diff --git a/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
index 44f428bfefb52f04d500fad05dfb9cf7ecc84b5d..5603b89b5dd5560887b6acf9f234ffba5976960c 100644
--- a/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
+++ b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
@@ -42,7 +42,7 @@ int main(int argc, char *argv[])
hdf5IO.Open("myVector.h5", adios2::Mode::Write);
/** Write variable for buffering */
- hdf5Writer.Write<float>(bpFloats, myFloats.data());
+ hdf5Writer.GetSync<float>(bpFloats, myFloats.data());
/** Create bp file, engine becomes unreachable after this*/
hdf5Writer.Close();
diff --git a/source/adios2/engine/bp/BPFileReader.cpp b/source/adios2/engine/bp/BPFileReader.cpp
index d329b29949bfd2251cee96bb08ce1c25dc0d3fc1..39791720603914c87e01b43d9425a58de6ff1f1c 100644
--- a/source/adios2/engine/bp/BPFileReader.cpp
+++ b/source/adios2/engine/bp/BPFileReader.cpp
@@ -19,7 +19,8 @@ namespace adios2
BPFileReader::BPFileReader(IO &io, const std::string &name, const Mode openMode,
MPI_Comm mpiComm)
: Engine("BPFileReader", io, name, openMode, mpiComm),
- m_BP3Deserializer(mpiComm, m_DebugMode), m_FileManager(mpiComm, m_DebugMode)
+ m_BP3Deserializer(mpiComm, m_DebugMode), m_FileManager(mpiComm, m_DebugMode),
+ m_SubFileManager(mpiComm, m_DebugMode)
{
Init();
}
@@ -57,13 +58,16 @@ void BPFileReader::InitTransports()
defaultTransportParameters["transport"] = "File";
m_IO.m_TransportsParameters.push_back(defaultTransportParameters);
}
+ // TODO Set Parameters
if (m_BP3Deserializer.m_RankMPI == 0)
{
const std::string metadataFile(
m_BP3Deserializer.GetBPMetadataFileName(m_Name));
+
+ const bool profile = m_BP3Deserializer.m_Profiler.IsActive;
m_FileManager.OpenFiles({}, {metadataFile}, adios2::Mode::Read,
- m_IO.m_TransportsParameters, true);
+ m_IO.m_TransportsParameters, profile);
}
}
@@ -104,4 +108,52 @@ void BPFileReader::InitBuffer()
ADIOS2_FOREACH_TYPE_1ARG(declare_type)
#undef declare_type
+void BPFileReader::ReadVariables(
+ IO &io, const std::map<std::string, SubFileInfoMap> &variablesSubFileInfo)
+{
+ const bool &profile = m_BP3Deserializer.m_Profiler.IsActive;
+
+ // sequentially request bytes from transport manager
+ // threaded here?
+ for (const auto &variableNamePair : variablesSubFileInfo) // variable name
+ {
+ const std::string variableName(variableNamePair.first);
+ unsigned int subFileTransportIndex = 0;
+
+ // or threaded here?
