Merge pull request #1024 from pnorbert/hdf5-blockinfo

Hdf5 blockinfo

source/adios2/engine/hdf5/HDF5ReaderP.cpp

@@ -331,9 +331,22 @@ void HDF5ReaderP::PerformGets()
     {                                                                          \
         GetSyncCommon(variable, data);                                         \
     }                                                                          \
+                                                                               \
     void HDF5ReaderP::DoGetDeferred(Variable<T> &variable, T *data)            \
     {                                                                          \
         GetDeferredCommon(variable, data);                                     \
+    }                                                                          \
+                                                                               \
+    std::map<size_t, std::vector<typename Variable<T>::Info>>                  \
+    HDF5ReaderP::DoAllStepsBlocksInfo(const Variable<T> &variable) const       \
+    {                                                                          \
+        return GetAllStepsBlocksInfo(variable);                                \
+    }                                                                          \
+                                                                               \
+    std::vector<typename Variable<T>::Info> HDF5ReaderP::DoBlocksInfo(         \
+        const Variable<T> &variable, const size_t step) const                  \
+    {                                                                          \
+        return GetBlocksInfo(variable, step);                                  \
     }
 
 ADIOS2_FOREACH_TYPE_1ARG(declare_type)

source/adios2/engine/hdf5/HDF5ReaderP.h

@@ -15,6 +15,9 @@
 #include "adios2/core/IO.h"
 #include "adios2/toolkit/interop/hdf5/HDF5Common.h"
 
+#include <map>
+#include <vector>
+
 namespace adios2
 {
 namespace core
@@ -56,7 +59,12 @@ class HDF5ReaderP : public Engine
     unsigned int m_StreamAt = 0; // stream step counter
 #define declare_type(T)                                                        \
     void DoGetSync(Variable<T> &, T *) final;                                  \
-    void DoGetDeferred(Variable<T> &, T *) final;
+    void DoGetDeferred(Variable<T> &, T *) final;                              \
+    std::map<size_t, std::vector<typename Variable<T>::Info>>                  \
+    DoAllStepsBlocksInfo(const Variable<T> &variable) const final;             \
+                                                                               \
+    std::vector<typename Variable<T>::Info> DoBlocksInfo(                      \
+        const Variable<T> &variable, const size_t step) const final;
     ADIOS2_FOREACH_TYPE_1ARG(declare_type)
 #undef declare_type
 
@@ -72,6 +80,18 @@ class HDF5ReaderP : public Engine
     template <class T>
     void GetDeferredCommon(Variable<T> &variable, T *data);
 
+    template <class T>
+    std::map<size_t, std::vector<typename Variable<T>::Info>>
+    GetAllStepsBlocksInfo(const Variable<T> &variable) const;
+
+    template <class T>
+    std::vector<typename Variable<T>::Info>
+    GetBlocksInfo(const Variable<T> &variable, const size_t step) const;
+
+    template <class T>
+    std::vector<typename core::Variable<T>::Info>
+    BlocksInfoCommon(const core::Variable<T> &variable) const;
+
     template <class T>
     void UseHDFRead(Variable<T> &variable, T *values, hid_t h5Type);
 

source/adios2/engine/hdf5/HDF5ReaderP.tcc

@@ -59,6 +59,52 @@ void HDF5ReaderP::GetDeferredCommon(Variable<T> &variable, T *data)
 #endif
 }
 
+template <class T>
+std::vector<typename core::Variable<T>::Info>
+HDF5ReaderP::BlocksInfoCommon(const core::Variable<T> &variable) const
+{
+    std::vector<typename core::Variable<T>::Info> blocksInfo;
+
+    typename core::Variable<T>::Info blockInfo;
+    blockInfo.Start = variable.m_Start;
+    blockInfo.Count = variable.m_Shape;
+    if (variable.m_ShapeID == ShapeID::GlobalValue ||
+        variable.m_ShapeID == ShapeID::LocalValue)
+    {
+        blockInfo.IsValue = true;
+    }
+    else
+    {
+        blockInfo.IsValue = false;
+    }
+    blocksInfo.push_back(blockInfo);
+
+    return blocksInfo;
+}
+
+template <class T>
+std::map<size_t, std::vector<typename Variable<T>::Info>>
+HDF5ReaderP::GetAllStepsBlocksInfo(const Variable<T> &variable) const
+{
+    std::map<size_t, std::vector<typename core::Variable<T>::Info>>
+        allStepsBlocksInfo;
+
+    for (size_t step = variable.m_AvailableStepsStart;
+         step < variable.m_AvailableStepsCount; ++step)
+    {
+        allStepsBlocksInfo[step - variable.m_AvailableStepsStart] =
+            BlocksInfoCommon(variable);
+    }
+    return allStepsBlocksInfo;
+}
+
+template <class T>
+std::vector<typename Variable<T>::Info>
+HDF5ReaderP::GetBlocksInfo(const Variable<T> &variable, const size_t step) const
+{
+    BlocksInfoCommon(variable);
+}
+
 } // end namespace engine
 } // end namespace core
 } // end namespace adios2

