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HDF5: Delete and re-create attribute when overwriting with diff. type #1697

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merged 3 commits into from
Dec 4, 2024
Merged

HDF5: Delete and re-create attribute when overwriting with diff. type #1697

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f82503d
HDF5: Delete and re-create attribute when overwriting with diff. type
franzpoeschel Nov 19, 2024
84b8d83
WIP: Change datatype in test
franzpoeschel Nov 26, 2024
6ee8426
Add forgotten H5Aclose() call
franzpoeschel Dec 4, 2024
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42 changes: 37 additions & 5 deletions src/IO/HDF5/HDF5IOHandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1694,8 +1694,7 @@ void HDF5IOHandlerImpl::writeAttribute(
"[HDF5] Internal error: Failed to get HDF5 datatype during attribute "
"write");
std::string name = parameters.name;
if (H5Aexists(node_id, name.c_str()) == 0)
{
auto create_attribute_anew = [&]() {
hid_t dataspace = getH5DataSpace(att);
VERIFY(
dataspace >= 0,
Expand All @@ -1717,14 +1716,47 @@ void HDF5IOHandlerImpl::writeAttribute(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataspace during "
"attribute write");
}
else
};
if (H5Aexists(node_id, name.c_str()) != 0)
{
attribute_id = H5Aopen(node_id, name.c_str(), H5P_DEFAULT);
VERIFY(
node_id >= 0,
attribute_id >= 0,
"[HDF5] Internal error: Failed to open HDF5 attribute during "
"attribute write");
/*
* Only reuse the old attribute if it had the same type.
*/
hid_t type_id = H5Aget_type(attribute_id);
VERIFY(
type_id >= 0,
"[HDF5] Internal error: Failed to inquire HDF5 attribute type "
"during attribute write");
auto equal = H5Tequal(type_id, dataType);
VERIFY(
equal >= 0,
"[HDF5] Internal error: Failed to compare HDF5 attribute types "
"during attribute write");
if (equal == 0) // unequal
{
status = H5Aclose(attribute_id);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close previous HDF5 "
"attribute "
"during attribute write");
status = H5Adelete(node_id, name.c_str());
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to delete previous HDF5 "
"attribute "
"during attribute write");
create_attribute_anew();
}
}
else
{
create_attribute_anew();
}

using DT = Datatype;
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10 changes: 10 additions & 0 deletions test/SerialIOTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -7522,6 +7522,8 @@ void groupbased_read_write(std::string const &ext)

E_x.setAttribute("updated_in_run", 0);
E_y.setAttribute("updated_in_run", 0);
E_y.setAttribute("changed_datatype_in_run", 0);
write.close();
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.close() calls added for stricter error check, the destructors will swallow exceptions.

}

{
Expand All @@ -7540,6 +7542,8 @@ void groupbased_read_write(std::string const &ext)

E_x.setAttribute("updated_in_run", 1);
E_y.setAttribute("updated_in_run", 1);
E_y.setAttribute("changed_datatype_in_run", "one");
write.close();
}

{
Expand All @@ -7551,6 +7555,9 @@ void groupbased_read_write(std::string const &ext)
REQUIRE(E_x_0_fromRun0.getAttribute("updated_in_run").get<int>() == 0);
REQUIRE(E_x_1_fromRun1.getAttribute("updated_in_run").get<int>() == 1);
REQUIRE(E_y_0_fromRun1.getAttribute("updated_in_run").get<int>() == 1);
REQUIRE(
E_y_0_fromRun1.getAttribute("changed_datatype_in_run")
.get<std::string>() == "one");

auto chunk_E_x_0_fromRun0 = E_x_0_fromRun0.loadChunk<int>({0}, {1});
auto chunk_E_x_1_fromRun1 = E_x_1_fromRun1.loadChunk<int>({0}, {1});
Expand All @@ -7561,6 +7568,7 @@ void groupbased_read_write(std::string const &ext)
REQUIRE(*chunk_E_x_0_fromRun0 == 0);
REQUIRE(*chunk_E_x_1_fromRun1 == 1);
REQUIRE(*chunk_E_y_0_fromRun1 == 1);
read.close();
}

// check that truncation works correctly
Expand All @@ -7574,12 +7582,14 @@ void groupbased_read_write(std::string const &ext)

E_x.storeChunkRaw(&data, {0}, {1});
E_x.setAttribute("updated_in_run", 2);
write.close();
}

{
Series read(filename, Access::READ_ONLY);
REQUIRE(read.iterations.size() == 1);
REQUIRE(read.iterations.count(2) == 1);
read.close();
}
}

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