From 2b91f85a2c05309a071ec47a5755e49bc9d54d83 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Mon, 5 Jun 2017 17:13:47 -0400
Subject: [PATCH] BP file output now compatible with bpdump
---
source/adios2/core/IO.h | 2 +-
source/adios2/core/VariableBase.cpp | 4 +--
.../adios2/toolkit/format/bp1/BP1Writer.cpp | 36 +++++++++++++------
source/adios2/toolkit/format/bp1/BP1Writer.h | 5 ++-
.../adios2/toolkit/format/bp1/BP1Writer.tcc | 22 +++---------
.../toolkit/interop/adios1/ADIOS1Common.h | 2 +-
6 files changed, 36 insertions(+), 35 deletions(-)
diff --git a/source/adios2/core/IO.h b/source/adios2/core/IO.h
index 215dbbfd9..87df704d8 100644
--- a/source/adios2/core/IO.h
+++ b/source/adios2/core/IO.h
@@ -42,7 +42,7 @@ public:
/** from ADIOS class passed to Engine created with Open
* if no new communicator is passed */
- MPI_Comm m_MPIComm = MPI_COMM_SELF;
+ MPI_Comm m_MPIComm;
/** true: extra exceptions checks */
const bool m_DebugMode = false;
diff --git a/source/adios2/core/VariableBase.cpp b/source/adios2/core/VariableBase.cpp
index 40632a61e..db50a21db 100644
--- a/source/adios2/core/VariableBase.cpp
+++ b/source/adios2/core/VariableBase.cpp
@@ -112,8 +112,8 @@ void VariableBase::SetMemorySelection(const SelectionBoundingBox &selection)
}
}
- ConvertUint64VectorToSizetVector(selection.m_Count, m_MemoryCount);
- ConvertUint64VectorToSizetVector(selection.m_Start, m_MemoryStart);
+ m_MemoryCount = selection.m_Count;
+ m_MemoryStart = selection.m_Start;
}
void VariableBase::SetStepSelection(const unsigned int startStep,
diff --git a/source/adios2/toolkit/format/bp1/BP1Writer.cpp b/source/adios2/toolkit/format/bp1/BP1Writer.cpp
index 34639d7fb..daaf29b8c 100644
--- a/source/adios2/toolkit/format/bp1/BP1Writer.cpp
+++ b/source/adios2/toolkit/format/bp1/BP1Writer.cpp
@@ -248,14 +248,19 @@ void BP1Writer::WriteDimensionsRecord(const Dims localDimensions,
void BP1Writer::WriteDimensionsRecord(const Dims localDimensions,
const Dims globalDimensions,
const Dims offsets,
- const unsigned int skip,
std::vector<char> &buffer,
- size_t &position) noexcept
+ size_t &position,
+ const bool isCharacteristic) noexcept
{
- auto lf_WriteFlaggedDim = [](std::vector<char> &buffer, size_t &position,
- const size_t dimension) {
- constexpr char no = 'n';
- CopyToBuffer(buffer, position, &no);
+ auto lf_CopyDimension = [](std::vector<char> &buffer, size_t &position,
+ const size_t dimension,
+ const bool isCharacteristic) {
+ if (!isCharacteristic)
+ {
+ constexpr char no = 'n';
+ CopyToBuffer(buffer, position, &no);
+ }
+
CopyToBuffer(buffer, position,
reinterpret_cast<const uint64_t *>(&dimension));
};
@@ -263,19 +268,28 @@ void BP1Writer::WriteDimensionsRecord(const Dims localDimensions,
// BODY Starts here
if (offsets.empty())
{
+ unsigned int globalBoundsSkip = 18;
+ if (isCharacteristic)
+ {
+ globalBoundsSkip = 16;
+ }
+
for (const auto &localDimension : localDimensions)
{
- lf_WriteFlaggedDim(buffer, position, localDimension);
- position += skip;
+ lf_CopyDimension(buffer, position, localDimension,
+ isCharacteristic);
+ position += globalBoundsSkip;
}
}
else
{
for (unsigned int d = 0; d < localDimensions.size(); ++d)
{
- lf_WriteFlaggedDim(buffer, position, localDimensions[d]);
- lf_WriteFlaggedDim(buffer, position, globalDimensions[d]);
- lf_WriteFlaggedDim(buffer, position, offsets[d]);
+ lf_CopyDimension(buffer, position, localDimensions[d],
+ isCharacteristic);
+ lf_CopyDimension(buffer, position, globalDimensions[d],
+ isCharacteristic);
+ lf_CopyDimension(buffer, position, offsets[d], isCharacteristic);
}
}
}