+ for (const auto &subFileIndexPair : variableNamePair.second)
+ {
+ const unsigned int subFileIndex = subFileIndexPair.first;
+ const std::string subFile(
+ m_BP3Deserializer.GetBPSubFileName(m_Name, subFileIndex));
+
+ m_SubFileManager.OpenFiles({}, {subFile}, adios2::Mode::Read,
+ std::vector<Params>(), profile);
+
+ for (const auto &stepPair : subFileIndexPair.second) // step
+ {
+ const size_t step = stepPair.first;
+
+ for (const auto &blockInfo : stepPair.second)
+ {
+ const auto &seek = blockInfo.Seeks;
+ const size_t blockStart = seek.first;
+ const size_t blockSize = seek.second - seek.first;
+ std::vector<char> contiguousData(blockSize);
+ m_SubFileManager.ReadFile(contiguousData.data(), blockStart,
+ blockSize, subFileTransportIndex);
+
+ // will go to BP3Deserializer along with contiguous data
+
+ // Variable Data
+ // blockInfo.IntersectionBox;
+ } // end block
+ } // end step
+ ++subFileTransportIndex;
+ } // end subfile
+ } // end variable
+
+ m_SubFileManager.CloseFiles();
+}
+
} // end namespace adios2
diff --git a/source/adios2/engine/bp/BPFileReader.h b/source/adios2/engine/bp/BPFileReader.h
index a1d1731b4b0ec7ecd2c16a3cb8ef1aff8bdcfb90..4c123500ec1c589382a6a4065897d5e76a6630c1 100644
--- a/source/adios2/engine/bp/BPFileReader.h
+++ b/source/adios2/engine/bp/BPFileReader.h
@@ -42,6 +42,7 @@ public:
private:
format::BP3Deserializer m_BP3Deserializer;
transportman::TransportMan m_FileManager;
+ transportman::TransportMan m_SubFileManager;
void Init();
void InitTransports();
@@ -59,6 +60,10 @@ private:
template <class T>
void GetDeferredCommon(Variable<T> &variable, T *data);
+
+ void
+ ReadVariables(IO &io,
+ const std::map<std::string, SubFileInfoMap> &variablesInfo);
};
} // end namespace adios2
diff --git a/source/adios2/engine/bp/BPFileReader.tcc b/source/adios2/engine/bp/BPFileReader.tcc
index 860567c315d92968542920bda13d09a8f85845df..57c81eff376dd20814598bba81897ee99f178323 100644
--- a/source/adios2/engine/bp/BPFileReader.tcc
+++ b/source/adios2/engine/bp/BPFileReader.tcc
@@ -19,6 +19,7 @@ namespace adios2
template <class T>
void BPFileReader::GetSyncCommon(Variable<T> &variable, T *data)
{
+ // subfile info
const std::map<std::string, SubFileInfoMap> variableSubfileInfo =
m_BP3Deserializer.GetSyncVariableSubFileInfo(variable);
}
@@ -26,6 +27,8 @@ void BPFileReader::GetSyncCommon(Variable<T> &variable, T *data)
template <class T>
void BPFileReader::GetDeferredCommon(Variable<T> &variable, T *data)
{
+ // returns immediately
+ m_BP3Deserializer.GetDeferredVariable(variable, data);
}
} // end namespace adios2
diff --git a/source/adios2/helper/adiosType.h b/source/adios2/helper/adiosType.h
index d1cffddea3d8e85c00c7e3fac3f165192ae95d23..9d4154ec616031578fc3dd54fe7f788909516d19 100644
--- a/source/adios2/helper/adiosType.h
+++ b/source/adios2/helper/adiosType.h
@@ -27,6 +27,7 @@ struct SubFileInfo
{
Box<Dims> IntersectionBox; ///< first = Start point, second = End point
Box<size_t> Seeks; ///< first = Start seek, second = End seek
+ std::vector<char> Data;
};
/**
diff --git a/source/adios2/toolkit/format/bp3/BP3Base.cpp b/source/adios2/toolkit/format/bp3/BP3Base.cpp
index 8d22296562aa65c67d7bbc623b041a575f73377a..ea585c4d4416b921cbd14579240744a2f1a04759 100644
--- a/source/adios2/toolkit/format/bp3/BP3Base.cpp
+++ b/source/adios2/toolkit/format/bp3/BP3Base.cpp
@@ -118,34 +118,24 @@ std::string BP3Base::GetBPMetadataFileName(const std::string &name) const
std::vector<std::string>
BP3Base::GetBPNames(const std::vector<std::string> &baseNames) const noexcept
{
- auto lf_GetBPName = [](const std::string &baseName,
- const int rank) -> std::string {
-
