Merge pull request #328 from pnorbert/heat

Heat

examples/heatTransfer/heat_adios1.xml

+<?xml version="1.0"?>
+<!-- Config XML file fo the  
+     - heatTransfer_write_adios2 
+     - heatTransfer_read
+     executables in build/bin -->
+
+<adios-config>
+
+    <!--====================================
+           Configuration for the Writer 
+        ====================================-->
+
+    <io name="writer">
+        <engine type="ADIOS1Writer">
+
+            <!-- for vectorized memory operations, make sure your system 
+                 enables threads--> 
+            <parameter key="Threads" value="2"/>
+
+            <!-- Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+            
+        </engine>
+
+        <transport type="File">
+            
+            <!-- POSIX, stdio (C FILE*), fstream (C++) -->
+            <parameter key="Library" value="MPI"/>
+            
+            <!-- For read/write, Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours. open/close always in Microseconds -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+            
+        </transport>
+        
+    </io>
+
+
+    <!--====================================
+           Configuration for the Reader 
+        ====================================-->
+
+    <io name="reader">
+        <engine type="ADIOS1Reader">
+            
+            <!-- for vectorized memory operations, make sure your system 
+                 enables threads--> 
+            <parameter key="Threads" value="2"/>
+
+            <!-- Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+
+        </engine>
+
+        <transport type="File">
+            
+            <!-- POSIX, stdio (C FILE*), fstream (C++) -->
+            <parameter key="Library" value="POSIX"/>
+            
+            <!-- For read/write, Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours. open/close always in Microseconds -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+            
+        </transport>
+        
+    </io>
+</adios-config>

examples/heatTransfer/heat.xml → examples/heatTransfer/heat_bpfile.xml

@@ -11,7 +11,7 @@
         ====================================-->
 
     <io name="writer">
-        <engine type="ADIOS1Writer">
+        <engine type="BPFileWriter">
             
             <!-- for vectorized memory operations, make sure your system 
                  enables threads--> 

examples/heatTransfer/read/CMakeLists.txt

@@ -10,6 +10,4 @@ if(ADIOS2_HAVE_MPI)
      ReadSettings.cpp
   )
   target_link_libraries(heatTransfer_read adios2 MPI::MPI_C)
-  target_compile_definitions(heatTransfer_read PRIVATE
-   -DDEFAULT_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}/../heat.xml)
 endif()

examples/heatTransfer/read/heatRead.cpp

@@ -89,13 +89,18 @@ int main(int argc, char *argv[])
         while (true)
         {
             adios2::StepStatus status =
-                bpReader.BeginStep(adios2::StepMode::NextAvailable);
+                bpReader.BeginStep(adios2::StepMode::NextAvailable, 10.0f);
             if (status != adios2::StepStatus::OK)
+            {
                 break;
+            }
+
+            // Variable objects disappear between steps so we need this every
+            // step
+            vT = bpReaderIO.InquireVariable<double>("T");
 
             if (firstStep)
             {
-                vT = bpReaderIO.InquireVariable<double>("T");
                 unsigned int gndx = vT->m_Shape[0];
                 unsigned int gndy = vT->m_Shape[1];
 
@@ -108,9 +113,6 @@ int main(int argc, char *argv[])
                 settings.DecomposeArray(gndx, gndy);
                 T = new double[settings.readsize[0] * settings.readsize[1]];
 
-                // Create a 2D selection for the subset
-                vT->SetSelection(adios2::Box<adios2::Dims>(settings.offset,
-                                                           settings.readsize));
                 firstStep = false;
                 MPI_Barrier(mpiReaderComm); // sync processes just for stdout
             }
@@ -119,8 +121,14 @@ int main(int argc, char *argv[])
             {
                 std::cout << "Processing step " << step << std::endl;
             }
+
+            // Create a 2D selection for the subset
+            vT->SetSelection(
+                adios2::Box<adios2::Dims>(settings.offset, settings.readsize));
+
             // Arrays are read by scheduling one or more of them
             // and performing the reads at once
+
             bpReader.GetDeferred<double>(*vT, T);
             bpReader.PerformGets();
 

