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Tweak min blocks interface to avoid leak in Shape() #3458

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merged 3 commits into from
Feb 2, 2023
Merged

Tweak min blocks interface to avoid leak in Shape() #3458

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0021c10
Tweak min blocks interface to avoid leak in Shape()
eisenhauer Feb 1, 2023
8f1484a
Don't call AvailableVariables() unless we know that BeginStep succeeded
eisenhauer Feb 2, 2023
81524a0
BP5Deserializer should use RegisterCreatedVariable()
eisenhauer Feb 2, 2023
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5 changes: 3 additions & 2 deletions source/adios2/core/Engine.h
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Original file line number Diff line number Diff line change
Expand Up @@ -486,9 +486,10 @@ class Engine
}

// in this call, Step is RELATIVE, not absolute
virtual Dims *VarShape(const VariableBase &, const size_t Step) const
virtual bool VarShape(const VariableBase &, const size_t Step,
Dims &Shape) const
{
return nullptr;
return false;
}

virtual bool VariableMinMax(const VariableBase &, const size_t Step,
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8 changes: 3 additions & 5 deletions source/adios2/core/VariableBase.cpp
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Expand Up @@ -628,12 +628,10 @@ Dims VariableBase::Shape(const size_t step) const

if (m_Engine)
{
Dims tmp;
// see if the engine implements Variable Shape inquiry
auto ShapePtr = m_Engine->VarShape(*this, step);
if (ShapePtr)
{
return *ShapePtr;
}
if (m_Engine->VarShape(*this, step, tmp))
return tmp;
}
if (m_FirstStreamingStep && step == adios2::EngineCurrentStep)
{
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5 changes: 3 additions & 2 deletions source/adios2/engine/bp5/BP5Reader.cpp
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Expand Up @@ -684,9 +684,10 @@ MinVarInfo *BP5Reader::MinBlocksInfo(const VariableBase &Var,
return m_BP5Deserializer->MinBlocksInfo(Var, Step);
}

Dims *BP5Reader::VarShape(const VariableBase &Var, const size_t Step) const
bool BP5Reader::VarShape(const VariableBase &Var, const size_t Step,
Dims &Shape) const
{
return m_BP5Deserializer->VarShape(Var, Step);
return m_BP5Deserializer->VarShape(Var, Step, Shape);
}

bool BP5Reader::VariableMinMax(const VariableBase &Var, const size_t Step,
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3 changes: 2 additions & 1 deletion source/adios2/engine/bp5/BP5Reader.h
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Expand Up @@ -57,7 +57,8 @@ class BP5Reader : public BP5Engine, public Engine
void PerformGets() final;

MinVarInfo *MinBlocksInfo(const VariableBase &, const size_t Step) const;
Dims *VarShape(const VariableBase &, const size_t Step) const;
bool VarShape(const VariableBase &Var, const size_t Step,
Dims &Shape) const;
bool VariableMinMax(const VariableBase &, const size_t Step,
MinMaxStruct &MinMax);

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7 changes: 4 additions & 3 deletions source/adios2/engine/sst/SstReader.cpp
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Expand Up @@ -691,12 +691,13 @@ void SstReader::DoGetStructDeferred(VariableStruct &variable, void *data)
m_BP5Deserializer->QueueGet(variable, data);
}

Dims *SstReader::VarShape(const VariableBase &Var, const size_t Step) const
bool SstReader::VarShape(const VariableBase &Var, const size_t Step,
Dims &Shape) const
{
if (m_WriterMarshalMethod != SstMarshalBP5)
return nullptr;
return false;

return m_BP5Deserializer->VarShape(Var, Step);
return m_BP5Deserializer->VarShape(Var, Step, Shape);
}

bool SstReader::VariableMinMax(const VariableBase &Var, const size_t Step,
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3 changes: 2 additions & 1 deletion source/adios2/engine/sst/SstReader.h
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Expand Up @@ -51,7 +51,8 @@ class SstReader : public Engine
void PerformGets();
void Flush(const int transportIndex = -1) final;
MinVarInfo *MinBlocksInfo(const VariableBase &, const size_t Step) const;
Dims *VarShape(const VariableBase &, const size_t Step) const;
bool VarShape(const VariableBase &Var, const size_t Step,
Dims &Shape) const;
bool VariableMinMax(const VariableBase &, const size_t Step,
MinMaxStruct &MinMax);

