diff --git a/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp b/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
index 6ab37a388f24beb17266d3828f77a1df4a906028..047b88dfb0502e284a78bfb21ce61059fafb1160 100644
--- a/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
+++ b/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
@@ -96,7 +96,10 @@ int main(int argc, char *argv[])
"Hello from rank: " + std::to_string(rank) +
" and timestep: " + std::to_string(timeStep));
- bpWriter.PutSync(bpString, myString);
+ if (rank == 0)
+ {
+ bpWriter.PutSync(bpString, myString);
+ }
bpWriter.EndStep();
}
@@ -116,6 +119,9 @@ int main(int argc, char *argv[])
adios2::Variable<float> *bpFloats000 =
ioReader.InquireVariable<float>("bpFloats000");
+ adios2::Variable<std::string> *bpString =
+ ioReader.InquireVariable<std::string>("bpString");
+
if (bpFloats000 != nullptr)
{
bpFloats000->SetSelection({{rank * Nx}, {Nx}});
@@ -125,7 +131,7 @@ int main(int argc, char *argv[])
bpReader.GetSync(*bpFloats000, data.data());
std::cout << "Data timestep " << bpFloats000->m_StepsStart
- << " from rank " << rank << "\n";
+ << " from rank " << rank << ": ";
for (const auto datum : data)
{
std::cout << datum << " ";
@@ -136,8 +142,17 @@ int main(int argc, char *argv[])
{
std::cout << "Variable bpFloats000 not found\n";
}
+
+ if (bpString != nullptr)
+ {
+ bpString->SetStepSelection({3, 1});
+
+ std::string myString;
+ bpReader.GetSync(*bpString, myString);
+ std::cout << myString << "\n";
+ }
+
bpReader.Close();
- //}
}
}
catch (std::invalid_argument &e)
diff --git a/source/adios2/engine/bp/BPFileReader.tcc b/source/adios2/engine/bp/BPFileReader.tcc
index 5fbecc0d91da68c15efa2691760f8e1b4dcb6487..743b4028909f2be8a42a2d6fbffde7e04253c9fc 100644
--- a/source/adios2/engine/bp/BPFileReader.tcc
+++ b/source/adios2/engine/bp/BPFileReader.tcc
@@ -16,10 +16,17 @@
namespace adios2
{
+template <>
+inline void BPFileReader::GetSyncCommon(Variable<std::string> &variable,
+ std::string *data)
+{
+ variable.SetData(data);
+ m_BP3Deserializer.GetStringFromMetadata(variable);
+}
+
template <class T>
-void BPFileReader::GetSyncCommon(Variable<T> &variable, T *data)
+inline void BPFileReader::GetSyncCommon(Variable<T> &variable, T *data)
{
- // subfile info
variable.SetData(data);
const std::map<std::string, SubFileInfoMap> variableSubfileInfo =
diff --git a/source/adios2/toolkit/format/bp3/BP3Base.tcc b/source/adios2/toolkit/format/bp3/BP3Base.tcc
index ffd66cba53c7bb0652c894a07d075bd65077cf6f..3a807d2614805a3aa1743636fcc1a752a045ab6d 100644
--- a/source/adios2/toolkit/format/bp3/BP3Base.tcc
+++ b/source/adios2/toolkit/format/bp3/BP3Base.tcc
@@ -160,7 +160,7 @@ int8_t BP3Base::GetDataType<cldouble>() const noexcept
}
template <class T>
-inline BP3Base::Characteristics<T> BP3Base::ReadElementIndexCharacteristics(
+BP3Base::Characteristics<T> BP3Base::ReadElementIndexCharacteristics(
const std::vector<char> &buffer, size_t &position, const DataTypes dataType,
const bool untilTimeStep) const
{
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp b/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
index 99b668ffdde584408dc5d0a5c23ceefaffd7ce17..edf25648c899194f12f0c2daeea31721e66b6cd5 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
@@ -65,6 +65,36 @@ void BP3Deserializer::ClipContiguousMemory(
#undef declare_type
}
+void BP3Deserializer::GetStringFromMetadata(
+ Variable<std::string> &variable) const
+{
+ std::string *data = variable.GetData();
+ const auto &buffer = m_Metadata.m_Buffer;
+
+ for (size_t i = 0; i < variable.m_StepsCount; ++i)
+ {
+ *(data + i) = "";
+ const size_t step = variable.m_StepsStart + i;
+ auto itStep = variable.m_IndexStepBlockStarts.find(step);
+
+ if (itStep == variable.m_IndexStepBlockStarts.end())
+ {
+ continue;
+ }
+
+ for (auto position : itStep->second)
+ {
+ const Characteristics<std::string> characteristics =
+ ReadElementIndexCharacteristics<std::string>(
+ buffer, position, type_string, false);
+
+ *(data + i) = characteristics.Statistics.Value;
+ }
+
+ variable.m_Value = *(data + i);
+ }
+}
+
// PRIVATE
void BP3Deserializer::ParseMinifooter()
{
@@ -139,6 +169,13 @@ void BP3Deserializer::ParseVariablesIndex(IO &io)
switch (header.DataType)
{
+ // TODO: string
+ case (type_string):
+ {
+ DefineVariableInIO<std::string>(header, io, buffer, position);
+ break;
+ }
+
case (type_byte):
{
DefineVariableInIO<signed char>(header, io, buffer, position);
@@ -225,7 +262,7 @@ void BP3Deserializer::ParseVariablesIndex(IO &io)
position);
break;
}
- // TODO: string
+
} // end switch
};
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.h b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
index eb24da84f86b34ecdc080272f5d7a8e35429d48e..1cb508b6272dbf6d04d8880510b518442e1f8df0 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.h
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
@@ -59,6 +59,8 @@ public:
const Box<Dims> &blockBox,
const Box<Dims> &intersectionBox) const;
+ void GetStringFromMetadata(Variable<std::string> &variable) const;
+
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 f36d3fb7fd4a279716490e62f9221d24370eb54d..3d49306b639e086e0ed07fe2d033680913d835e3 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
@@ -37,11 +37,74 @@ void BP3Deserializer::GetDeferredVariable(Variable<T> &variable, T *data)
}
// PRIVATE
+template <>
+inline void BP3Deserializer::DefineVariableInIO<std::string>(
+ const ElementIndexHeader &header, IO &io, const std::vector<char> &buffer,
+ size_t position) const
+{
+ const size_t initialPosition = position;
+
+ const Characteristics<std::string> characteristics =
+ ReadElementIndexCharacteristics<std::string>(
+ buffer, position, static_cast<DataTypes>(header.DataType));
+
+ std::string variableName(header.Name);
+ if (!header.Path.empty())
+ {
+ variableName = header.Path + PathSeparator + header.Name;
+ }
+
+ Variable<std::string> *variable = nullptr;
+ if (characteristics.Statistics.IsValue)
+ {
+ std::lock_guard<std::mutex> lock(m_Mutex);
+ variable = &io.DefineVariable<std::string>(variableName);
+ variable->m_Value =
+ characteristics.Statistics.Value; // assigning first step
+ }
+ else
+ {
+ // TODO: throw exception?