diff --git a/source/adios2/toolkit/format/bp1/BP1Writer.h b/source/adios2/toolkit/format/bp1/BP1Writer.h
index d3caf67f3..d193753c1 100644
--- a/source/adios2/toolkit/format/bp1/BP1Writer.h
+++ b/source/adios2/toolkit/format/bp1/BP1Writer.h
@@ -186,9 +186,8 @@ private:
/** Overloaded version for data buffer */
void WriteDimensionsRecord(const Dims localDimensions,
const Dims globalDimensions, const Dims offsets,
- const unsigned int skip,
- std::vector<char> &buffer,
- size_t &position) noexcept;
+ std::vector<char> &buffer, size_t &position,
+ const bool isCharacteristic = false) noexcept;
/** Writes min max */
template <class T>
diff --git a/source/adios2/toolkit/format/bp1/BP1Writer.tcc b/source/adios2/toolkit/format/bp1/BP1Writer.tcc
index 31eac673a..eef815c26 100644
--- a/source/adios2/toolkit/format/bp1/BP1Writer.tcc
+++ b/source/adios2/toolkit/format/bp1/BP1Writer.tcc
@@ -175,16 +175,15 @@ void BP1Writer::WriteVariableMetadataInData(
CopyToBuffer(buffer, position, &dimensionsLength); // length
WriteDimensionsRecord(variable.m_Count, variable.m_Shape, variable.m_Start,
- 18, buffer, position);
+ buffer, position);
// CHARACTERISTICS
- // FIX
WriteVariableCharacteristics(variable, stats, buffer, position);
// Back to varLength including payload size
- // remove its own size (8) from length
+ // not need to remove its own size (8) from length from bpdump
const uint64_t varLength =
- position - varLengthPosition + variable.PayLoadSize() - 8;
+ position - varLengthPosition + variable.PayLoadSize();
size_t backPosition = varLengthPosition;
CopyToBuffer(buffer, backPosition, &varLength);
@@ -301,10 +300,6 @@ void BP1Writer::WriteCharacteristicRecord(const uint8_t characteristicID,
{
const std::uint8_t id = characteristicID;
CopyToBuffer(buffer, position, &id);
-
- const std::uint16_t lengthOfCharacteristic = sizeof(T);
- CopyToBuffer(buffer, position, &lengthOfCharacteristic);
-
CopyToBuffer(buffer, position, &value);
++characteristicsCounter;
}
@@ -372,25 +367,18 @@ void BP1Writer::WriteVariableCharacteristics(
// DIMENSIONS
uint8_t characteristicID = characteristic_dimensions;
CopyToBuffer(buffer, position, &characteristicID);
- const uint8_t dimensions = variable.m_Count.size();
-
- // 24 = 3 local, global, offset x 8 bytes/each
- const int16_t lengthOfDimensionsCharacteristic = 24 * dimensions + 3;
- CopyToBuffer(buffer, position, &lengthOfDimensionsCharacteristic);
+ const uint8_t dimensions = variable.m_Count.size();
CopyToBuffer(buffer, position, &dimensions); // count
const uint16_t dimensionsLength = 24 * dimensions;
CopyToBuffer(buffer, position, &dimensionsLength); // length
WriteDimensionsRecord(variable.m_Count, variable.m_Shape, variable.m_Start,
- 16, buffer, position);
+ buffer, position, true); // isCharacteristic = true
++characteristicsCounter;
// VALUE for SCALAR or STAT min, max for ARRAY
WriteBoundsRecord(variable.m_SingleValue, stats, characteristicsCounter,
buffer, position);
- // TIME INDEX
- WriteCharacteristicRecord(characteristic_time_index, characteristicsCounter,
- stats.TimeIndex, buffer, position);
// END OF CHARACTERISTICS
// Back to characteristics count and length
diff --git a/source/adios2/toolkit/interop/adios1/ADIOS1Common.h b/source/adios2/toolkit/interop/adios1/ADIOS1Common.h
index 05327d92b..c5e2297f4 100644
--- a/source/adios2/toolkit/interop/adios1/ADIOS1Common.h
+++ b/source/adios2/toolkit/interop/adios1/ADIOS1Common.h
@@ -73,7 +73,7 @@ public:
void Close();
private:
- MPI_Comm m_MPIComm = MPI_COMM_SELF;
+ MPI_Comm m_MPIComm;
const bool m_DebugMode = false;
void Init();
--
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