Merge pull request #190 from williamfgc/memory

Memory

examples/heatTransfer/write/CMakeLists.txt

@@ -16,6 +16,8 @@ if(ADIOS2_HAVE_MPI)
     PRIVATE ${MPI_C_INCLUDE_PATH}
   )
   target_link_libraries(heatTransfer_write_adios2 adios2 ${MPI_C_LIBRARIES})
+  target_compile_definitions(heatTransfer_write_adios2 PRIVATE
+   -DDEFAULT_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}/config.xml)
 
   if(ADIOS2_HAVE_ADIOS1)
     find_package(ADIOS1 REQUIRED)

examples/heatTransfer/write/IO_adios2.cpp

@@ -14,6 +14,13 @@
 
 #include <adios2.h>
 
+#define str_helper(X) #X
+#define str(X) str_helper(X)
+#ifndef DEFAULT_CONFIG
+#define DEFAULT_CONFIG config.xml
+#endif
+#define DEFAULT_CONFIG_STR str(DEFAULT_CONFIG)
+
 static int rank_saved;
 adios2::ADIOS *ad = nullptr;
 std::shared_ptr<adios2::Engine> bpWriter;
@@ -24,7 +31,8 @@ IO::IO(const Settings &s, MPI_Comm comm)
 {
     rank_saved = s.rank;
     m_outputfilename = s.outputfile + ".bp";
-    ad = new adios2::ADIOS("config.xml", comm, adios2::DebugON);
+    ad = new adios2::ADIOS(std::string(DEFAULT_CONFIG_STR), comm,
+                           adios2::DebugON);
 
     // Define method for engine creation
 

examples/heatTransfer/write/config.xml

+<?xml version="1.0"?>
+<!-- Config XML file fo the  heatTransfer_write_adios2 executable in .
+     build/bin from IO_adios2.cpp -->
+
+<adios-config>
+    <io name="output">
+        <engine type="BPFileWriter">
+            
+            <!-- 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>
+</adios-config>

source/adios2/ADIOSTypes.h

@@ -2,7 +2,8 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * ADIOSTypes.h
+ * ADIOSTypes.h : public header that contains "using/typedef" alias, defaults
+ * and parameters options as enum classes
  *
  *  Created on: Mar 23, 2017
  *      Author: Chuck Atkins chuck.atkins@kitware.com
@@ -31,7 +32,8 @@
 namespace adios2
 {
 
-/** Variable shape type identifier */
+/** Variable shape type identifier, assigned automatically from the signature of
+ *  DefineVariable */
 enum class ShapeID
 {
     GlobalValue, ///< single global value, common case
@@ -84,12 +86,12 @@ enum class TransportType
     WAN
 };
 
-/** Just for info purposes */
+/** Currently available engines, just for info purposes */
 enum class IOEngine
 {
     Unknown,
     BPFileWriter, ///< produces bp files
-    BPFileReader, ///< read bp files
+    BPFileReader, ///< read bp files (not yet implemented)
     HDF5Writer,   ///<
     HDF5Reader,   ///<
     ADIOS1Writer,
@@ -150,14 +152,19 @@ const std::string DefaultTimeUnit("Microseconds");
 constexpr TimeUnit DefaultTimeUnitEnum(TimeUnit::Microseconds);
 
 /** default initial bp buffer size, 16Kb, in bytes */
-constexpr size_t DefaultInitialBufferSize(16384);
-/** default maximum bp buffer size, 16Mb, in bytes */
-constexpr size_t DefaultMaxBufferSize(16777216);
-/** default buffer growth factor (from STL vector = 2.) */
-constexpr float DefaultBufferGrowthFactor(2.);
+constexpr size_t DefaultInitialBufferSize(16 * 1024);
+
+/** default maximum bp buffer size, unlimited, in bytes.
+ *  Needs to be studied for optimizing applications */
+constexpr size_t DefaultMaxBufferSize(std::numeric_limits<size_t>::max() - 1);
+
+/** default buffer growth factor. Needs to be studied
+ * for optimizing applications*/
+constexpr float DefaultBufferGrowthFactor(1.05);
+
 /** default size for writing/reading files using POSIX/fstream/stdio write
- *  1Gb - 1Kb (tolerance)*/
-constexpr size_t DefaultMaxFileBatchSize(1024 * 1024 * 1024 - 1024);
+ *  2Gb - 100Kb (tolerance)*/
+constexpr size_t DefaultMaxFileBatchSize(2147381248);
 
 // adios alias values and types
 constexpr bool DebugON = true;

source/adios2/toolkit/format/bp1/BP1Base.cpp

@@ -182,7 +182,7 @@ void BP1Base::InitParameterBufferGrowth(const std::string value)
         if (!success || m_GrowthFactor <= 1.f)
         {
             throw std::invalid_argument(
-                "ERROR: IO SetParameter buffer_growth value "
+                "ERROR: BufferGrowthFactor value "
                 "can't be less or equal than 1 (default = 1.5), or couldn't "
                 "convert number, in call to Open\n");
         }
@@ -196,10 +196,8 @@ void BP1Base::InitParameterBufferGrowth(const std::string value)
 void BP1Base::InitParameterInitBufferSize(const std::string value)
 {
     const std::string errorMessage(
-        "ERROR: couldn't convert value of init_buffer_size IO "
-        "SetParameter, valid syntax: InitialBufferSize=10Gb, "
-        "InitialBufferSize=1000Mb, InitialBufferSize=16Kb (minimum default), "
-        " in call to Open");
+        "ERROR: wrong value for InitialBufferSize, it must be larger than "
+        "16Kb (minimum default), in call to Open\n");
 
     if (m_DebugMode)
     {

source/adios2/toolkit/format/bp1/BP1Writer.cpp

@@ -117,6 +117,15 @@ void BP1Writer::WriteProcessGroupIndex(
 
 void BP1Writer::Advance()
 {
+    // enforce memory policy here to restrict buffer size for each timestep
+    // this is flushing
+
+    if (m_MaxBufferSize == DefaultMaxBufferSize)
+    {
+        // current position + 1Kb chunk tolerance
+        m_MaxBufferSize = m_HeapBuffer.m_DataPosition + 64;
+    }
+
     if (m_Profiler.IsActive)
     {
         m_Profiler.Timers.at("buffering").Resume();