testing/utils/iotest/CMakeLists.txt

@@ -16,7 +16,7 @@ set(mpicmd ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG})
 #------------------------------------------
 
 #
-#  Pipe2 InsituMPI version 
+#  Pipe2 BP version 
 #
   set(WORKDIR ${CMAKE_CURRENT_BINARY_DIR}/Pipe2.BP)
   file(MAKE_DIRECTORY ${WORKDIR})
@@ -83,6 +83,76 @@ set_property(TEST Utils.IOTest.Pipe2.BP.ValidateRead
 )
 
 
+if (ADIOS2_HAVE_HDF5)
+  #
+  #  Pipe2 HDF5 version 
+  #
+  set(WORKDIR ${CMAKE_CURRENT_BINARY_DIR}/Pipe2.HDF5)
+  file(MAKE_DIRECTORY ${WORKDIR})
+
+  #  HDF5 file version Write part
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.Write
+    COMMAND ${mpicmd} 2 ${PROJECT_BINARY_DIR}/bin/adios_iotest -a 1 -c ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.txt -x ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.xml -d 2 1 --strong-scaling
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.DumpWrite
+    COMMAND ${CMAKE_COMMAND}
+      -DARGS=-laD
+      -DINPUT_FILE=pipe2_write.h5
+      -DOUTPUT_FILE=IOTest.Pipe2.HDF5.Write.bpls.txt
+      -P "${PROJECT_BINARY_DIR}/$<CONFIG>/bpls.cmake"
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+
+  set_property(TEST Utils.IOTest.Pipe2.HDF5.DumpWrite
+    PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.Write
+  )
+
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.ValidateWrite
+    COMMAND ${CMAKE_COMMAND}
+      -E compare_files
+      ${CMAKE_CURRENT_SOURCE_DIR}/IOTest.Pipe2.HDF5.Write.bpls.txt
+      ${WORKDIR}/IOTest.Pipe2.HDF5.Write.bpls.txt
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+  set_property(TEST Utils.IOTest.Pipe2.HDF5.ValidateWrite
+    PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.DumpWrite
+  )
+
+  #  HDF5 file version Read part
+
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.Read
+    COMMAND ${mpicmd} 2 ${PROJECT_BINARY_DIR}/bin/adios_iotest -a 2 -c ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.txt -x ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.xml -d 2 1 --strong-scaling
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.DumpRead
+    COMMAND ${CMAKE_COMMAND}
+      -DARGS=-laD
+      -DINPUT_FILE=pipe2_read.h5
+      -DOUTPUT_FILE=IOTest.Pipe2.HDF5.Read.bpls.txt
+      -P "${PROJECT_BINARY_DIR}/$<CONFIG>/bpls.cmake"
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+
+  set_property(TEST Utils.IOTest.Pipe2.HDF5.DumpRead
+    PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.Read
+  )
+
+  add_test(NAME Utils.IOTest.Pipe2.HDF5.ValidateRead
+    COMMAND ${CMAKE_COMMAND}
+      -E compare_files
+      ${CMAKE_CURRENT_SOURCE_DIR}/IOTest.Pipe2.HDF5.Read.bpls.txt
+      ${WORKDIR}/IOTest.Pipe2.HDF5.Read.bpls.txt
+    WORKING_DIRECTORY ${WORKDIR} 
+  )
+  set_property(TEST Utils.IOTest.Pipe2.HDF5.ValidateRead
+    PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.DumpRead
+  )
+
+endif (ADIOS2_HAVE_HDF5)
+
 #
 math(EXPR HAVE_2_PROCS "${MPIEXEC_MAX_NUMPROCS} - 1")
 if (${HAVE_2_PROCS}) 