- const std::string bpBaseName = AddExtension(baseName, ".bp");
-
- // path/root.bp.dir/root.bp.rank
- std::string bpRootName = bpBaseName;
- const auto lastPathSeparator(bpBaseName.find_last_of(PathSeparator));
-
- if (lastPathSeparator != std::string::npos)
- {
- bpRootName = bpBaseName.substr(lastPathSeparator);
- }
- const std::string bpName(bpBaseName + ".dir/" + bpRootName + "." +
- std::to_string(rank));
- return bpName;
- };
-
std::vector<std::string> bpNames;
bpNames.reserve(baseNames.size());
for (const auto &baseName : baseNames)
{
- bpNames.push_back(lf_GetBPName(baseName, m_RankMPI));
+ bpNames.push_back(
+ GetBPRankName(baseName, static_cast<unsigned int>(m_RankMPI)));
}
return bpNames;
}
+std::string BP3Base::GetBPSubFileName(const std::string &name,
+ const unsigned int subFileIndex) const
+ noexcept
+{
+ return GetBPRankName(name, subFileIndex);
+}
+
// PROTECTED
void BP3Base::InitOnOffParameter(const std::string value, bool ¶meter,
const std::string hint)
@@ -459,16 +449,16 @@ BP3Base::ReadElementIndexHeader(const std::vector<char> &buffer,
ElementIndexHeader header;
header.Length = ReadValue<uint32_t>(buffer, position);
header.MemberID = ReadValue<uint32_t>(buffer, position);
- header.GroupName = ReadBP1String(buffer, position);
- header.Name = ReadBP1String(buffer, position);
- header.Path = ReadBP1String(buffer, position);
+ header.GroupName = ReadBP3String(buffer, position);
+ header.Name = ReadBP3String(buffer, position);
+ header.Path = ReadBP3String(buffer, position);
header.DataType = ReadValue<int8_t>(buffer, position);
header.CharacteristicsSetsCount = ReadValue<uint64_t>(buffer, position);
return header;
}
-std::string BP3Base::ReadBP1String(const std::vector<char> &buffer,
+std::string BP3Base::ReadBP3String(const std::vector<char> &buffer,
size_t &position) const noexcept
{
const size_t size =
@@ -500,6 +490,24 @@ void BP3Base::ProfilerStop(const std::string process)
}
}
+std::string BP3Base::GetBPRankName(const std::string &name,
+ const unsigned int rank) const noexcept
+{
+ const std::string bpName = AddExtension(name, ".bp");
+
+ // path/root.bp.dir/root.bp.rank
+ std::string bpRoot = bpName;
+ const auto lastPathSeparator(bpName.find_last_of(PathSeparator));
+
+ if (lastPathSeparator != std::string::npos)
+ {
+ bpRoot = bpName.substr(lastPathSeparator);
+ }
+ const std::string bpRankName(bpName + ".dir/" + bpRoot + "." +
+ std::to_string(rank));
+ return bpRankName;
+}
+
#define declare_template_instantiation(T) \
template BP3Base::ResizeResult BP3Base::ResizeBuffer( \
const Variable<T> &variable); \
diff --git a/source/adios2/toolkit/format/bp3/BP3Base.h b/source/adios2/toolkit/format/bp3/BP3Base.h
index 5758f3e0abb63553d5fdfc0482f0533d75ad4fb4..3fe4a06c9bd8f3d806b3a1be82fd60133ac17e2f 100644
--- a/source/adios2/toolkit/format/bp3/BP3Base.h
+++ b/source/adios2/toolkit/format/bp3/BP3Base.h
@@ -165,6 +165,10 @@ public:
std::string GetBPMetadataFileName(const std::string &name) const noexcept;
+ std::string GetBPSubFileName(const std::string &name,
+ const unsigned int subFileIndex) const
+ noexcept;
+
/** Return type of the CheckAllocation function. */
enum class ResizeResult
{
@@ -418,7 +422,7 @@ protected:
* @param position
* @return
*/
- std::string ReadBP1String(const std::vector<char> &buffer,
+ std::string ReadBP3String(const std::vector<char> &buffer,
size_t &position) const noexcept;
void ProfilerStart(const std::string process);
@@ -433,6 +437,9 @@ private:
*/
template <class T>
size_t GetVariableIndexSize(const Variable<T> &variable) const noexcept;
+
+ std::string GetBPRankName(const std::string &name,
+ const unsigned int rank) const noexcept;
};
