diff --git a/source/adios2/capsule/heap/STLVector.cpp b/source/adios2/capsule/heap/STLVector.cpp
index 2b6b9a289fcded2c1cc3fddcd36673befd82fe87..9893948669be5570d12044e9fbf32b968603d3fd 100644
--- a/source/adios2/capsule/heap/STLVector.cpp
+++ b/source/adios2/capsule/heap/STLVector.cpp
@@ -2,37 +2,38 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * Heap.cpp
+ * STLVector.cpp
*
* Created on: Dec 22, 2016
* Author: wfg
*/
-#include "STLVector.h"
-
+/// \cond EXCLUDE_FROM_DOXYGEN
#include <new> //std::bad_alloc
#include <stdexcept> //std::runtime_error
+/// \endcond
+
+#include "STLVector.h"
namespace adios
{
namespace capsule
{
-STLVector::STLVector(std::string accessMode, int rankMPI, bool debugMode)
-: Capsule{"Heap", std::move(accessMode), rankMPI, debugMode}
+STLVector::STLVector(const bool debugMode)
+: Capsule("heap/STLVector", debugMode)
{
- m_Data.reserve(16777216);
}
char *STLVector::GetData() { return m_Data.data(); }
char *STLVector::GetMetadata() { return m_Metadata.data(); }
-std::size_t STLVector::GetDataSize() const { return m_Data.size(); }
+size_t STLVector::GetDataSize() const { return m_Data.size(); }
-std::size_t STLVector::GetMetadataSize() const { return m_Metadata.size(); }
+size_t STLVector::GetMetadataSize() const { return m_Metadata.size(); }
-void STLVector::ResizeData(const std::size_t size)
+void STLVector::ResizeData(const size_t size)
{
if (m_DebugMode == true)
{
@@ -53,7 +54,7 @@ void STLVector::ResizeData(const std::size_t size)
}
}
-void STLVector::ResizeMetadata(const std::size_t size)
+void STLVector::ResizeMetadata(const size_t size)
{
if (m_DebugMode == true)
{
diff --git a/source/adios2/capsule/heap/STLVector.h b/source/adios2/capsule/heap/STLVector.h
index aaa7bd095cedb6d252c7d7ec1d7c28787613a0dd..ae00013690608e90a87597a6a52185ad08a8c0c1 100644
--- a/source/adios2/capsule/heap/STLVector.h
+++ b/source/adios2/capsule/heap/STLVector.h
@@ -30,31 +30,27 @@ class STLVector : public Capsule
{
public:
- std::vector<char> m_Data; ///< data buffer allocated using the STL in heap
- /// memory, default size = 16 Mb
- std::vector<char>
- m_Metadata; ///< metadata buffer allocated using the STL in
- /// heap memory, default size = 100 Kb
+ /** data buffer allocated using the STL in heap */
+ std::vector<char> m_Data;
+ /** might be used in cases other than files */
+ std::vector<char> m_Metadata;
/**
* Unique constructor
- * @param accessMode read, write or append
- * @param rankMPI MPI rank
- * @param debugMode true: extra checks, slower
+ * @param debugMode true: exceptions checks
*/
- STLVector(const std::string accessMode, const int rankMPI,
- const bool debugMode = false);
+ STLVector(const bool debugMode = false);
~STLVector() = default;
char *GetData();
char *GetMetadata();
- std::size_t GetDataSize() const;
- std::size_t GetMetadataSize() const;
+ size_t GetDataSize() const;
+ size_t GetMetadataSize() const;
- void ResizeData(const std::size_t size);
- void ResizeMetadata(const std::size_t size);
+ void ResizeData(const size_t size);
+ void ResizeMetadata(const size_t size);
};
} // end namespace capsule
diff --git a/source/adios2/capsule/shmem/ShmSystemV.cpp b/source/adios2/capsule/shmem/ShmSystemV.cpp
index c241b6eab36ecd106ab9feec7df510320e31c570..b9c78211c7921cb367c4537722d660475b78e8ec 100644
--- a/source/adios2/capsule/shmem/ShmSystemV.cpp
+++ b/source/adios2/capsule/shmem/ShmSystemV.cpp
@@ -8,35 +8,37 @@
