From 6608f692e17900251e69c3b31182fa400a9a3c56 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Thu, 20 Apr 2017 17:42:04 -0400
Subject: [PATCH] Started to implement BP1 memory buffer policy
Created public function ResizeBuffer in BP1Writer
---
source/adios2/core/adiosFunctions.cpp | 62 ++++++---------
source/adios2/core/adiosFunctions.h | 21 +----
source/adios2/engine/bp/BPFileWriter.cpp | 6 +-
source/adios2/utilities/format/bp1/BP1Base.h | 13 ++++
.../adios2/utilities/format/bp1/BP1Writer.cpp | 9 ++-
.../adios2/utilities/format/bp1/BP1Writer.h | 70 +++++++++--------
.../adios2/utilities/format/bp1/BP1Writer.tcc | 77 +++++++++++--------
7 files changed, 131 insertions(+), 127 deletions(-)
diff --git a/source/adios2/core/adiosFunctions.cpp b/source/adios2/core/adiosFunctions.cpp
index ffb5c81f4..12988d0ac 100644
--- a/source/adios2/core/adiosFunctions.cpp
+++ b/source/adios2/core/adiosFunctions.cpp
@@ -24,6 +24,7 @@
#include <stdexcept>
#include <thread> //std::thread
+#include "adios2/ADIOSTypes.h"
#include "adios2/core/Support.h"
#ifdef ADIOS2_HAVE_BZIP2
@@ -661,54 +662,37 @@ void ConvertUint64VectorToSizetVector(const std::vector<std::uint64_t> &in,
}
}
-bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
- const std::size_t maxBufferSize,
- std::vector<char> &buffer)
+int GrowBuffer(const size_t incomingDataSize, const float growthFactor,
+ std::vector<char> &buffer, const size_t position)
{
- // Check if data in buffer needs to be reallocated
- const std::size_t requiredDataSize =
- buffer.size() + newSize + 100; // adding some bytes for tolerance
- // might need to write payload in batches
- bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;
+ const size_t currentCapacity = buffer.capacity();
+ const size_t availableSpace = currentCapacity - position;
+ const double gf = static_cast<double>(growthFactor);
- if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
+ if (incomingDataSize < availableSpace)
{
- doTransportsFlush = true;
+ return 0;
}
- return doTransportsFlush;
-}
+ const size_t neededCapacity = incomingDataSize + position;
+ const double numerator = std::log(static_cast<double>(neededCapacity) /
+ static_cast<double>(currentCapacity));
+ const double denominator = std::log(gf);
-int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
- std::vector<char> &buffer)
-{
- const std::size_t currentCapacity = buffer.capacity();
- const std::size_t availableSpace = currentCapacity - buffer.size();
- const double gf = static_cast<double>(growthFactor);
+ const double n = std::ceil(numerator / denominator);
+ const size_t newSize =
+ static_cast<size_t>(std::ceil(std::pow(gf, n) * currentCapacity));
- if (incomingDataSize > availableSpace)
+ try
{
- const std::size_t neededCapacity = incomingDataSize + buffer.size();
- const double numerator = std::log(static_cast<double>(neededCapacity) /
- static_cast<double>(currentCapacity));
- const double denominator = std::log(gf);
-
- double n = std::ceil(numerator / denominator);
- const std::size_t newSize = static_cast<std::size_t>(
- std::ceil(std::pow(gf, n) * currentCapacity));
-
- try
- {
- buffer.reserve(newSize);
- }
- catch (std::bad_alloc &e)
- {
- return -1;
- }
-
- return 1;
+ buffer.resize(newSize);
}
- return 0;
+ catch (std::bad_alloc &e)
+ {
+ return -1;
