Add JoinedArray test in staging-common, limit to BP4 currently

testing/adios2/engine/staging-common/CMakeLists.txt

@@ -36,6 +36,8 @@ set (PROGS TestCommonWrite
     TestLocalRead
     TestStructWrite
     TestStructRead
+    TestWriteJoined
+    TestReadJoined
     TestOnDemandWrite
     TestOnDemandRead)
 
@@ -114,7 +116,7 @@ if(ADIOS2_HAVE_MPI AND MPIEXEC_EXECUTABLE)
    endforeach()
 endif()
 
-set (SIMPLE_TESTS "1x1;1x1.Attrs;1x1.ModAttrs;1x1DefSync;1x1VarDestruction;1x1.SpanMinMax;1x1.Local2;1x1Struct")
+set (SIMPLE_TESTS "1x1;1x1.Attrs;1x1.ModAttrs;1x1DefSync;1x1VarDestruction;1x1.SpanMinMax;1x1.Local2;1x1Struct;1x1Joined")
 set (BP5File_ONLY_TESTS "1x1DataWrite")
 
 set (SIMPLE_FORTRAN_TESTS "")
@@ -131,7 +133,7 @@ endif()
 set (SIMPLE_MPI_TESTS "")
 set (SIMPLE_MPI_FORTRAN_TESTS "")
 if (ADIOS2_HAVE_MPI)
-  set (SIMPLE_MPI_TESTS "2x1;1x2;3x5;5x3;DelayedReader_3x5;3x5LockGeometry;2x1.Local;1x2.Local;3x5.Local;5x3.Local;1x1.LocalVarying;5x3.LocalVarying;2x1ZeroDataVar;2x1ZeroDataR64;2x2.NoData;2x2.HalfNoData;2x1.SharedNothing;2x1.SharedIO;2x1.SharedVar;2x1.SharedNothingSync;2x1.SharedIOSync;2x1.SharedVarSync;3x5EarlyExit")
+  set (SIMPLE_MPI_TESTS "2x1;1x2;3x5;5x3;DelayedReader_3x5;3x5LockGeometry;2x1.Local;1x2.Local;3x5.Local;5x3.Local;1x1.LocalVarying;5x3.LocalVarying;2x1ZeroDataVar;2x1ZeroDataR64;2x2.NoData;2x2.HalfNoData;2x1.SharedNothing;2x1.SharedIO;2x1.SharedVar;2x1.SharedNothingSync;2x1.SharedIOSync;2x1.SharedVarSync;3x5EarlyExit;;5x1Joined")
   list (APPEND SPECIAL_TESTS "2x1.NoPreload;2x3.ForcePreload;PreciousTimestep.3x2;PreciousTimestepDiscard.3x2")
   if (ADIOS2_HAVE_Fortran)
     set (SIMPLE_MPI_FORTRAN_TESTS "FtoC.3x5;CtoF.3x5;FtoF.3x5")
@@ -170,6 +172,9 @@ MutateTestSet( COMM_MIN_SST_TESTS "CommMin" writer "CPCommPattern=Min" "${BASIC_
 # temporarily remove PreciousTimestep CommPeer tests
 list (REMOVE_ITEM COMM_PEER_SST_TESTS "PreciousTimestep")
 