+ }
+
+ // going back to get variable index position
+ variable->m_IndexStart =
+ initialPosition - (header.Name.size() + header.GroupName.size() +
+ header.Path.size() + 23);
+
+ const size_t endPosition =
+ variable->m_IndexStart + static_cast<size_t>(header.Length) + 4;
+
+ position = initialPosition;
+
+ size_t currentStep = 0; // Starts at 1 in bp file
+
+ while (position < endPosition)
+ {
+ const size_t subsetPosition = position;
+
+ // read until step is found
+ const Characteristics<std::string> subsetCharacteristics =
+ ReadElementIndexCharacteristics<std::string>(
+ buffer, position, static_cast<DataTypes>(header.DataType),
+ false);
+
+ if (subsetCharacteristics.Statistics.Step > currentStep)
+ {
+ currentStep = subsetCharacteristics.Statistics.Step;
+ variable->m_AvailableStepsCount =
+ subsetCharacteristics.Statistics.Step;
+ }
+ variable->m_IndexStepBlockStarts[currentStep].push_back(subsetPosition);
+ position = subsetPosition + subsetCharacteristics.EntryLength + 5;
+ }
+}
+
template <class T>
-void BP3Deserializer::DefineVariableInIO(const ElementIndexHeader &header,
- IO &io,
- const std::vector<char> &buffer,
- size_t position) const
+inline void
+BP3Deserializer::DefineVariableInIO(const ElementIndexHeader &header, IO &io,
+ const std::vector<char> &buffer,
+ size_t position) const
{
const size_t initialPosition = position;
diff --git a/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp b/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp
index e0d72e8078667aa3b5262cba35a22fbf8d0f6f14..4aa708d8266a5af2b9c3e4c1c7229e1051a2484b 100644
--- a/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp
+++ b/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp
@@ -160,10 +160,10 @@ TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
adios2::Engine &bpReader = io.Open(fname, adios2::Mode::Read);
- // auto var_iString = io.InquireVariable<std::string>("iString");
- // ASSERT_NE(var_iString, nullptr);
- // ASSERT_EQ(var_iString->m_Shape.size(), 0);
- // ASSERT_EQ(var_iString->m_AvailableStepsCount, NSteps);
+ auto var_iString = io.InquireVariable<std::string>("iString");
+ ASSERT_NE(var_iString, nullptr);
+ ASSERT_EQ(var_iString->m_Shape.size(), 0);
+ ASSERT_EQ(var_iString->m_AvailableStepsCount, NSteps);
auto var_i8 = io.InquireVariable<int8_t>("i8");
ASSERT_NE(var_i8, nullptr);
@@ -228,7 +228,8 @@ TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
// TODO: other types
SmallTestData testData;
- std::vector<char> IString(testData.S1.size());
+
+ std::string IString;
std::array<int8_t, Nx> I8;
std::array<int16_t, Nx> I16;
std::array<int32_t, Nx> I32;
@@ -260,6 +261,8 @@ TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
for (size_t t = 0; t < NSteps; ++t)
{
+ var_iString->SetStepSelection({t + 1, 1});
+
var_i8->SetStepSelection({t + 1, 1});
var_i16->SetStepSelection({t + 1, 1});
var_i32->SetStepSelection({t + 1, 1});
@@ -277,6 +280,8 @@ TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
SmallTestData currentTestData = generateNewSmallTestData(
m_TestData, static_cast<int>(t), mpiRank, mpiSize);
+ bpReader.GetSync(*var_iString, IString);
+
bpReader.GetDeferred(*var_i8, I8.data());
bpReader.GetDeferred(*var_i16, I16.data());
bpReader.GetDeferred(*var_i32, I32.data());
@@ -292,6 +297,8 @@ TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
bpReader.PerformGets();
+ EXPECT_EQ(IString, currentTestData.S1);
+
for (size_t i = 0; i < Nx; ++i)
{
std::stringstream ss;