+ }
+
+ return 1;
}
bool IsLittleEndian() noexcept
diff --git a/source/adios2/core/adiosFunctions.h b/source/adios2/core/adiosFunctions.h
index 07f05fae2..bfedf18b0 100644
--- a/source/adios2/core/adiosFunctions.h
+++ b/source/adios2/core/adiosFunctions.h
@@ -195,33 +195,18 @@ void ConvertUint64VectorToSizetVector(const std::vector<std::uint64_t> &in,
*/
std::string DimsToCSV(const std::vector<std::size_t> &dims);
-/**
- * Common strategy to check for heap buffer allocation for data and metadata
- * typically calculated in Write
- * @param newSize new data size
- * @param growthFactor user provided growth factor for index and data memory
- * buffers ( default = 1.5 )
- * @param maxBufferSize user provided maximum buffer size
- * @param buffer to be reallocated
- * @return true: must do a transport flush, false: buffer sizes are enough
- * to
- * contain incoming data, no need for transport flush
- */
-bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
- const std::size_t maxBufferSize,
- std::vector<char> &buffer);
-
/**
* Grows a buffer by a factor of n . growthFactor . currentCapacity to
* accommodate for incomingDataSize
* @param incomingDataSize size of new data required to be stored in buffer
* @param growthFactor buffer grows in multiples of the growth buffer
* @param buffer to be resized
+ * @param position, current buffer position
* @return -1: failed to allocate (bad_alloc), 0: didn't have to allocate
* (enough space), 1: successful allocation
*/
-int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
- std::vector<char> &buffer);
+int GrowBuffer(const size_t incomingDataSize, const float growthFactor,
+ std::vector<char> &buffer, const size_t position);
/**
* Check if system is little endian
diff --git a/source/adios2/engine/bp/BPFileWriter.cpp b/source/adios2/engine/bp/BPFileWriter.cpp
index 3e650472b..314519912 100644
--- a/source/adios2/engine/bp/BPFileWriter.cpp
+++ b/source/adios2/engine/bp/BPFileWriter.cpp
@@ -273,7 +273,7 @@ void BPFileWriter::Close(const int transportIndex)
if (allClose == true) // aggregate and write profiling.log
{
- m_BP1Writer.DumpProfilingLogFile(m_Name, m_RankMPI, m_Transports);
+ m_BP1Writer.WriteProfilingLogFile(m_Name, m_RankMPI, m_Transports);
}
}
}
@@ -395,8 +395,8 @@ void BPFileWriter::InitTransports()
{
auto itProfile = parameters.find("profile_units");
bool doProfiling = false;
- Support::Resolutions resolution =
- Support::Resolutions::s; // default is seconds
+ // default is seconds for this engine
+ Support::Resolutions resolution = Support::Resolutions::s;
if (itProfile != parameters.end())
{
if (itProfile->second == "mus" ||
diff --git a/source/adios2/utilities/format/bp1/BP1Base.h b/source/adios2/utilities/format/bp1/BP1Base.h
index 80b891462..0c9a2ff52 100644
--- a/source/adios2/utilities/format/bp1/BP1Base.h
+++ b/source/adios2/utilities/format/bp1/BP1Base.h
@@ -62,6 +62,8 @@ public:
*/
BP1Base(MPI_Comm mpiComm, const bool debugMode);
+ virtual ~BP1Base() = default;
+
/**
* Checks if input name has .bp extension and returns a .bp directory name
* @param name input (might or not have .bp)
@@ -80,6 +82,17 @@ public:
void OpenRankFiles(const std::string name, const std::string accessMode,
Transport &file) const;
+ /**
+ * Return type of the CheckAllocation function.