+# no SSE engine does Joined
+list (FILTER COMM_MIN_SST_TESTS EXCLUDE REGEX "Joined*")
+
 MutateTestSet( FFS_SST_TESTS "FFS" writer "MarshalMethod=FFS" "${COMM_MIN_SST_TESTS};${COMM_PEER_SST_TESTS}" )
 MutateTestSet( FFS_SST_TESTS "BP5" writer "MarshalMethod=BP5" "${COMM_MIN_SST_TESTS};${COMM_PEER_SST_TESTS}" )
 MutateTestSet( BP_SST_TESTS "BP" writer "MarshalMethod=BP" "${COMM_MIN_SST_TESTS};${COMM_PEER_SST_TESTS}" )
@@ -220,6 +225,8 @@ if(NOT WIN32)    # not on windows
     endforeach()
     # BP3 fails to handle lots of timesteps
     list (FILTER BP_TESTS EXCLUDE REGEX "Bulk.*")
+    # BP3 doesn't do Joined
+    list (FILTER BP_TESTS EXCLUDE REGEX "Joined.*")
     foreach(test ${BP_TESTS})
         add_common_test(${test} BP3)
     endforeach()
@@ -228,6 +235,8 @@ endif()
 #  BP5 tests
 if(ADIOS2_HAVE_BP5)
     set (BP5_TESTS ${ALL_SIMPLE_TESTS} ${SPECIAL_TESTS})
+    # BP5 doesn't do Joined
+    list (FILTER BP5_TESTS EXCLUDE REGEX "Joined.*")
     # Delayed reader not worth testing on file engines
     list (FILTER BP5_TESTS EXCLUDE REGEX "DelayedReader")
     # Discard not a feature of BP5
@@ -253,6 +262,8 @@ if(NOT MSVC)    # not on windows
     # BP4 streaming tests start with all the simple tests, but with a timeout added on open
     LIST (APPEND BP4_STREAM_TESTS ${ALL_SIMPLE_TESTS} ${SPECIAL_TESTS})
     MutateTestSet( BP4_STREAM_TESTS "BPS" reader "OpenTimeoutSecs=10,BeginStepPollingFrequencySecs=0.1" "${BP4_STREAM_TESTS}")
+    # no BP4 streaming doesn't do Joined?
+    list (FILTER BP4_STREAM_TESTS EXCLUDE REGEX "Joined*")
     # SharedVars fail with BP4_streaming*
     list (FILTER BP4_STREAM_TESTS EXCLUDE REGEX ".*SharedVar.BPS$")
    # Discard not a feature of BP4
@@ -325,6 +336,8 @@ if(NOT MSVC)    # not on windows
     list (FILTER FILESTREAM_TESTS EXCLUDE REGEX ".*VarDestruction.*")
     # BP3 and BP4 don't do structs
     list (FILTER FILESTREAM_TESTS EXCLUDE REGEX ".*1x1Struct.*")
+    # no FileStream doesn't do Joined
+    list (FILTER FILESTREAM_TESTS EXCLUDE REGEX "Joined*")
 
     foreach(test ${FILESTREAM_TESTS})
         add_common_test(${test} FileStream)
@@ -358,6 +371,9 @@ if(NOT MSVC AND ADIOS2_HAVE_HDF5 AND (NOT ADIOS2_HAVE_MPI OR HDF5_IS_PARALLEL))
     list (FILTER HDF5_TESTS EXCLUDE REGEX ".*ModAttr.*")
     # HDF5 engine doesn't do structs (but HDF5 does)
     list (FILTER HDF5_TESTS EXCLUDE REGEX ".*1x1Struct.*")
+    # HDF5 doesn't do Joined
+    list (FILTER HDF5_TESTS EXCLUDE REGEX "Joined*")
+
     foreach(test ${HDF5_TESTS})
         add_common_test(${test} HDF5)
     endforeach()

