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Add ADIOS2 parameter modifiable_attributes
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@franzpoeschel
franzpoeschel committed Aug 18, 2022
1 parent d8b744d commit 7044d3d
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Showing 3 changed files with 98 additions and 19 deletions.
10 changes: 10 additions & 0 deletions include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,16 @@ class ADIOS2IOHandlerImpl

UseSpan m_useSpanBasedPutByDefault = UseSpan::Auto;

enum class ModifiableAttributes : char
{
Yes,
No,
Unspecified
};

ModifiableAttributes m_modifiableAttributes =
ModifiableAttributes::Unspecified;

inline SupportedSchema schema() const
{
switch (m_schema)
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39 changes: 29 additions & 10 deletions src/IO/ADIOS/ADIOS2IOHandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -156,6 +156,14 @@ void ADIOS2IOHandlerImpl::init(json::TracingJSON cfg)
: UseSpan::No;
}

if (m_config.json().contains("modifiable_attributes"))
{
m_modifiableAttributes =
m_config["modifiable_attributes"].json().get<bool>()
? ModifiableAttributes::Yes
: ModifiableAttributes::No;
}

auto engineConfig = config(ADIOS2Defaults::str_engine);
if (!engineConfig.json().is_null())
{
Expand Down Expand Up @@ -1638,8 +1646,10 @@ namespace detail
adios2::IO IO = filedata.m_IO;
impl->m_dirty.emplace(std::move(file));

if (parameters.changesOverSteps ==
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No)
if (impl->m_modifiableAttributes ==
ADIOS2IOHandlerImpl::ModifiableAttributes::No &&
parameters.changesOverSteps ==
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No)
{
std::string t = IO.AttributeType(fullName);
if (!t.empty()) // an attribute is present <=> it has a type
Expand Down Expand Up @@ -1676,6 +1686,10 @@ namespace detail
}

auto &value = std::get<T>(parameters.resource);
bool modifiable = impl->m_modifiableAttributes ==
ADIOS2IOHandlerImpl::ModifiableAttributes::Yes ||
parameters.changesOverSteps !=
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No;

if constexpr (IsUnsupportedComplex_v<T>)
{
Expand All @@ -1691,8 +1705,7 @@ namespace detail
value.size(),
/* variableName = */ "",
/* separator = */ "/",
/* allowModification = */ parameters.changesOverSteps !=
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No);
/* allowModification = */ modifiable);
if (!attr)
{
throw std::runtime_error(
Expand All @@ -1708,8 +1721,7 @@ namespace detail
value.size(),
/* variableName = */ "",
/* separator = */ "/",
/* allowModification = */ parameters.changesOverSteps !=
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No);
/* allowModification = */ modifiable);
if (!attr)
{
throw std::runtime_error(
Expand All @@ -1727,8 +1739,7 @@ namespace detail
representation,
/* variableName = */ "",
/* separator = */ "/",
/* allowModification = */ parameters.changesOverSteps !=
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No);
/* allowModification = */ modifiable);
if (!attr)
{
throw std::runtime_error(
Expand All @@ -1743,8 +1754,7 @@ namespace detail
value,
/* variableName = */ "",
/* separator = */ "/",
/* allowModification = */ parameters.changesOverSteps !=
Parameter<Operation::WRITE_ATT>::ChangesOverSteps::No);
/* allowModification = */ modifiable);
if (!attr)
{
throw std::runtime_error(
Expand Down Expand Up @@ -2276,6 +2286,15 @@ namespace detail
m_impl->m_schema = ADIOS2Schema::schema_2022_07_26;
}

if (m_impl->m_modifiableAttributes ==
ADIOS2IOHandlerImpl::ModifiableAttributes::Unspecified)
{
m_impl->m_modifiableAttributes =
m_impl->m_iterationEncoding == IterationEncoding::variableBased
? ADIOS2IOHandlerImpl::ModifiableAttributes::Yes
: ADIOS2IOHandlerImpl::ModifiableAttributes::No;
}

