWriteReadBlosc2, ADIOS2BPWriteReadBlosc23DSel)
 {
     Blosc2Accuracy3DSel(std::get<0>(GetParam()), std::get<1>(GetParam()), std::get<2>(GetParam()));
 }
+TEST_P(BPWriteReadBlosc2, ADIOS2BPWriteReadBlosc2Null)
+{
+    Blosc2NullBlocks(std::get<0>(GetParam()), std::get<1>(GetParam()), std::get<2>(GetParam()));
+}
 
 INSTANTIATE_TEST_SUITE_P(
     Blosc2Accuracy, BPWriteReadBlosc2,