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18 changes: 10 additions & 8 deletions source/adios2/toolkit/format/bp5/BP5Deserializer.cpp
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Expand Up @@ -498,6 +498,7 @@ void *BP5Deserializer::VarSetup(core::Engine *engine, const char *variableName,
{ \
core::Variable<T> *variable = \
&(engine->m_IO.DefineVariable<T>(variableName)); \
engine->RegisterCreatedVariable(variable); \
variable->SetData((T *)data); \
variable->m_AvailableStepsCount = 1; \
return (void *)variable; \
Expand Down Expand Up @@ -547,6 +548,7 @@ void *BP5Deserializer::ArrayVarSetup(core::Engine *engine,
{
core::VariableStruct *variable = &(engine->m_IO.DefineStructVariable(
variableName, *Def, VecShape, VecStart, VecCount));
engine->RegisterCreatedVariable(variable);
variable->m_ReadStructDefinition = ReaderDef;
return (void *)variable;
}
Expand All @@ -555,6 +557,7 @@ void *BP5Deserializer::ArrayVarSetup(core::Engine *engine,
{ \
core::Variable<T> *variable = \
&(engine->m_IO.DefineVariable<T>(variableName)); \
engine->RegisterCreatedVariable(variable); \
variable->m_Shape = VecShape; \
variable->m_Start = VecStart; \
variable->m_Count = VecCount; \
Expand Down Expand Up @@ -2100,13 +2103,13 @@ void BP5Deserializer::GetAbsoluteSteps(const VariableBase &Var,
}
}

Dims *BP5Deserializer::VarShape(const VariableBase &Var,
const size_t RelStep) const
bool BP5Deserializer::VarShape(const VariableBase &Var, const size_t RelStep,
Dims &Shape) const
{
BP5VarRec *VarRec = LookupVarByKey((void *)&Var);
if (VarRec->OrigShapeID != ShapeID::GlobalArray)
{
return nullptr;
return false;
}
size_t AbsStep = RelStep;
if (m_RandomAccessMode)
Expand All @@ -2127,16 +2130,15 @@ Dims *BP5Deserializer::VarShape(const VariableBase &Var,
(MetaArrayRec *)GetMetadataBase(VarRec, AbsStep, WriterRank);
if (writer_meta_base && writer_meta_base->Shape)
{
Dims *Shape = new Dims();
Shape->reserve(writer_meta_base->Dims);
Shape.resize(writer_meta_base->Dims);
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If Shape has a bigger size than the writer_meta_base, resize will remove the values but not update the size. Would this be a problem? This is not the case in any of the test so I assume no, but just want to point this out.

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I wouldn't think it would be a problem. In all the current uses, Shape passed in by reference is an fresh Dims value with default size 0. So, I think no worries...

for (size_t i = 0; i < writer_meta_base->Dims; i++)
{
Shape->push_back(writer_meta_base->Shape[i]);
Shape[i] = writer_meta_base->Shape[i];
}
return Shape;
return true;
}
}
return nullptr;
return false;
}

bool BP5Deserializer::VariableMinMax(const VariableBase &Var, const size_t Step,
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2 changes: 1 addition & 1 deletion source/adios2/toolkit/format/bp5/BP5Deserializer.h
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Expand Up @@ -84,7 +84,7 @@ class BP5Deserializer : virtual public BP5Base
MinVarInfo *AllRelativeStepsMinBlocksInfo(const VariableBase &var);
MinVarInfo *AllStepsMinBlocksInfo(const VariableBase &var);
MinVarInfo *MinBlocksInfo(const VariableBase &Var, const size_t Step);
Dims *VarShape(const VariableBase &, const size_t Step) const;
bool VarShape(const VariableBase &, const size_t Step, Dims &Shape) const;
bool VariableMinMax(const VariableBase &var, const size_t Step,
MinMaxStruct &MinMax);
void GetAbsoluteSteps(const VariableBase &variable,
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2 changes: 2 additions & 0 deletions testing/adios2/engine/staging-common/TestCommonRead.cpp
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Expand Up @@ -85,6 +85,8 @@ TEST_F(CommonReadTest, ADIOS2CommonRead1D8)
}
ts = std::chrono::steady_clock::now();
adios2::StepStatus status = engine.BeginStep();
auto av = io.AvailableVariables();

Seconds timeBeginStep = std::chrono::steady_clock::now() - ts;
begin_statuses.push_back(status);
begin_times.push_back(timeBeginStep);
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