// set engine type
{
m_IO.SetEngine(m_engineType);
Expand Down
68 changes: 59 additions & 9 deletions test/SerialIOTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5237,10 +5237,9 @@ TEST_CASE("git_adios2_sample_test", "[serial][adios2]")

void variableBasedSeries(std::string const &file)
{
std::string selectADIOS2 = R"({"backend": "adios2"})";
constexpr Extent::value_type extent = 1000;
{
Series writeSeries(file, Access::CREATE, selectADIOS2);
auto testWrite = [&file](std::string const &jsonConfig) {
Series writeSeries(file, Access::CREATE, jsonConfig);
writeSeries.setIterationEncoding(IterationEncoding::variableBased);
REQUIRE(
writeSeries.iterationEncoding() ==
Expand All @@ -5260,6 +5259,8 @@ void variableBasedSeries(std::string const &file)
"iteration_is_larger_than_two", "it truly is");
}

iteration.setAttribute("changing_value", i);

// this tests changing extents and dimensionalities
// across iterations
auto E_y = iteration.meshes["E"]["y"];
Expand Down Expand Up @@ -5294,14 +5295,17 @@ void variableBasedSeries(std::string const &file)

iteration.close();
}
}
};

REQUIRE(auxiliary::directory_exists(file));

auto testRead = [&file, &extent, &selectADIOS2](
std::string const &jsonConfig) {
auto testRead = [&file, &extent](
std::string const &parseMode,
bool supportsModifiableAttributes) {
Series readSeries(
file, Access::READ_LINEAR, json::merge(selectADIOS2, jsonConfig));
file,
Access::READ_LINEAR,
json::merge(R"(backend = "adios2")", parseMode));

size_t last_iteration_index = 0;
for (auto iteration : readSeries.readIterations())
Expand All @@ -5318,6 +5322,13 @@ void variableBasedSeries(std::string const &file)
"iteration_is_larger_than_two"));
}

// If modifiable attributes are unsupported, the attribute is
// written once in step 0 and then never changed
// A warning is printed upon trying to write
REQUIRE(
iteration.getAttribute("changing_value").get<unsigned>() ==
(supportsModifiableAttributes ? iteration.iterationIndex : 0));

auto E_x = iteration.meshes["E"]["x"];
REQUIRE(E_x.getDimensionality() == 1);
REQUIRE(E_x.getExtent()[0] == extent);
Expand Down Expand Up @@ -5383,8 +5394,47 @@ void variableBasedSeries(std::string const &file)
REQUIRE(last_iteration_index == 9);
};

testRead("{\"defer_iteration_parsing\": true}");
testRead("{\"defer_iteration_parsing\": false}");
std::string jsonConfig = R"(
{
"backend": "adios2",
"adios2": {
"modifiable_attributes": true
}
})";
testWrite(jsonConfig);
testRead(
"{\"defer_iteration_parsing\": true}",
/*supportsModifiableAttributes = */ true);
testRead(
"{\"defer_iteration_parsing\": false}",
/*supportsModifiableAttributes = */ true);

jsonConfig = R"(
{
"backend": "adios2"
})";
testWrite(jsonConfig);
testRead(
"{\"defer_iteration_parsing\": true}",
/*supportsModifiableAttributes = */ true);
testRead(
"{\"defer_iteration_parsing\": false}",
/*supportsModifiableAttributes = */ true);

jsonConfig = R"(
{
"backend": "adios2",
"adios2": {
"modifiable_attributes": false
}
})";
testWrite(jsonConfig);
testRead(
"{\"defer_iteration_parsing\": true}",
/*supportsModifiableAttributes = */ false);
testRead(
"{\"defer_iteration_parsing\": false}",
/*supportsModifiableAttributes = */ false);
}

#if openPMD_HAVE_ADIOS2
Expand Down

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