* Author: wfg
*/
-#include "ShmSystemV.h"
-
#include <sys/shm.h>
+/// \cond EXCLUDE_FROM_DOXYGEN
#include <ios> //std::ios_base::failure
#include <utility>
+/// \endcond
+
+#include "ShmSystemV.h"
namespace adios
{
-ShmSystemV::ShmSystemV(std::string accessMode, int rankMPI,
- const std::string &pathName, size_t dataSize,
- size_t metadataSize, bool debugMode)
-: Capsule{"ShmSystemV", std::move(accessMode), rankMPI, debugMode},
- m_DataSize{dataSize}, m_MetadataSize{metadataSize}
+ShmSystemV::ShmSystemV(const std::string &pathName, const int rankMPI,
+ const size_t dataSize, const size_t metadataSize,
+ const bool debugMode)
+: Capsule("ShmSystemV", debugMode), m_DataSize(dataSize),
+ m_MetadataSize(metadataSize)
{
// Data Shared memory sector
const std::string dataPath(pathName + "/adios.shm.data." +
- std::to_string(m_RankMPI));
- m_DataKey = ftok(dataPath.c_str(), m_RankMPI + 1);
+ std::to_string(rankMPI));
+ // 2nd field must be greater than zero and unique
+ m_DataKey = ftok(dataPath.c_str(), rankMPI + 1);
m_DataShmID = shmget(m_DataKey, m_DataSize, IPC_CREAT | 0666);
m_Data = static_cast<char *>(shmat(m_DataShmID, nullptr, 0));
// Metadata Shared memory sector
const std::string metadataPath(pathName + "/adios.shm.metadata." +
- std::to_string(m_RankMPI));
- m_MetadataKey =
- ftok(metadataPath.c_str(),
- m_RankMPI + 1); // 2nd field must be greater than zero and unique
+ std::to_string(rankMPI));
+ // 2nd field must be greater than zero and unique
+ m_MetadataKey = ftok(metadataPath.c_str(), rankMPI + 1);
m_MetadataShmID = shmget(m_MetadataKey, m_MetadataSize, IPC_CREAT | 0666);
m_Metadata = static_cast<char *>(shmat(m_MetadataShmID, nullptr, 0));
diff --git a/source/adios2/capsule/shmem/ShmSystemV.h b/source/adios2/capsule/shmem/ShmSystemV.h
index 68631624b214716fac3e54a272835c5917fab43b..ca8872bfcb32d073c685c5cd7e44aed7a62064c4 100644
--- a/source/adios2/capsule/shmem/ShmSystemV.h
+++ b/source/adios2/capsule/shmem/ShmSystemV.h
@@ -24,15 +24,16 @@ class ShmSystemV : public Capsule
public:
/**
- * Create a Capsule in shared memory using System V shm API
- * @param accessMode
- * @param pathName used to create the key as a unique identifier
- * @param dataSize size of allocated memory segment for data
- * @param metadataSize size of allocated memory segment for metadata
- * @param debugMode true: extra checks, slower
- */
- ShmSystemV(std::string accessMode, int rankMPI, const std::string &pathName,
- size_t dataSize, size_t metadataSize, bool debugMode = false);
+ * Create a Capsule in shared memory using System V shm API
+ * @param accessMode
+ * @param pathName used to create the key as a unique identifier
+ * @param dataSize size of allocated memory segment for data
+ * @param metadataSize size of allocated memory segment for metadata
+ * @param debugMode true: extra checks, slower
+ */
+ ShmSystemV(const std::string &pathName, const int rankMPI,
+ const size_t dataSize, const size_t metadataSize,
+ const bool debugMode = false);
~ShmSystemV() = default;
@@ -43,24 +44,21 @@ public:
size_t GetMetadataSize() const; ///< get current metadata buffer size
private:
- char *m_Data = nullptr; ///< reference to a shared memory data buffer
- /// created with shmget
+ /** reference to a shared memory data buffer */
+ char *m_Data = nullptr;
const size_t m_DataSize; ///< size of the allocated shared memory segment
key_t m_DataKey; ///< key associated with the data buffer, created with ftok
