New API to allow storing only stats for primary variables (#4328)

* Move the decision to write data for derived variables in VariableBase Co-authored-by: Greg Eisenhauer <eisen@cc.gatech.edu> * C and C++ bindings for setting the write mode of a variable * Fortran API for changing the write mode for primary variables * Python API for changing the write mode for primary variables * Change the API to StoreStatsOnly instead of SetWriteMode Co-authored-by: Norbert Podhorszki <pnorbert@ornl.gov> * Testing in CXX and C for the StatsOnly write mode * Testing for the Fortran bindings for the StatsOnly write mode * Testing for the Python bindings for the StatsOnly write mode --------- Co-authored-by: Greg Eisenhauer <eisen@cc.gatech.edu> Co-authored-by: Norbert Podhorszki <pnorbert@ornl.gov>
ornladios · Sep 17, 2024 · 532747a · 532747a
1 parent d975ac0
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diff --git a/bindings/C/adios2/c/adios2_c_variable.cpp b/bindings/C/adios2/c/adios2_c_variable.cpp
@@ -77,6 +77,23 @@ adios2_error adios2_set_shape(adios2_variable *variable, const size_t ndims, con
     }
 }
 
+adios2_error adios2_store_stats_only(adios2_variable *variable, const adios2_bool mode)
+{
+    try
+    {
+        adios2::core::VariableBase *variableBase =
+            reinterpret_cast<adios2::core::VariableBase *>(variable);
+        variableBase->StoreStatsOnly(mode);
+
+        return adios2_error_none;
+    }
+    catch (...)
+    {
+        return static_cast<adios2_error>(
+            adios2::helper::ExceptionToError("adios2_set_memory_space"));
+    }
+}
+
 adios2::MemorySpace adios2_ToMemorySpace(const adios2_memory_space Cmem)
 {
     adios2::MemorySpace mem = adios2::MemorySpace::Detect;

diff --git a/bindings/C/adios2/c/adios2_c_variable.h b/bindings/C/adios2/c/adios2_c_variable.h
@@ -29,6 +29,12 @@ extern "C" {
  */
 adios2_error adios2_set_shape(adios2_variable *variable, const size_t ndims, const size_t *shape);
 
+/**
+ * Set the write mode of a variable
+ * @param false - write data; true - write only stats
+ */
+adios2_error adios2_store_stats_only(adios2_variable *variable, const adios2_bool mode);
+
 /**
  * Sets the memory space for all following Puts/Gets
  * to either host (default) or device

diff --git a/bindings/CXX11/adios2/cxx11/Variable.cpp b/bindings/CXX11/adios2/cxx11/Variable.cpp
@@ -31,6 +31,12 @@ namespace adios2
     }                                                                                              \
                                                                                                    \
     template <>                                                                                    \
+    void Variable<T>::StoreStatsOnly(const bool mode)                                              \
+    {                                                                                              \
+        m_Variable->StoreStatsOnly(mode);                                                          \
+    }                                                                                              \
+                                                                                                   \
+    template <>                                                                                    \
     void Variable<T>::SetMemorySpace(const MemorySpace mem)                                        \
     {                                                                                              \
         m_Variable->SetMemorySpace(mem);                                                           \

diff --git a/bindings/CXX11/adios2/cxx11/Variable.h b/bindings/CXX11/adios2/cxx11/Variable.h
@@ -147,6 +147,12 @@ class Variable
     /** Checks if object is valid, e.g. if( variable ) { //..valid } */
     explicit operator bool() const noexcept;
 
+    /**
+     * Set the write mode of a variable
+     * @param false - write data; true - write only stats
+     */
+    void StoreStatsOnly(const bool mode);
+
     /**
      * Sets the memory space for all following Puts/Gets
      * to either host (default) or device

diff --git a/bindings/Fortran/f2c/adios2_f2c_variable.cpp b/bindings/Fortran/f2c/adios2_f2c_variable.cpp
@@ -97,6 +97,13 @@ void FC_GLOBAL(adios2_variable_steps_f2c,
     }
 }
 
