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HDF5IOHandler: Support for float128 on ARM64/PPC64 (#1364)
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* HDF5IOHandler: Support for float128 data types with 80bit precision on ARM64/PPC64

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Cleanup

Unify little/big endian, use double80 also in other places

Long double size 8 -> 16

Use malloc to avoid alignment issues

Same treatment for complex long double

Add this for readAttribute too

Avoid non-native datatypes in writing

* Make this fix little-endian only

* Add comment

* Suggestions from review

* Use new instead of malloc everywhere

Also, add a more explanative comment

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Franz Pöschel <[email protected]>
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@skalarproduktraum @pre-commit-ci @franzpoeschel
3 people authored Jul 26, 2023
1 parent 5e89ef9 commit e7d7a4b
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Showing 2 changed files with 177 additions and 4 deletions.
10 changes: 10 additions & 0 deletions include/openPMD/IO/HDF5/HDF5IOHandlerImpl.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,16 @@ class HDF5IOHandlerImpl : public AbstractIOHandlerImpl
hid_t m_H5T_CFLOAT;
hid_t m_H5T_CDOUBLE;
hid_t m_H5T_CLONG_DOUBLE;
/* See https://github.com/openPMD/openPMD-api/issues/1363
* long double values written on AMD64 architectures cannot be read on
* ARM64/PPC64 architectures without doing some special tricks.
* We generally don't implement custom conversions, but instead pass-through
* the cross-platform support of HDF5.
* But this case is common and important enough to warrant a custom
* workaround.
*/
hid_t m_H5T_LONG_DOUBLE_80_LE;
hid_t m_H5T_CLONG_DOUBLE_80_LE;

protected:
#if openPMD_HAVE_MPI
Expand Down
171 changes: 167 additions & 4 deletions src/IO/HDF5/HDF5IOHandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
#include "openPMD/auxiliary/Filesystem.hpp"
#include "openPMD/auxiliary/Mpi.hpp"
#include "openPMD/auxiliary/StringManip.hpp"
#include "openPMD/auxiliary/TypeTraits.hpp"
#include "openPMD/backend/Attribute.hpp"

#include <hdf5.h>
Expand Down Expand Up @@ -73,6 +74,8 @@ HDF5IOHandlerImpl::HDF5IOHandlerImpl(
, m_H5T_CFLOAT{H5Tcreate(H5T_COMPOUND, sizeof(float) * 2)}
, m_H5T_CDOUBLE{H5Tcreate(H5T_COMPOUND, sizeof(double) * 2)}
, m_H5T_CLONG_DOUBLE{H5Tcreate(H5T_COMPOUND, sizeof(long double) * 2)}
, m_H5T_LONG_DOUBLE_80_LE{H5Tcopy(H5T_IEEE_F64BE)}
, m_H5T_CLONG_DOUBLE_80_LE{H5Tcreate(H5T_COMPOUND, 16 * 2)}
{
// create a h5py compatible bool type
VERIFY(
Expand Down Expand Up @@ -107,6 +110,28 @@ HDF5IOHandlerImpl::HDF5IOHandlerImpl(
H5Tinsert(m_H5T_CLONG_DOUBLE, "r", 0, H5T_NATIVE_LDOUBLE);
H5Tinsert(m_H5T_CLONG_DOUBLE, "i", sizeof(long double), H5T_NATIVE_LDOUBLE);

// Create a type that understands 128bit floats with 80 bits of precision
// even on those platforms that do not have it (ARM64, PPC64).
// Otherwise, files created on e.g. AMD64 platforms might not be readable
// on such platforms.
H5Tset_size(m_H5T_LONG_DOUBLE_80_LE, 16);
H5Tset_order(m_H5T_LONG_DOUBLE_80_LE, H5T_ORDER_LE);
H5Tset_precision(m_H5T_LONG_DOUBLE_80_LE, 80);
H5Tset_fields(m_H5T_LONG_DOUBLE_80_LE, 79, 64, 15, 0, 64);
H5Tset_ebias(m_H5T_LONG_DOUBLE_80_LE, 16383);
H5Tset_norm(m_H5T_LONG_DOUBLE_80_LE, H5T_NORM_NONE);

VERIFY(
m_H5T_LONG_DOUBLE_80_LE >= 0,
"[HDF5] Internal error: Failed to create 128-bit long double");