testing/utils/iotest/IOTest.Pipe2.HDF5.Read.bpls.txt

@@ -0,0 +1,14 @@
+  double   a     3*{100, 200} = 0 / 0
+        step 0: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+        step 1: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+        step 2: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+  float    b     3*{100} = 0 / 0
+        step 0: 
+          block 0: [ 0:99] = 0 / 0
+        step 1: 
+          block 0: [ 0:99] = 0 / 0
+        step 2: 
+          block 0: [ 0:99] = 0 / 0

testing/utils/iotest/IOTest.Pipe2.HDF5.Write.bpls.txt

@@ -0,0 +1,21 @@
+  double   a     3*{100, 200} = 0 / 0
+        step 0: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+        step 1: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+        step 2: 
+          block 0: [ 0:99,   0:199] = 0 / 0
+  float    b     3*{100} = 0 / 0
+        step 0: 
+          block 0: [ 0:99] = 0 / 0
+        step 1: 
+          block 0: [ 0:99] = 0 / 0
+        step 2: 
+          block 0: [ 0:99] = 0 / 0
+  float    c     3*{100, 200, 300} = 0 / 0
+        step 0: 
+          block 0: [ 0:99,   0:199,   0:299] = 0 / 0
+        step 1: 
+          block 0: [ 0:99,   0:199,   0:299] = 0 / 0
+        step 2: 
+          block 0: [ 0:99,   0:199,   0:299] = 0 / 0

testing/utils/iotest/pipe2-HDF5.txt

@@ -0,0 +1,50 @@
+# Config file for Task 1 in a pipeline
+#   - Produce variables  a  b  c 
+#   - Write variables    a  b  c     to    pipe2_write.h5
+
+# Config file for Task 2 in a pipeline
+#   - Read in variables  a  b  from Task 1 (ignore c) from pipe2_write.h5
+#     using a different decomposition
+#   - Write variables    a  b        to   pipe2_read.h5
+
+
+group  io_T1
+  # item  type    varname     N   [dim1 dim2 ... dimN  decomp1 decomp2 ... decompN]
+  array   double  a           2    100   200              X       YZ
+  array   float   b           1    100                    XYZ 
+  array   float   c           3    100   200   300        XY      z     1
+
+group  io_T2_in
+  # item  type    varname     N   [dim1 dim2 ... dimN  decomp1 decomp2 ... decompN]
+  array   double  a           2    100   200              XY      Z
+  array   float   b           1    100                    XYZ 
+
+group  io_T2_out
+  # use all variables read into io_T2_in in the output 
+  link group io_T2_in
+
+
+
+# Task 1 actions
+app 1
+  steps   3
+  sleep   0.1      
+  # write all of io_T1 into pipe2_write.h5
+  write   pipe2_write.h5    io_T1
+
+# Task 2 actions
+app 2
+  steps   over pipe2_write.h5   
+  # read a & b from pipe2_write.h5 using io_T2_in definition with blocking wait
+  read  next  pipe2_write.h5    io_T2_in  -1   a   b
+
+  # Sleep and write only if read was successful:
+  cond pipe2_write.h5   sleep   0.1 
+  # write io_T2 into pipe2_read.h5
+  cond pipe2_write.h5   write   pipe2_read.h5    io_T2_out  
+
+  sleep   0.123456789
+
+
+
+

testing/utils/iotest/pipe2-HDF5.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0"?>
+<adios-config>
+
+    <!-- example engines 
+
+        <engine type="BPFile"/>
+        <engine type="HDF5"/>
+        <engine type="SST"/>
+        <engine type="InSituMPI"/>
+
+     -->
+
+
+    <!--===========================================
+           Configuration for io_T1 group
+        ==========================================-->
+
+    <io name="io_T1">
+        <engine type="HDF5">
+        </engine>
+    </io>
+
+
+    <!--=========================================
+           Configuration for io_T2_in group
+           It should match the io_T1 output group
+        =========================================-->
+
+    <io name="io_T2_in">
+        <engine type="HDF5">
+        </engine>
+    </io>
+
+    <!--=========================================
+           Configuration for io_T2_out group
+        =========================================-->
+
+    <io name="io_T2_out">
+        <engine type="HDF5">
+        </engine>
+    </io>
+
+
+</adios-config>