+void FC_GLOBAL(adios2_store_stats_only_f2c, ADIOS2_SET_WRITE_MODE_F2C)(adios2_variable **variable,
+                                                                       const adios2_bool *mode,
+                                                                       int *ierr)
+{
+    *ierr = static_cast<int>(adios2_store_stats_only(*variable, *mode));
+}
+
 void FC_GLOBAL(adios2_set_memory_space_f2c, ADIOS2_SET_MEMORY_SPACE_F2C)(adios2_variable **variable,
                                                                          const int *mem, int *ierr)
 {

diff --git a/bindings/Fortran/modules/adios2_variable_mod.f90 b/bindings/Fortran/modules/adios2_variable_mod.f90
@@ -19,6 +19,7 @@ module adios2_variable_mod
     external adios2_set_selection_f2c
     external adios2_set_shape_f2c
     external adios2_set_step_selection_f2c
+    external adios2_store_stats_only_f2c
     external adios2_variable_name_f2c
     external adios2_variable_name_length_f2c
     external adios2_variable_ndims_f2c
@@ -131,6 +132,14 @@ subroutine adios2_set_selection(variable, ndims, start_dims, count_dims, &
                                       count_dims, ierr)
     end subroutine
 
+    subroutine adios2_store_stats_only(variable, mode, ierr)
+        type(adios2_variable), intent(in) :: variable
+        logical, intent(in) :: mode
+        integer, intent(out) :: ierr
+
+        call adios2_store_stats_only_f2c(variable%f2c, mode, ierr)
+    end subroutine
+
     subroutine adios2_set_memory_selection(variable, ndims, &
                                            memory_start_dims, &
                                            memory_count_dims, &

diff --git a/bindings/Python/py11Variable.cpp b/bindings/Python/py11Variable.cpp
@@ -27,6 +27,12 @@ void Variable::SetShape(const Dims &shape)
     m_VariableBase->SetShape(shape);
 }
 
+void Variable::StoreStatsOnly(const bool mode)
+{
+    helper::CheckForNullptr(m_VariableBase, "in call to Variable::StoreStatsOnly");
+    m_VariableBase->StoreStatsOnly(mode);
+}
+
 void Variable::SetBlockSelection(const size_t blockID)
 {
     helper::CheckForNullptr(m_VariableBase, "in call to Variable::SetBlockSelection");

diff --git a/bindings/Python/py11Variable.h b/bindings/Python/py11Variable.h
@@ -39,6 +39,8 @@ class Variable
 
     void SetShape(const Dims &shape);
 
+    void StoreStatsOnly(const bool mode);
+
     void SetBlockSelection(const size_t blockID);
 
     void SetSelection(const Box<Dims> &selection);

diff --git a/bindings/Python/py11glue.cpp b/bindings/Python/py11glue.cpp
@@ -369,6 +369,7 @@ PYBIND11_MODULE(ADIOS2_PYTHON_MODULE_NAME, m)
                  return opBool;
              })
         .def("SetShape", &adios2::py11::Variable::SetShape)
+        .def("StoreStatsOnly", &adios2::py11::Variable::StoreStatsOnly)
         .def("SetBlockSelection", &adios2::py11::Variable::SetBlockSelection)
         .def("SetSelection", &adios2::py11::Variable::SetSelection)
         .def("SetStepSelection", &adios2::py11::Variable::SetStepSelection)

diff --git a/python/adios2/variable.py b/python/adios2/variable.py
@@ -211,3 +211,9 @@ def remove_operations(self):
         Remove operations (operators) assigned to this Variable.
         """
         self.impl.RemoveOperations()
+
+    def store_stats_only(self, mode):
+        """
+        Select writing mode for variable (write data or just stats)
+        """
+        self.impl.StoreStatsOnly(mode)
diff --git a/source/adios2/core/VariableBase.cpp b/source/adios2/core/VariableBase.cpp
@@ -42,6 +42,8 @@ VariableBase::VariableBase(const std::string &name, const DataType type, const s
 
 size_t VariableBase::TotalSize() const noexcept { return helper::GetTotalSize(m_Count); }
 