+ */
+ enum class ResizeResult
+ {
+ FAILURE, //!< FAILURE, caught a std::bad_alloc
+ UNCHANGED, //!< UNCHANGED, no need to resize (sufficient capacity)
+ SUCCESS, //!< SUCCESS, resize was successful
+ FLUSH //!< FLUSH, need to flush to transports for current variable
+ };
+
protected:
/** might be used in large payload copies to buffer */
unsigned int m_Threads = 1;
diff --git a/source/adios2/utilities/format/bp1/BP1Writer.cpp b/source/adios2/utilities/format/bp1/BP1Writer.cpp
index 76814161e..666a3e6ed 100644
--- a/source/adios2/utilities/format/bp1/BP1Writer.cpp
+++ b/source/adios2/utilities/format/bp1/BP1Writer.cpp
@@ -156,12 +156,12 @@ void BP1Writer::Close(Transport &transport, bool &isFirstClose,
}
}
-void BP1Writer::DumpProfilingLogFile(
- const std::string name, const unsigned int rank,
+void BP1Writer::WriteProfilingLogFile(
+ const std::string &name, const unsigned int rank,
const std::vector<std::shared_ptr<Transport>> &transports) noexcept
{
const std::string fileName(GetDirectoryName(name) + "/profiling.log");
- const std::string rankLog = GetRankProfilingLog(rank, transports);
+ const std::string rankLog(GetRankProfilingLog(rank, transports));
m_BP1Aggregator.WriteProfilingLog(fileName, rankLog);
}
@@ -447,6 +447,9 @@ std::string BP1Writer::GetRankProfilingLog(
// Explicit instantiation of only public templates
#define declare_template_instantiation(T) \
+ template BP1Writer::ResizeResult BP1Writer::ResizeBuffer( \
+ const Variable<T> &variable); \
+ \
template void BP1Writer::WriteVariablePayload( \
const Variable<T> &variable) noexcept; \
\
diff --git a/source/adios2/utilities/format/bp1/BP1Writer.h b/source/adios2/utilities/format/bp1/BP1Writer.h
index afffaa187..821217336 100644
--- a/source/adios2/utilities/format/bp1/BP1Writer.h
+++ b/source/adios2/utilities/format/bp1/BP1Writer.h
@@ -43,51 +43,35 @@ public:
*/
BP1Writer(MPI_Comm mpiComm, const bool debugMode = false);
- /**
- * Calculates the Process Index size in bytes according to the BP format,
- * including list of method with no parameters (for now)
- * @param name
- * @param timeStepName
- * @param numberOfTransports
- * @return size of pg index
- */
- size_t GetProcessGroupIndexSize(const std::string name,
- const std::string timeStepName,
- const size_t numberOfTransports) const
- noexcept;
+ virtual ~BP1Writer() = default;
/**
* Writes a process group index PGIndex and list of methods (from
- * transports),
- * done at Open or aggregation of new time step
- * Version that operates on a single heap buffer and metadataset.
+ * transports). Done at Open or Advance.
* @param isFortran
- * @param name
+ * @param name group name, taking the rank
* @param processID
* @param transports
- * @param buffer
- * @param metadataSet
*/
void WriteProcessGroupIndex(
const bool isFortran, const std::string name, const uint32_t processID,
const std::vector<std::shared_ptr<Transport>> &transports) noexcept;
/**
- * Returns the estimated variable index size
- * @param group
- * @param variableName
+ *
* @param variable
- * @param verbosity
- * @return variable index size
+ * @return
+ * -1: allocation failed,
+ * 0: no allocation needed,
+ * 1: reallocation is sucessful
+ * 2: need a transport flush
*/
template <class T>
- size_t GetVariableIndexSize(const Variable<T> &variable) const noexcept;
+ ResizeResult ResizeBuffer(const Variable<T> &variable);
/**
* Write metadata for a given variable
* @param variable
- * @param heap
- * @param metadataSet
*/
template <class T>
void WriteVariableMetadata(const Variable<T> &variable) noexcept;
@@ -96,16 +80,11 @@ public:
* Expensive part this is only for heap buffers need to adapt to vector of
* capsules
* @param variable
- * @param buffer
*/
template <class T>
void WriteVariablePayload(const Variable<T> &variable) noexcept;
- /**
- * Flattens data
- * @param metadataSet
- * @param buffer
- */
+ /** Flattens data buffer */
void Advance();
/**
@@ -120,14 +99,34 @@ public:
void Close(Transport &transport, bool &isFirstClose,
const bool doAggregation) noexcept;
- void DumpProfilingLogFile(
- const std::string name, const unsigned int rank,
+ void WriteProfilingLogFile(
+ const std::string &name, const unsigned int rank,
const std::vector<std::shared_ptr<Transport>> &transports) noexcept;
private:
/** BP format version */
const std::uint8_t m_Version = 3;
+ /**
+ * Calculates the Process Index size in bytes according to the BP format,
+ * including list of method with no parameters (for now)
+ * @param name
+ * @param timeStepName
+ * @param numberOfTransports
+ * @return size of pg index
+ */
+ size_t GetProcessGroupIndexSize(const std::string name,
+ const std::string timeStepName,
+ const size_t numberOfTransports) const
+ noexcept;
+
+ /**
+ * Returns the estimated variable index size
+ * @param variable
+ */
+ template <class T>
+ size_t GetVariableIndexSize(const Variable<T> &variable) const noexcept;
+
/**
* Get variable statistics
* @param variable
@@ -277,6 +276,9 @@ private:
};
#define declare_template_instantiation(T) \
+ extern template BP1Writer::ResizeResult BP1Writer::ResizeBuffer( \
+ const Variable<T> &variable) noexcept; \
+ \
extern template void BP1Writer::WriteVariablePayload( \
const Variable<T> &variable) noexcept; \
\
diff --git a/source/adios2/utilities/format/bp1/BP1Writer.tcc b/source/adios2/utilities/format/bp1/BP1Writer.tcc
index dab05715c..50facc41a 100644
--- a/source/adios2/utilities/format/bp1/BP1Writer.tcc
+++ b/source/adios2/utilities/format/bp1/BP1Writer.tcc
@@ -19,40 +19,20 @@ namespace format
// PUBLIC
template <class T>
-size_t BP1Writer::GetVariableIndexSize(const Variable<T> &variable) const
- noexcept
+BP1Writer::ResizeResult BP1Writer::ResizeBuffer(const Variable<T> &variable)
{
- // size_t indexSize = varEntryLength + memberID + lengthGroupName +
- // groupName + lengthVariableName + lengthOfPath + path + datatype
- size_t indexSize = 23; // without characteristics
- indexSize += variable.m_Name.size();
-
- // characteristics 3 and 4, check variable number of dimensions
- const size_t dimensions = variable.DimensionsSize();
- indexSize += 28 * dimensions; // 28 bytes per dimension
- indexSize += 1; // id
+ size_t variableData =
+ GetVariableIndexSize(variable) + variable.PayLoadSize();
+ size_t requiredCapacity = variableData + m_Heap.m_DataPosition;
- // characteristics, offset + payload offset in data
- indexSize += 2 * (1 + 8);
- // characteristic 0, if scalar add value, for now only allowing string
- if (dimensions == 1)
+ if (requiredCapacity > m_MaxBufferSize && m_MaxBufferSize > 0) // is set
{
- indexSize += sizeof(T);
- indexSize += 1; // id
- // must have an if here
- indexSize += 2 + variable.m_Name.size();
- indexSize += 1; // id
- }
-
- // characteristic statistics
- if (m_Verbosity == 0) // default, only min and max
- {
- indexSize += 2 * (sizeof(T) + 1);
- indexSize += 1 + 1; // id
+ if (m_Heap.GetDataSize() < m_MaxBufferSize)
+ {
+ m_Heap.ResizeData(m_MaxBufferSize);
+ return ResizeResult::FLUSH;
+ }
}
-
- return indexSize + 12; // extra 12 bytes in case of attributes
- // need to add transform characteristics
}
template <class T>
@@ -88,6 +68,43 @@ void BP1Writer::WriteVariablePayload(const Variable<T> &variable) noexcept
}
// PRIVATE
+template <class T>
+size_t BP1Writer::GetVariableIndexSize(const Variable<T> &variable) const
+ noexcept
+{
+ // size_t indexSize = varEntryLength + memberID + lengthGroupName +
+ // groupName + lengthVariableName + lengthOfPath + path + datatype
+ size_t indexSize = 23; // without characteristics
+ indexSize += variable.m_Name.size();
+
+ // characteristics 3 and 4, check variable number of dimensions
+ const size_t dimensions = variable.DimensionsSize();
+ indexSize += 28 * dimensions; // 28 bytes per dimension
+ indexSize += 1; // id
+
+ // characteristics, offset + payload offset in data
+ indexSize += 2 * (1 + 8);
+ // characteristic 0, if scalar add value, for now only allowing string
+ if (dimensions == 1)
+ {
+ indexSize += sizeof(T);
+ indexSize += 1; // id
+ // must have an if here
+ indexSize += 2 + variable.m_Name.size();
+ indexSize += 1; // id
+ }
+
+ // characteristic statistics
+ if (m_Verbosity == 0) // default, only min and max
+ {
+ indexSize += 2 * (sizeof(T) + 1);
+ indexSize += 1 + 1; // id
+ }
+
+ return indexSize + 12; // extra 12 bytes in case of attributes
+ // need to add transform characteristics
+}
+
template <class T>
BP1Writer::Stats<typename TypeInfo<T>::ValueType>
BP1Writer::GetStats(const Variable<T> &variable) const noexcept
--
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