testing/adios2/engine/staging-common/TestReadJoined.cpp

@@ -0,0 +1,158 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ */
+#include <cstdint>
+#include <cstring>
+
+#include <chrono>
+#include <iostream>
+#include <stdexcept>
+#include <thread>
+
+#include <adios2.h>
+
+#include <gtest/gtest.h>
+
+#include "TestData.h"
+
+#include "ParseArgs.h"
+
+class CommonReadTest : public ::testing::Test
+{
+public:
+    CommonReadTest() = default;
+};
+
+typedef std::chrono::duration<double> Seconds;
+
+#if ADIOS2_USE_MPI
+MPI_Comm testComm;
+#endif
+
+const int nsteps = 3;
+const size_t Ncols = 4;
+const std::vector<int> nblocksPerProcess = {2, 3, 2, 1, 3, 2};
+int nMyTotalRows[nsteps];
+int nTotalRows[nsteps];
+
+// ADIOS2 Common read
+TEST_F(CommonReadTest, ADIOS2CommonRead1D8)
+{
+    // Each process would write a 1x8 array and all processes would
+    // form a mpiSize * Nx 1D array
+    int mpiRank = 0, mpiSize = 1;
+
+#if ADIOS2_USE_MPI
+    MPI_Comm_rank(testComm, &mpiRank);
+    MPI_Comm_size(testComm, &mpiSize);
+#endif
+
+    // Write test data using ADIOS2
+
+#if ADIOS2_USE_MPI
+    adios2::ADIOS adios(testComm);
+#else
+    adios2::ADIOS adios;
+#endif
+    adios2::IO inIO = adios.DeclareIO("Input");
+
+    inIO.SetEngine(engine);
+    inIO.SetParameters(engineParams);
+
+    adios2::Engine reader = inIO.Open(fname, adios2::Mode::Read);
+
+    if (!mpiRank)
+    {
+        std::cout << "Reading as stream with BeginStep/EndStep on " << mpiSize
+                  << "processes :" << std::endl;
+    }
+
+    int step = 0;
+    while (true)
+    {
+        adios2::StepStatus status = reader.BeginStep(adios2::StepMode::Read);
+
+        if (status != adios2::StepStatus::OK)
+        {
+            break;
+        }
+
+        auto rows_var = inIO.InquireVariable<int>("totalrows");
+        auto var = inIO.InquireVariable<double>("table");
+        EXPECT_TRUE(var);
+
+        if (!mpiRank)
+        {
+            std::cout << "Step " << step << " table shape (" << var.Shape()[0]
+                      << ", " << var.Shape()[1] << ")" << std::endl;
+        }
+
+        int Nrows;
+        reader.Get(rows_var, Nrows);
+        EXPECT_EQ(var.Shape()[0], Nrows);
+        EXPECT_EQ(var.Shape()[1], Ncols);
+
+        var.SetSelection({{0, 0}, {(size_t)Nrows, Ncols}});
+
+        // Check data on rank 0
+        if (!mpiRank)
+        {
+            std::vector<double> data(Nrows * Ncols);
+            reader.Get(var, data.data());
+            reader.PerformGets();
+            for (size_t i = 0; i < (size_t)Nrows; ++i)
+            {
+                for (size_t j = 0; j < Ncols; ++j)
+                {
+                    EXPECT_GE(data[i * Ncols + j], (step + 1) * 1.0);
+                    EXPECT_LT(data[i * Ncols + j], (nsteps + 1) * 1.0 + 0.9999);
+                }
+            }
+        }
+
+        reader.EndStep();
+        ++step;
+    }
+    reader.Close();
+    EXPECT_EQ(step, nsteps);
+}
+
+//******************************************************************************
+// main
+//******************************************************************************
+
+int main(int argc, char **argv)
+{
+    int result;
+    ::testing::InitGoogleTest(&argc, argv);
+    ParseArgs(argc, argv);
+
+#if ADIOS2_USE_MPI
+    int provided;
+    int thread_support_level = (engine == "SST" || engine == "sst")
+                                   ? MPI_THREAD_MULTIPLE
+                                   : MPI_THREAD_SINGLE;
+
+    // MPI_THREAD_MULTIPLE is only required if you enable the SST MPI_DP
+    MPI_Init_thread(nullptr, nullptr, thread_support_level, &provided);
+
+    int key;
+    MPI_Comm_rank(MPI_COMM_WORLD, &key);
+
+    const unsigned int color = 2;
+    MPI_Comm_split(MPI_COMM_WORLD, color, key, &testComm);
+#endif
+
+    result = RUN_ALL_TESTS();
+
+#if ADIOS2_USE_MPI
+#ifdef CRAY_MPICH_VERSION
+    MPI_Barrier(MPI_COMM_WORLD);
+#else
+    MPI_Finalize();
+#endif
+#endif
+
+    return result;
+}

testing/adios2/engine/staging-common/TestSupp.cmake

@@ -64,6 +64,7 @@ set (STAGING_COMMON_TEST_SUPP_VERBOSE OFF)
 
 set (1x1_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1")
 set (1x1Struct_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 -r $<TARGET_FILE:TestStructRead> -w $<TARGET_FILE:TestStructWrite> ")
+set (1x1Joined_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 -r $<TARGET_FILE:TestReadJoined> -w $<TARGET_FILE:TestWriteJoined> ")
 set (1x1GetSync_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 --rarg=--read_mode --rarg=sync")
 set (1x1DontCloseWriter_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 --warg=--dont_close")
 set (1x1DontCloseReader_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 --rarg=--dont_close")
@@ -90,6 +91,7 @@ set (3x5LockGeometry_CMD "run_test.py.$<CONFIG> -nw 3 -nr 5 --warg=--num_steps -
 set (1x1EarlyExit_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1 --warg=--num_steps --warg=50 --rarg=--num_steps --rarg=5 --rarg=--early_exit")
 set (3x5EarlyExit_CMD "run_test.py.$<CONFIG> -nw 3 -nr 5 --warg=--num_steps --warg=50 --rarg=--num_steps --rarg=5 --rarg=--early_exit")
 set (3x5LockGeometry_TIMEOUT 60)
+set (5x1Joined_CMD "run_test.py.$<CONFIG> -nw 5 -nr 1 -r $<TARGET_FILE:TestReadJoined> -w $<TARGET_FILE:TestWriteJoined> ")
 set (5x3_CMD "run_test.py.$<CONFIG> -nw 5 -nr 3")
 set (5x3DontClose_CMD "run_test.py.$<CONFIG> -nw 5 -nr 3 --rarg=--dont_close --warg=--dont_close")
 set (1x1.Local_CMD "run_test.py.$<CONFIG> -nw 1 -nr 1  -w $<TARGET_FILE:TestCommonWriteLocal> -r $<TARGET_FILE:TestCommonReadLocal>")