+void VariableBase::StoreStatsOnly(const bool mode) { m_WriteData = !(mode); }
+
 #if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
 ArrayOrdering VariableBase::GetArrayLayout() { return m_ArrayLayout; }
 

diff --git a/source/adios2/core/VariableBase.h b/source/adios2/core/VariableBase.h
@@ -51,6 +51,9 @@ class VariableBase
      *  VariableStruct -> from constructor sizeof(struct) */
     const size_t m_ElementSize;
 
+    /** Write data for the variable (True - default) or only write stats (False) */
+    bool m_WriteData = true;
+
     /* User requested memory space */
     MemorySpace m_MemSpace = MemorySpace::Detect;
 #if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
@@ -128,6 +131,12 @@ class VariableBase
      */
     size_t TotalSize() const noexcept;
 
+    /**
+     * Set the write mode of a variable
+     * @param false - write data; true - write only stats
+     */
+    void StoreStatsOnly(const bool mode);
+
 #if defined(ADIOS2_HAVE_KOKKOS) || defined(ADIOS2_HAVE_GPU_SUPPORT)
     /**
      * Get the layout used by the user buffers

diff --git a/source/adios2/core/VariableDerived.cpp b/source/adios2/core/VariableDerived.cpp
@@ -14,6 +14,8 @@ VariableDerived::VariableDerived(const std::string &name, adios2::derived::Expre
                expr.GetCount(), isConstant),
   m_DerivedType(varType), m_NameToType(nameToType), m_Expr(expr)
 {
+    if (varType != DerivedVarType::StoreData)
+        m_WriteData = false;
 }
 
 DerivedVarType VariableDerived::GetDerivedType() { return m_DerivedType; }

diff --git a/source/adios2/toolkit/format/bp5/BP5Serializer.cpp b/source/adios2/toolkit/format/bp5/BP5Serializer.cpp
@@ -751,14 +751,7 @@ void BP5Serializer::Marshal(void *Variable, const char *Name, const DataType Typ
     core::VariableDerived *VD = dynamic_cast<core::VariableDerived *>(VB);
 #endif
 
-    bool WriteData = true;
-#ifdef ADIOS2_HAVE_DERIVED_VARIABLE
-    if (VD)
-    {
-        // All other types of Derived types we don't write data
-        WriteData = (VD->GetDerivedType() == DerivedVarType::StoreData);
-    }
-#endif
+    bool WriteData = VB->m_WriteData;
     BP5MetadataInfoStruct *MBase;
 
     BP5WriterRec Rec = LookupWriterRec(Variable);