int m_DataShmID; ///< data shared memory buffer id
- char *m_Metadata =
- nullptr; ///< reference to a shared memory metadata buffer
- /// created with shmget
- const size_t
- m_MetadataSize; ///< size of the allocated shared memory segment
- key_t m_MetadataKey; ///< key associated with the metadata buffer, created
- /// with ftok
- int m_MetadataShmID; ///< metadata shared memory buffer id
+ /** reference to a shared memory metadata buffer created with shmget */
+ char *m_Metadata = nullptr;
+ const size_t m_MetadataSize; ///< size of the allocated segment
+ key_t m_MetadataKey; ///< ftok metadata buffer key
+ int m_MetadataShmID; ///< metadata shared memory buffer id
- void CheckShm() const; ///< checks if all shared memory allocations are
- /// correct, throws std::bad_alloc, called from
- /// constructor if debug mode is true
+ /** checks if all shared memory allocations are correct, throws
+ std::bad_alloc, called from constructor if debug mode is true */
+ void CheckShm() const;
};
} // end namespace adios
diff --git a/source/adios2/core/Capsule.cpp b/source/adios2/core/Capsule.cpp
index 60888e8f85ee0bd4bad144c8e7c28b75033ef25a..2388c03fdf73556dc8658ae247eddf60ab8e1cd6 100644
--- a/source/adios2/core/Capsule.cpp
+++ b/source/adios2/core/Capsule.cpp
@@ -10,15 +10,11 @@
#include "Capsule.h"
-#include <utility>
-
namespace adios
{
-Capsule::Capsule(const std::string type, const std::string accessMode,
- int rankMPI, bool debugMode)
-: m_Type{std::move(type)}, m_AccessMode{std::move(accessMode)},
- m_RankMPI{rankMPI}, m_DebugMode{debugMode}
+Capsule::Capsule(const std::string type, const bool debugMode)
+: m_Type(type), m_DebugMode(debugMode)
{
}
diff --git a/source/adios2/core/Capsule.h b/source/adios2/core/Capsule.h
index c3e3cdcebef36517998014186d664affea40342f..51e7098dc61899e59b65a814f9c0785a877a337f 100644
--- a/source/adios2/core/Capsule.h
+++ b/source/adios2/core/Capsule.h
@@ -5,7 +5,7 @@
* Capsule.h
*
* Created on: Dec 7, 2016
- * Author: wfgtemplates and pointers
+ * Author: wfg
*/
#ifndef ADIOS2_CORE_CAPSULE_H_
@@ -29,40 +29,40 @@ class Capsule
{
public:
- const std::string m_Type; ///< buffer type
- const std::string m_AccessMode; ///< 'w': write, 'r': read, 'a': append
+ /** Derived class ID */
+ const std::string m_Type;
- std::size_t m_DataPosition = 0; ///< position in current data buffer (not
- /// included data flushed to transports)
- std::size_t m_DataAbsolutePosition = 0; ///< include bytes flushed
+ /** position in current data buffer */
+ size_t m_DataPosition = 0;
- std::size_t m_MetadataPosition = 0; ///< position in metadata buffer
+ /** position in current data buffer + bytes flushed in transports */
+ size_t m_DataAbsolutePosition = 0;
+
+ /** position in metadata buffer */
+ size_t m_MetadataPosition = 0;
/**
- * Base class constructor providing type from derived class and accessMode
- * @param type derived class type
- * @param accessMode 'w':write, 'r':read, 'a':append
- * @param rankMPI current MPI rank
- * @param debugMode
+ * Unique constructor
+ * @param type derived class
+ * @param debugMode true: extra exception checks
*/
- Capsule(const std::string type, const std::string accessMode,
- const int rankMPI, const bool debugMode);
+ Capsule(const std::string type, const bool debugMode);
virtual ~Capsule() = default;
- virtual char *GetData() = 0; ///< return the pointer to the raw data buffer