#define declare_template_instantiation(T) \
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.h b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
index aaa265f775a8858b9ee60e82dfbd48b2be24d522..3eb88183c899492e702ca6562af65e62c3856956 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.h
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
@@ -54,6 +54,10 @@ public:
std::map<std::string, SubFileInfoMap>
PerformGetsVariablesSubFileInfo(IO &io);
+ template <class T>
+ void ClipContiguousMemory(const std::vector<char> &contiguousMemory,
+ Variable<T> &variable);
+
private:
std::map<std::string, SubFileInfoMap> m_DeferredVariables;
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc b/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
index fe99e5e5428e935af1fb05e940d668a91f6ec9a8..9bf793f956f8adb1cf00145faebefe68e7ba75b9 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
@@ -33,8 +33,7 @@ template <class T>
void BP3Deserializer::GetDeferredVariable(Variable<T> &variable, T *data)
{
variable.SetData(data);
- SubFileInfoMap emptyMap;
- m_DeferredVariables[variable.m_Name] = emptyMap;
+ m_DeferredVariables[variable.m_Name] = SubFileInfoMap();
}
// PRIVATE
diff --git a/source/adios2/toolkit/transportman/TransportMan.cpp b/source/adios2/toolkit/transportman/TransportMan.cpp
index 1b396c1b7f7948413cc204c1a5c6d3b380277066..ce81f04a1c8c6b1908d55916583c62e90edb5335 100644
--- a/source/adios2/toolkit/transportman/TransportMan.cpp
+++ b/source/adios2/toolkit/transportman/TransportMan.cpp
@@ -40,7 +40,8 @@ void TransportMan::OpenFiles(const std::vector<std::string> &baseNames,
const std::vector<Params> ¶metersVector,
const bool profile)
{
- for (auto i = 0; i < names.size(); ++i)
+
+ for (size_t i = 0; i < names.size(); ++i)
{
const Params ¶meters = parametersVector[i];
const std::string type(parameters.at("transport"));
@@ -51,11 +52,23 @@ void TransportMan::OpenFiles(const std::vector<std::string> &baseNames,
{
CreateDirectory(baseNames[i]);
}
- OpenFileTransport(names[i], openMode, parameters, profile);
+
+ std::shared_ptr<Transport> file =
+ OpenFileTransport(names[i], openMode, parameters, profile);
+ m_Transports.insert({i, file});
}
}
}
+void TransportMan::OpenFileID(const std::string &name, const unsigned int id,
+ const Mode openMode, const Params ¶meters,
+ const bool profile)
+{
+
+ std::shared_ptr<Transport> file =
+ OpenFileTransport(name, openMode, parameters, profile);
+}
+
std::vector<std::string> TransportMan::GetFilesBaseNames(
const std::string &baseName,
const std::vector<Params> ¶metersVector) const
@@ -108,8 +121,9 @@ std::vector<std::string> TransportMan::GetTransportsTypes() noexcept
std::vector<std::string> types;
types.reserve(m_Transports.size());
- for (const auto &transport : m_Transports)
+ for (const auto &transportPair : m_Transports)
{
+ const std::shared_ptr<Transport> &transport = transportPair.second;
types.push_back(transport->m_Type + "_" + transport->m_Library);
}
return types;
@@ -121,8 +135,9 @@ TransportMan::GetTransportsProfilers() noexcept
std::vector<profiling::IOChrono *> profilers;
profilers.reserve(m_Transports.size());
- for (const auto &transport : m_Transports)
+ for (const auto &transportPair : m_Transports)
{
+ const auto &transport = transportPair.second;
profilers.push_back(&transport->m_Profiler);
}
return profilers;
@@ -133,8 +148,9 @@ void TransportMan::WriteFiles(const char *buffer, const size_t size,
{
if (transportIndex == -1)
{
- for (auto &transport : m_Transports)
+ for (auto &transportPair : m_Transports)
{
+ auto &transport = transportPair.second;
if (transport->m_Type == "File")
{
// make this truly asynch?