diff --git a/testing/adios2/bindings/C/CMakeLists.txt b/testing/adios2/bindings/C/CMakeLists.txt
@@ -9,3 +9,4 @@ gtest_add_tests_helper(NullWriteRead MPI_ALLOW "" Bindings.C. "")
 gtest_add_tests_helper(WriteAggregateReadLocal MPI_ONLY BP Bindings.C. "")
 gtest_add_tests_helper(AvailableVariablesAttribites MPI_ONLY BP Bindings.C. "")
 gtest_add_tests_helper(MemorySpace MPI_NONE BP Bindings.C. "")
+gtest_add_tests_helper(WriteStatsOnly MPI_ALLOW BP Bindings.C. "")
diff --git a/testing/adios2/bindings/C/TestBPWriteStatsOnly.cpp b/testing/adios2/bindings/C/TestBPWriteStatsOnly.cpp
@@ -0,0 +1,88 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * TestBPWriteStatsOnly.cpp : test the C bindings when only stats are written
+ */
+
+#include <adios2_c.h>
+#include <gtest/gtest.h>
+#include <vector>
+
+class ADIOS2_C_API : public ::testing::Test
+{
+public:
+    ADIOS2_C_API() { adiosH = adios2_init_serial(); }
+
+    ~ADIOS2_C_API() { adios2_finalize(adiosH); }
+
+    adios2_adios *adiosH;
+};
+
+TEST_F(ADIOS2_C_API, ADIOS2BPWriteStatsOnly)
+{
+#if ADIOS2_USE_MPI
+    const char fname[] = "ADIOS2_C_API.ADIOS2BPWriteStatsOnly_MPI.bp";
+#else
+    const char fname[] = "ADIOS2_C_API.ADIOS2BPWriteStatsOnly.bp";
+#endif
+    // write
+    {
+        adios2_io *ioH = adios2_declare_io(adiosH, "CWriteStats");
+        adios2_set_engine(ioH, "BPFile");
+
+        size_t shape[2];
+        shape[0] = 5;
+        shape[1] = 2;
+
+        size_t start[2];
+        start[0] = 0;
+        start[1] = 0;
+
+        size_t count[2];
+        count[0] = 5;
+        count[1] = 2;
+
+        int32_t data_I32[10] = {131072, 131073,  -131070, 131075,  -131068,
+                                131077, -131066, 131079,  -131064, 131081};
+        adios2_define_variable(ioH, "varI32", adios2_type_int32_t, 2, shape, start, count,
+                               adios2_constant_dims_true);
+        adios2_variable *varI32 = adios2_inquire_variable(ioH, "varI32");
+        adios2_store_stats_only(varI32, adios2_true);
+
+        adios2_engine *engineH = adios2_open(ioH, fname, adios2_mode_write);
+        adios2_put(engineH, varI32, data_I32, adios2_mode_deferred);
+        adios2_close(engineH);
+    }
+    // read shape
+    {
+        adios2_io *ioH = adios2_declare_io(adiosH, "Reader");
+        adios2_engine *engineH = adios2_open(ioH, fname, adios2_mode_readRandomAccess);
+        size_t steps;
+        adios2_steps(&steps, engineH);
+        EXPECT_EQ(steps, 1);
+
+        std::vector<int32_t> inI32(10);
+        adios2_variable *varI32 = adios2_inquire_variable(ioH, "varI32");
+
+        // test that the shape function returns the correct dimensions
+        size_t cpu_shape[2];
+        adios2_error e = adios2_variable_shape(cpu_shape, varI32);
+        EXPECT_EQ(e, adios2_error_none);
+        EXPECT_EQ(cpu_shape[0], 5);
+        EXPECT_EQ(cpu_shape[1], 2);
+
+        e = adios2_get(engineH, varI32, inI32.data(), adios2_mode_sync);
+        EXPECT_EQ(e, adios2_error_runtime_error);
+        adios2_close(engineH);
+    }
+}
+
+int main(int argc, char **argv)
+{
+    int result;
+    ::testing::InitGoogleTest(&argc, argv);
+    result = RUN_ALL_TESTS();
+
+    return result;
+}
diff --git a/testing/adios2/bindings/fortran/CMakeLists.txt b/testing/adios2/bindings/fortran/CMakeLists.txt
@@ -60,6 +60,7 @@ fortran_add_test_helper(BPReadGlobalsByName MPI_ONLY)
 fortran_add_test_helper(BPWriteMemorySelectionRead2D MPI_ONLY)
 fortran_add_test_helper(BPWriteMemorySelectionRead3D MPI_ONLY)
 fortran_add_test_helper(NullEngine MPI_ONLY)
+fortran_add_test_helper(BPWriteStatsOnly MPI_NONE)
 fortran_add_test_helper(BPMemorySpace MPI_NONE)
 if(ADIOS2_HAVE_GPU_Support)
   fortran_add_test_helper(BPMemorySpaceGPU MPI_NONE)