- virtual char *
- GetMetadata() = 0; ///< return the pointer to the raw metadata buffer
+ /** pointer to the raw data buffer */
+ virtual char *GetData() = 0;
+ /** pointer to the raw metadata buffer */
+ virtual char *GetMetadata() = 0;
- virtual std::size_t GetDataSize() const = 0; ///< data buffer size
- virtual std::size_t GetMetadataSize() const = 0; ///< metadata buffer size
+ virtual size_t GetDataSize() const = 0; ///< data buffer memory size
+ virtual size_t GetMetadataSize() const = 0; ///< metadata buffer memory size
- virtual void ResizeData(std::size_t size); ///< resize data buffer
- virtual void ResizeMetadata(std::size_t size); ///< resize metadata buffer
+ virtual void ResizeData(size_t size); ///< resize data buffer
+ virtual void ResizeMetadata(size_t size); ///< resize metadata buffer
protected:
- const int m_RankMPI = 0; ///< current MPI rank
- const bool m_DebugMode = false; ///< true: extra checks
+ const bool m_DebugMode = false; ///< true: extra exception checks
};
} // end namespace
diff --git a/source/adios2/engine/bp/BPFileReader.cpp b/source/adios2/engine/bp/BPFileReader.cpp
index ef4951a0a65487bcf8b28d253092a92bdc140179..d74d94adac0ab80f5b2a5cef3b0cfb56803b6b7a 100644
--- a/source/adios2/engine/bp/BPFileReader.cpp
+++ b/source/adios2/engine/bp/BPFileReader.cpp
@@ -24,7 +24,7 @@ BPFileReader::BPFileReader(ADIOS &adios, const std::string &name,
const Method &method)
: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method,
" BPFileReader constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+ m_Heap(m_DebugMode)
{
Init();
}
diff --git a/source/adios2/engine/bp/BPFileReader.h b/source/adios2/engine/bp/BPFileReader.h
index cba6a54ea7724d530cef9a22ab351b13351a36b7..6f36b4f336810ec97aff3ff6b437c0a221a7092c 100644
--- a/source/adios2/engine/bp/BPFileReader.h
+++ b/source/adios2/engine/bp/BPFileReader.h
@@ -113,7 +113,7 @@ public:
private:
capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
+ m_Heap; ///< heap capsule, contains data and metadata buffers
// format::BP1Writer m_BP1Writer; ///< format object will provide the
// required
// BP functionality to be applied on m_Buffer and m_Transports
diff --git a/source/adios2/engine/bp/BPFileWriter.cpp b/source/adios2/engine/bp/BPFileWriter.cpp
index 013a19ec07d72c18371f3041fbb0b6ac29c528f4..ad033c333d7d0c5e507f0dd3e3ed04586df5f11a 100644
--- a/source/adios2/engine/bp/BPFileWriter.cpp
+++ b/source/adios2/engine/bp/BPFileWriter.cpp
@@ -25,9 +25,8 @@ BPFileWriter::BPFileWriter(ADIOS &adios, const std::string &name,
const Method &method)
: Engine(adios, "BPFileWriter", name, accessMode, mpiComm, method,
" BPFileWriter constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode),
- m_BP1Aggregator(m_MPIComm, m_DebugMode),
- m_MaxBufferSize(m_Buffer.m_Data.max_size())
+ m_Heap(m_DebugMode), m_BP1Aggregator(m_MPIComm, m_DebugMode),
+ m_MaxBufferSize(m_Heap.m_Data.max_size())
{
m_MetadataSet.TimeStep = 1; // to be compatible with ADIOS1.x
Init();
@@ -245,7 +244,7 @@ void BPFileWriter::Write(const std::string & /*variableName*/,
void BPFileWriter::Advance(float /*timeout_sec*/)
{
- m_BP1Writer.Advance(m_MetadataSet, m_Buffer);
+ m_BP1Writer.Advance(m_MetadataSet, m_Heap);
}
void BPFileWriter::Close(const int transportIndex)
@@ -255,15 +254,14 @@ void BPFileWriter::Close(const int transportIndex)
{
for (auto &transport : m_Transports)
{ // by reference or value or it doesn't matter?
