Merge pull request #1349 from williamfgc/hl_py_shape

High level Python API to allow changing shape of global array
ornladios · Apr 3, 2019 · e306c38 · e306c38
2 parents 2a711df + c1535bc
commit e306c38
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Showing 5 changed files with 48 additions and 12 deletions.
diff --git a/source/adios2/core/IO.cpp b/source/adios2/core/IO.cpp
@@ -251,7 +251,7 @@ std::map<std::string, Params> IO::GetAvailableVariables() noexcept
         Variable<T> &variable = *InquireVariable<T>(name);                     \
         variablesInfo[name]["AvailableStepsCount"] =                           \
             helper::ValueToString(variable.m_AvailableStepsCount);             \
-        variablesInfo[name]["Shape"] = helper::VectorToCSV(variable.m_Shape);  \
+        variablesInfo[name]["Shape"] = helper::VectorToCSV(variable.Shape());  \
         if (variable.m_SingleValue)                                            \
         {                                                                      \
             variablesInfo[name]["SingleValue"] = "true";                       \
@@ -262,9 +262,9 @@ std::map<std::string, Params> IO::GetAvailableVariables() noexcept
         {                                                                      \
             variablesInfo[name]["SingleValue"] = "false";                      \
             variablesInfo[name]["Min"] =                                       \
-                helper::ValueToString(variable.m_Min);                         \
+                helper::ValueToString(variable.Min());                         \
             variablesInfo[name]["Max"] =                                       \
-                helper::ValueToString(variable.m_Max);                         \
+                helper::ValueToString(variable.Max());                         \
         }                                                                      \
     }
         ADIOS2_FOREACH_STDTYPE_1ARG(declare_template_instantiation)

diff --git a/source/adios2/core/Stream.tcc b/source/adios2/core/Stream.tcc
@@ -73,12 +73,9 @@ void Stream::Write(const std::string &name, const T *data, const Dims &shape,
     }
     else
     {
-        if (!shape.empty())
+        if (!shape.empty() && !variable->m_SingleValue)
         {
-            if (!(shape.size() == 1 && shape.front() == adios2::LocalValueDim))
-            {
-                variable->SetShape(shape);
-            }
+            variable->SetShape(shape);
         }
 
         if (!start.empty() && !count.empty())

diff --git a/source/adios2/core/Variable.h b/source/adios2/core/Variable.h
@@ -130,17 +130,17 @@ class Variable : public VariableBase
 
     size_t SubStreamsInfoSize();
 
-    Dims Shape(const size_t step) const;
+    Dims Shape(const size_t step = adios2::EngineCurrentStep) const;
 
     Dims Count() const;
 
     size_t SelectionSize() const;
 
-    std::pair<T, T> MinMax(const size_t step) const;
+    std::pair<T, T> MinMax(const size_t step = adios2::DefaultSizeT) const;
 
-    T Min(const size_t step) const;
+    T Min(const size_t step = adios2::DefaultSizeT) const;
 
-    T Max(const size_t step) const;
+    T Max(const size_t step = adios2::DefaultSizeT) const;
 
     std::vector<std::vector<typename Variable<T>::Info>>
     AllStepsBlocksInfo() const;

diff --git a/testing/adios2/bindings/python/CMakeLists.txt b/testing/adios2/bindings/python/CMakeLists.txt
@@ -19,6 +19,8 @@ if(ADIOS2_HAVE_MPI)
                     SCRIPT TestBPReadMultisteps.py)
     python_add_test(NAME PythonBPWriteRead2D ${test_parameters} 
                     SCRIPT TestBPWriteRead2D.py)
+    python_add_test(NAME PythonBPChangingShapeHighLevelAPI ${test_parameters} 
+                    SCRIPT TestBPChangingShapeHighLevelAPI.py)
     if (ADIOS2_HAVE_HDF5)
         python_add_test(NAME PythonBPWriteReadHighLevelAPI_HDF5 
                         SCRIPT TestBPWriteTypesHighLevelAPI_HDF5.py)

diff --git a/testing/adios2/bindings/python/TestBPChangingShapeHighLevelAPI.py b/testing/adios2/bindings/python/TestBPChangingShapeHighLevelAPI.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#
+# TestChangingShape.py
+#
+#  Created on: April 2nd, 2019
+#      Author: Jeremy Logan
+
+import numpy as np
+from mpi4py import MPI
+import adios2
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
+
+# Test data
+nx = [10, 15]
+data = [np.zeros(nx[0]), np.ones(nx[1])]
+shape = [[size * nx[0]], [size * nx[1]]]
+start = [[rank * nx[0]], [rank * nx[1]]]
+count = [[nx[0]], [nx[1]]]
+
+# Write different sized arrays as separate steps
+with adios2.open('out.bp', 'w', comm) as f:
+    f.write('z', data[0], shape[0], start[0], count[0], end_step=True)
+    f.write('z', data[1], shape[1], start[1], count[1], end_step=True)
+
+# Read back arrays
+with adios2.open('out.bp', 'r', comm) as f:
+    for f_step in f:
+        shape_z = int(f_step.available_variables()['z']['Shape'])
+        print(shape_z)
+        assert(shape_z == int(shape[f_step.current_step()][0]))