diff --git a/testing/adios2/bindings/fortran/TestBPWriteStatsOnly.F90 b/testing/adios2/bindings/fortran/TestBPWriteStatsOnly.F90
@@ -0,0 +1,67 @@
+program TestBPWriteStatsOnly
+  use adios2
+
+  implicit none
+
+  type(adios2_adios) :: adios
+  type(adios2_io) :: ioPut, ioGet
+  type(adios2_engine) :: bpWriter, bpReader
+  type(adios2_variable) :: var_temperatures, var_temperaturesIn
+
+  integer(kind=4), dimension(:, :), allocatable :: temperatures_i4, &
+                                                   sel_temperatures_i4
+
+  integer(kind=8), dimension(2) :: ishape, istart, icount
+  integer(kind=4) :: ierr
+  integer :: step_status
+  integer :: in1, in2
+
+  in1 = 5
+  in2 = 10
+
+  icount = (/in1, in2/)
+  istart = (/0, 0/)
+  ishape = (/in1, in2/)
+
+  allocate (temperatures_i4(in1, in2))
+  temperatures_i4 = 1
+
+  ! Start adios2 Writer
+  call adios2_init(adios, ierr)
+  call adios2_declare_io(ioPut, adios, 'TestWrite', ierr)
+
+  call adios2_define_variable(var_temperatures, ioPut, &
+                              'temperatures_i4', adios2_type_integer4, &
+                              2, ishape, istart, icount, &
+                              adios2_constant_dims, ierr)
+  call adios2_store_stats_only(var_temperatures, .true., ierr)
+
+  call adios2_open(bpWriter, ioPut, 'TestBPWriteStatsOnly_f.bp', adios2_mode_write, &
+                   ierr)
+  call adios2_put(bpWriter, var_temperatures, temperatures_i4, ierr)
+  call adios2_close(bpWriter, ierr)
+  if (allocated(temperatures_i4)) deallocate (temperatures_i4)
+
+  call adios2_declare_io(ioGet, adios, 'TestRead', ierr)
+  call adios2_open(bpReader, ioGet, 'TestBPWriteStatsOnly_f.bp', &
+                   adios2_mode_read, ierr)
+
+  call adios2_begin_step(bpReader, adios2_step_mode_read, -1., &
+                         step_status, ierr)
+  call adios2_inquire_variable(var_temperaturesIn, ioGet, &
+                               'temperatures_i4', ierr)
+
+  allocate (sel_temperatures_i4(ishape(1), ishape(2)))
+  sel_temperatures_i4 = 0
+
+  call adios2_get(bpReader, var_temperaturesIn, sel_temperatures_i4, adios2_mode_sync, ierr)
+  if (ierr == 0) then
+    write(*,*) 'adios2_get for a variable storing only stats returned without error'
+    if (allocated(sel_temperatures_i4)) deallocate (sel_temperatures_i4)
+    call adios2_close(bpReader, ierr)
+    stop 1
+  end if
+  if (allocated(sel_temperatures_i4)) deallocate (sel_temperatures_i4)
+  call adios2_close(bpReader, ierr)
+
+end program TestBPWriteStatsOnly
diff --git a/testing/adios2/bindings/python/CMakeLists.txt b/testing/adios2/bindings/python/CMakeLists.txt
@@ -14,6 +14,7 @@ endfunction()
 
 python_add_test(NAME Bindings.Python.BPWriteReadTypes.Serial SCRIPT TestBPWriteReadTypes_nompi.py)
 python_add_test(NAME Bindings.Python.TypeExceptionOnGet.Serial SCRIPT TestGetException_nompi.py)
+python_add_test(NAME Bindings.Python.BPWriteStatsOnly.Serial SCRIPT TestBPWriteStatsOnly.py)
 
 if(ADIOS2_HAVE_MPI)
   add_python_mpi_test(BPWriteReadTypes)