Merge pull request #336 from guj/1204

1204

examples/heatTransfer/heat_hdf5.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="HDF5Writer">
+            
+            <!-- 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"/>
+
+            <!-- XXKb, XXMb, or XXXGb supported, default=16Kb 
+                (applications might choose an optimal value) -->
+            <parameter key="InitialBufferSize" value="16Kb"/> 
+            
+            <!-- XXKb, XXMb, or XXXGb supported, default=Unlimited (until 
+                 fails), maximum at each time step  
+                (applications might choose an optimal value) -->
+            <!-- <parameter key="MaxBufferSize" value="2Gb"/> -->
+
+            <!-- exponential growth factor > 1, default = 1.05 
+                 1.05  is good for a few large variables, for many small
+                 variables increase the value to 1.5 to 2 
+                 (optimal value is application dependent)--> 
+            <!-- <parameter key="BufferGrowthFactor" value="1.05"/> -->
+            
+        </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>
+
+
+    <!--====================================
+           Configuration for the Reader 
+        ====================================-->
+
+    <io name="reader">
+      <!-- <engine type="BPFileReader"> -->
+       <engine type="HDF5Reader"> 
+            
+            <!-- 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/write/IO_h5mixer.cpp

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * IO_ADIOS2.cpp
+ * IO_h5mixer.cpp
  *
  *  Created on: Feb 2017
  *      Author: Norbert Podhorszki
@@ -50,7 +50,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
 
     // Define method for engine creation
 
-    adios2::IO &h5io = ad->DeclareIO("output");
+    adios2::IO &h5io = ad->DeclareIO("writer");
     if (!h5io.InConfigFile())
     {
         // if not defined by user, we can change the default settings

examples/heatTransfer/write/IO_ph5.cpp

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * IO_ADIOS2.cpp
+ * IO_ph5.cpp
  *
  *  Created on: Feb 2017
  *      Author: Norbert Podhorszki

examples/heatTransfer/write/IO_ph5_adios2.cpp

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * IO_ADIOS2.cpp
+ * IO_ph5_adios2.cpp
  *
  *  Created on: Feb 2017
  *      Author: Norbert Podhorszki
@@ -37,7 +37,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
     // Define method for engine creation
     // 1. Get method def from config file or define new one
 
-    adios2::IO &h5io = ad->DeclareIO("output");
+    adios2::IO &h5io = ad->DeclareIO("writer");
     if (!h5io.InConfigFile())
     {
         // if not defined by user, we can change the default settings
@@ -69,7 +69,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
 IO::~IO()
 {
     h5writer->Close();
-    // delete ad;
+    delete ad;
 }
 
 void IO::write(int step, const HeatTransfer &ht, const Settings &s,

source/adios2/engine/hdf5/HDF5WriterP.cpp

@@ -46,7 +46,28 @@ void HDF5WriterP::Init()
             ", in call to ADIOS Open or HDF5Writer constructor\n");
     }
 
+#ifdef NEVER
     m_H5File.Init(m_Name, m_MPIComm, true);
+#else
+    // enforce .h5 ending
+    std::string suffix = ".h5";
+    std::string wrongSuffix = ".bp";
+
+    int ss = m_Name.size();
+    int wpos = m_Name.find(wrongSuffix);
+
+    if (wpos == ss - wrongSuffix.size())
+    {
+        // is a file with .bp ending
+        std::string updatedName = m_Name.substr(0, wpos) + suffix;
+        m_H5File.Init(updatedName, m_MPIComm, true);
+    }
+    else
+    {
+        m_H5File.Init(m_Name, m_MPIComm, true);
+    }
+
+#endif
 }
 
 #define declare_type(T)                                                        \