@@ -173,8 +189,10 @@ void TransportMan::CloseFiles(const int transportIndex)
{
if (transportIndex == -1)
{
- for (auto &transport : m_Transports)
+ for (auto &transportPair : m_Transports)
{
+ auto &transport = transportPair.second;
+
if (transport->m_Type == "File")
{
transport->Close();
@@ -191,8 +209,10 @@ void TransportMan::CloseFiles(const int transportIndex)
bool TransportMan::AllTransportsClosed() const noexcept
{
bool allClose = true;
- for (const auto &transport : m_Transports)
+ for (const auto &transportPair : m_Transports)
{
+ const auto &transport = transportPair.second;
+
if (transport->m_IsOpen)
{
allClose = false;
@@ -203,10 +223,10 @@ bool TransportMan::AllTransportsClosed() const noexcept
}
// PRIVATE
-void TransportMan::OpenFileTransport(const std::string &fileName,
- const Mode openMode,
- const Params ¶meters,
- const bool profile)
+std::shared_ptr<Transport>
+TransportMan::OpenFileTransport(const std::string &fileName,
+ const Mode openMode, const Params ¶meters,
+ const bool profile)
{
auto lf_SetFileTransport = [&](const std::string library,
std::shared_ptr<Transport> &transport) {
@@ -266,9 +286,9 @@ void TransportMan::OpenFileTransport(const std::string &fileName,
lf_GetTimeUnits(DefaultTimeUnit, parameters));
}
- // open and move transport to container
+ // open
transport->Open(fileName, openMode);
- m_Transports.push_back(std::move(transport)); // is move needed?
+ return transport;
}
void TransportMan::CheckFileType(const int transportIndex)
diff --git a/source/adios2/toolkit/transportman/TransportMan.h b/source/adios2/toolkit/transportman/TransportMan.h
index 8e571a470680134baf237dd276697e0abe7f3b6c..8171f562f3067a713327356d9ec8cb37f6c6471a 100644
--- a/source/adios2/toolkit/transportman/TransportMan.h
+++ b/source/adios2/toolkit/transportman/TransportMan.h
@@ -30,13 +30,14 @@ class TransportMan
{
public:
- /** contains all transports from IO AddTransport
+ /**
+ * Contains all transports
* <pre>
- * key : unique id from IO AddTransport
- * value : obejct derived from Transport.h class
+ * key : unique id
+ * value : object derived from Transport base class
* </pre>
*/
- std::vector<std::shared_ptr<Transport>> m_Transports;
+ std::unordered_map<size_t, std::shared_ptr<Transport>> m_Transports;
/**
* Unique base constructor
@@ -60,8 +61,13 @@ public:
const std::vector<Params> ¶metersVector,
const bool profile);
+ void OpenFileID(const std::string &name, const unsigned int id,
+ const Mode openMode, const Params ¶meters,
+ const bool profile);
+
/**
- * Gets each transport base name from either baseName at Open or name key in
+ * Gets each transport base name from either baseName at Open or name
+ * key in
* parameters
* Checks if transport name rules IO AddTransport have unique names for
* every type (for now)
@@ -128,8 +134,10 @@ protected:
MPI_Comm m_MPIComm;
const bool m_DebugMode = false;
- void OpenFileTransport(const std::string &fileName, const Mode openMode,
- const Params ¶meters, const bool profile);
+ std::shared_ptr<Transport> OpenFileTransport(const std::string &fileName,
+ const Mode openMode,
+ const Params ¶meters,
+ const bool profile);
void CheckFileType(const int transportIndex);
};