examples/heatTransfer/write/CMakeLists.txt

@@ -13,9 +13,7 @@ if(ADIOS2_HAVE_MPI)
   target_link_libraries(heatTransfer_write_adios2
     adios2 MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
   )
-  target_compile_definitions(heatTransfer_write_adios2 PRIVATE
-   -DDEFAULT_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}/config.xml
-  )
+
 
   if(ADIOS2_HAVE_ADIOS1)
     add_executable(heatTransfer_write_adios1

source/adios2/engine/adios1/ADIOS1Reader.cpp

@@ -26,8 +26,7 @@ ADIOS1Reader::ADIOS1Reader(IO &io, const std::string &name, const Mode mode,
     m_EndMessage = " in call to IO Open ADIOS1Reader " + m_Name + "\n";
 
     Init();
-    m_ADIOS1.Open(); // adios_read_init_method(m_ReadMethod, mpiComm, "");
-    m_ADIOS1.GenerateVariables(io);
+    m_ADIOS1.Open(io);
 }
 
 ADIOS1Reader::~ADIOS1Reader()
@@ -38,7 +37,7 @@ ADIOS1Reader::~ADIOS1Reader()
 StepStatus ADIOS1Reader::BeginStep(const StepMode mode,
                                    const float timeoutSeconds)
 {
-    return m_ADIOS1.AdvanceStep(mode, timeoutSeconds);
+    return m_ADIOS1.AdvanceStep(m_IO, mode, timeoutSeconds);
 }
 
 // PRIVATE

source/adios2/toolkit/interop/adios1/ADIOS1CommonRead.cpp

@@ -28,7 +28,6 @@ ADIOS1CommonRead::ADIOS1CommonRead(const std::string &fileName,
 : ADIOS1Common(fileName, mpiComm, debugMode)
 {
     Init();
-    adios_read_init_method(m_ReadMethod, m_MPIComm, "");
 }
 
 ADIOS1CommonRead::~ADIOS1CommonRead()
@@ -37,12 +36,13 @@ ADIOS1CommonRead::~ADIOS1CommonRead()
     adios_read_finalize_method(m_ReadMethod);
 }
 
-bool ADIOS1CommonRead::Open()
+bool ADIOS1CommonRead::Open(IO &io)
 {
     if (m_OpenAsFile)
     {
         m_fh =
             adios_read_open_file(m_FileName.c_str(), m_ReadMethod, m_MPIComm);
+        GenerateVariables(io);
     }
     else
     {
@@ -120,6 +120,8 @@ void ADIOS1CommonRead::DefineADIOS2Variable(IO &io, const char *name,
 
 void ADIOS1CommonRead::GenerateVariables(IO &io)
 {
+    if (!m_fh)
+        return;
     /* Create a Variable for each variable in the file */
     for (int varid = 0; varid < m_fh->nvars; varid++)
     {
@@ -217,6 +219,7 @@ void ADIOS1CommonRead::ScheduleReadCommon(const std::string &name,
                                           const bool readAsJoinedArray,
                                           void *data)
 {
+    const int adios1FromStep = fromStep - 1;
     if (readAsLocalValue)
     {
         /* Get all the requested values from metadata now */
@@ -226,12 +229,12 @@ void ADIOS1CommonRead::ScheduleReadCommon(const std::string &name,
             adios_inq_var_stat(m_fh, vi, 0, 1);
             int elemsize = adios_type_size(vi->type, nullptr);
             long long blockidx = 0;
-            for (int i = 0; i < fromStep; i++)
+            for (int i = 0; i < adios1FromStep; i++)
             {
                 blockidx += vi->nblocks[i];
             }
             char *dest = (char *)data;
-            for (int i = fromStep; i < fromStep + nSteps; i++)
+            for (int i = adios1FromStep; i < adios1FromStep + nSteps; i++)
             {
                 for (int j = 0; j < vi->nblocks[i]; j++)
                 {
@@ -257,8 +260,8 @@ void ADIOS1CommonRead::ScheduleReadCommon(const std::string &name,
         {
             sel = adios_selection_boundingbox(ldims.size(), start, count);
         }
-        adios_schedule_read(m_fh, sel, name.c_str(), (int)fromStep, (int)nSteps,
-                            data);
+        adios_schedule_read(m_fh, sel, name.c_str(), (int)adios1FromStep,
+                            (int)nSteps, data);
         adios_selection_delete(sel);
     }
 }
@@ -268,7 +271,7 @@ void ADIOS1CommonRead::PerformReads()
     adios_perform_reads(m_fh, static_cast<int>(ReadMode::Blocking));
 }
 