- m_BP1Writer.Close(m_MetadataSet, m_Buffer, *transport,
- m_IsFirstClose,
+ m_BP1Writer.Close(m_MetadataSet, m_Heap, *transport, m_IsFirstClose,
false); // false: not using aggregation for now
}
}
else
{
- m_BP1Writer.Close(m_MetadataSet, m_Buffer,
- *m_Transports[transportIndex], m_IsFirstClose,
+ m_BP1Writer.Close(m_MetadataSet, m_Heap, *m_Transports[transportIndex],
+ m_IsFirstClose,
false); // false: not using aggregation for now
}
@@ -559,7 +557,7 @@ void BPFileWriter::WriteProcessGroupIndex()
m_BP1Writer.WriteProcessGroupIndex(isFortran, std::to_string(m_RankMPI),
static_cast<std::uint32_t>(m_RankMPI),
- m_Transports, m_Buffer, m_MetadataSet);
+ m_Transports, m_Heap, m_MetadataSet);
}
} // end namespace adios
diff --git a/source/adios2/engine/bp/BPFileWriter.h b/source/adios2/engine/bp/BPFileWriter.h
index f6754ed382681feb4441ef9a9a58bbc247545945..1c0c533a3fd4efd98e69a9aafda18742e353a7cb 100644
--- a/source/adios2/engine/bp/BPFileWriter.h
+++ b/source/adios2/engine/bp/BPFileWriter.h
@@ -98,7 +98,7 @@ public:
void Close(const int transportIndex = -1);
private:
- capsule::STLVector m_Buffer; ///< heap capsule using STL std::vector<char>
+ capsule::STLVector m_Heap; ///< heap capsule using STL std::vector<char>
format::BP1Writer
m_BP1Writer; ///< format object will provide the required BP
/// functionality to be applied on m_Buffer and
@@ -160,7 +160,7 @@ private:
// m_Buffer.m_Data );
// WRITE INDEX to data buffer and metadata structure (in memory)//
- m_BP1Writer.WriteVariableMetadata(variable, m_Buffer, m_MetadataSet);
+ m_BP1Writer.WriteVariableMetadata(variable, m_Heap, m_MetadataSet);
if (m_TransportFlush == true) // in batches
{
@@ -172,7 +172,7 @@ private:
}
else // Write data to buffer
{
- m_BP1Writer.WriteVariablePayload(variable, m_Buffer, m_nThreads);
+ m_BP1Writer.WriteVariablePayload(variable, m_Heap, m_nThreads);
}
variable.m_AppValues =
diff --git a/source/adios2/engine/dataman/DataManReader.cpp b/source/adios2/engine/dataman/DataManReader.cpp
index bb520b5011ad22cce0c48ee25e973a4bccf4676e..6ecc32f09beff58eeeb04d064043f59f9109523f 100644
--- a/source/adios2/engine/dataman/DataManReader.cpp
+++ b/source/adios2/engine/dataman/DataManReader.cpp
@@ -25,7 +25,7 @@ DataManReader::DataManReader(ADIOS &adios, const std::string &name,
const Method &method)
: Engine(adios, "DataManReader", name, accessMode, mpiComm, method,
" DataManReader constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+ m_Heap(m_DebugMode)
{
Init();
}
diff --git a/source/adios2/engine/dataman/DataManReader.h b/source/adios2/engine/dataman/DataManReader.h
index 003fad9776b587b96bfcb0b7a60247f4549509ba..4475c31059cf2bf86469f230b158968e9a8cf0c5 100644
--- a/source/adios2/engine/dataman/DataManReader.h
+++ b/source/adios2/engine/dataman/DataManReader.h
@@ -101,7 +101,7 @@ public:
private:
capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
+ m_Heap; ///< heap capsule, contains data and metadata buffers
format::BP1Writer
m_BP1Writer; ///< format object will provide the required BP
/// functionality to be applied on m_Buffer and
diff --git a/source/adios2/engine/dataman/DataManWriter.cpp b/source/adios2/engine/dataman/DataManWriter.cpp
index c125c10cbbb21b16d6341830213ab1992bc2feaa..1cf180ffe0fb5bbf3ec55ea8e8756ce948cdd4c5 100644
--- a/source/adios2/engine/dataman/DataManWriter.cpp
+++ b/source/adios2/engine/dataman/DataManWriter.cpp
@@ -25,7 +25,7 @@ DataManWriter::DataManWriter(ADIOS &adios, const std::string name,
const Method &method)
: Engine(adios, "DataManWriter", name, accessMode, mpiComm, method,
" DataManWriter constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+ m_Heap(m_DebugMode)
{
Init();
}
diff --git a/source/adios2/engine/dataman/DataManWriter.h b/source/adios2/engine/dataman/DataManWriter.h
index 0edaeb2e1a067d95caba640c3ec30328d2343cff..44567dddff6d6fc6b497d17cfbe713b738c413db 100644
--- a/source/adios2/engine/dataman/DataManWriter.h
+++ b/source/adios2/engine/dataman/DataManWriter.h
@@ -98,7 +98,7 @@ public:
private:
capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
+ m_Heap; ///< heap capsule, contains data and metadata buffers
format::BP1Writer
m_BP1Writer; ///< format object will provide the required BP
/// functionality to be applied on m_Buffer and