-StepStatus ADIOS1CommonRead::AdvanceStep(const StepMode mode,
+StepStatus ADIOS1CommonRead::AdvanceStep(IO &io, const StepMode mode,
                                          const float timeout_sec)
 {
     if (m_OpenAsFile)
@@ -277,21 +280,41 @@ StepStatus ADIOS1CommonRead::AdvanceStep(const StepMode mode,
                                     "Advance() on a file which was opened for "
                                     "read as File\n");
     }
+
     if (mode != StepMode::NextAvailable && mode != StepMode::LatestAvailable)
     {
         throw std::invalid_argument(
             "ERROR: ADIOS1Reader.Advance() only allows "
             "for NextAvailable or LatestAvailable modes.\n");
     }
-    int last = (mode == StepMode::NextAvailable ? 0 : 1);
-    float *to = const_cast<float *>(&timeout_sec);
-    adios_advance_step(m_fh, last, *to);
+
+    if (m_IsBeforeFirstStep)
+    {
+        /* ADIOS1 already has the first step open after Open(), in ADIOS2 we
+         * wait for
+         * the first call to BeginStep(), which calls this function.
+         */
+
+        m_IsBeforeFirstStep = false;
+        adios_errno = err_no_error;
+    }
+    else
+    {
+        int last = (mode == StepMode::NextAvailable ? 0 : 1);
+        float *timeout = const_cast<float *>(&timeout_sec);
+        adios_advance_step(m_fh, last, *timeout);
+        if (adios_errno != err_step_notready)
+        {
+            io.RemoveAllVariables();
+        }
+    }
 
     StepStatus status;
     switch (adios_errno)
     {
     case err_no_error:
         status = StepStatus::OK;
+        GenerateVariables(io);
         break;
     case err_end_of_stream:
         status = StepStatus::EndOfStream;
@@ -403,6 +426,7 @@ void ADIOS1CommonRead::InitTransports(
             }
         }
     }
+    adios_read_init_method(m_ReadMethod, m_MPIComm, "");
 }
 
 /*

source/adios2/toolkit/interop/adios1/ADIOS1CommonRead.h

@@ -48,7 +48,7 @@ public:
 
     void InitParameters(const Params &parameters);
     void InitTransports(const std::vector<Params> &transportsParameters);
-    bool Open(); // return true if file is opened successfully
+    bool Open(IO &io); // return true if file is opened successfully
     void GenerateVariables(IO &io);
 
     void ScheduleReadCommon(const std::string &name, const Dims &offs,
@@ -57,7 +57,8 @@ public:
                             const bool readAsJoinedArray, void *data);
 
     void PerformReads();
-    StepStatus AdvanceStep(const StepMode mode, const float timeout_sec = 0.0);
+    StepStatus AdvanceStep(IO &io, const StepMode mode,
+                           const float timeout_sec = 0.0);
     void ReleaseStep();
 
     ADIOS_VARINFO *InqVar(const std::string &varName);
@@ -73,6 +74,11 @@ private:
     bool m_OpenAsFile = false;
     ADIOS_FILE *m_fh = nullptr; ///< ADIOS1 file handler
 
+    // In streaming mode, Open() does not generate the variable map.
+    // The first BeginStep() call does that to publish the variables of the
+    // first step
+    bool m_IsBeforeFirstStep = true;
+
     void Init();
 
     void DefineADIOS2Variable(IO &io, const char *name, const ADIOS_VARINFO *vi,