H5Tinsert(m_H5T_CLONG_DOUBLE_80_LE, "r", 0, m_H5T_LONG_DOUBLE_80_LE);
H5Tinsert(m_H5T_CLONG_DOUBLE_80_LE, "i", 16, m_H5T_LONG_DOUBLE_80_LE);

VERIFY(
m_H5T_LONG_DOUBLE_80_LE >= 0,
"[HDF5] Internal error: Failed to create 128-bit complex long double");

m_chunks = auxiliary::getEnvString("OPENPMD_HDF5_CHUNKS", "auto");
// JSON option can overwrite env option:
if (config.json().contains("hdf5"))
Expand Down Expand Up @@ -188,6 +213,14 @@ HDF5IOHandlerImpl::~HDF5IOHandlerImpl()
std::cerr
<< "[HDF5] Internal error: Failed to close complex double type\n";
status = H5Tclose(m_H5T_CLONG_DOUBLE);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close complex long "
"double type\n";
status = H5Tclose(m_H5T_LONG_DOUBLE_80_LE);
if (status < 0)
std::cerr
<< "[HDF5] Internal error: Failed to close long double type\n";
status = H5Tclose(m_H5T_CLONG_DOUBLE_80_LE);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close complex long "
"double type\n";
Expand Down Expand Up @@ -1006,13 +1039,17 @@ void HDF5IOHandlerImpl::openDataset(
d = DT::FLOAT;
else if (H5Tequal(dataset_type, H5T_NATIVE_DOUBLE))
d = DT::DOUBLE;
else if (H5Tequal(dataset_type, H5T_NATIVE_LDOUBLE))
else if (
H5Tequal(dataset_type, H5T_NATIVE_LDOUBLE) ||
H5Tequal(dataset_type, m_H5T_LONG_DOUBLE_80_LE))
d = DT::LONG_DOUBLE;
else if (H5Tequal(dataset_type, m_H5T_CFLOAT))
d = DT::CFLOAT;
else if (H5Tequal(dataset_type, m_H5T_CDOUBLE))
d = DT::CDOUBLE;
else if (H5Tequal(dataset_type, m_H5T_CLONG_DOUBLE))
else if (
H5Tequal(dataset_type, m_H5T_CLONG_DOUBLE) ||
H5Tequal(dataset_type, m_H5T_CLONG_DOUBLE_80_LE))
d = DT::CLONG_DOUBLE;
else if (H5Tequal(dataset_type, H5T_NATIVE_USHORT))
d = DT::USHORT;
Expand Down Expand Up @@ -1761,6 +1798,38 @@ void HDF5IOHandlerImpl::readDataset(
{typeid(std::complex<long double>).name(), m_H5T_CLONG_DOUBLE},
});
hid_t dataType = getH5DataType(a);
if (H5Tequal(dataType, H5T_NATIVE_LDOUBLE))
{
// We have previously determined in openDataset() that this dataset is
// of type long double.
// We cannot know if that actually was H5T_NATIVE_LDOUBLE or if it was
// the worked-around m_H5T_LONG_DOUBLE_80_LE.
// Check this.
hid_t checkDatasetTypeAgain = H5Dget_type(dataset_id);
if (!H5Tequal(checkDatasetTypeAgain, H5T_NATIVE_LDOUBLE))
{
dataType = m_H5T_LONG_DOUBLE_80_LE;
}
status = H5Tclose(checkDatasetTypeAgain);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset type during "
"dataset reading");
}
else if (H5Tequal(dataType, m_H5T_CLONG_DOUBLE))
{
// Same deal for m_H5T_CLONG_DOUBLE
hid_t checkDatasetTypeAgain = H5Dget_type(dataset_id);
if (!H5Tequal(checkDatasetTypeAgain, m_H5T_CLONG_DOUBLE))
{
dataType = m_H5T_CLONG_DOUBLE_80_LE;
}
status = H5Tclose(checkDatasetTypeAgain);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset type during "
"dataset reading");
}
VERIFY(
dataType >= 0,
"[HDF5] Internal error: Failed to get HDF5 datatype during dataset "
Expand Down Expand Up @@ -1952,6 +2021,14 @@ void HDF5IOHandlerImpl::readAttribute(
status = H5Aread(attr_id, attr_type, &l);
a = Attribute(l);
}
else if (H5Tequal(attr_type, m_H5T_LONG_DOUBLE_80_LE))
{
char bfr[16];
status = H5Aread(attr_id, attr_type, bfr);
H5Tconvert(
attr_type, H5T_NATIVE_LDOUBLE, 1, bfr, nullptr, H5P_DEFAULT);
a = Attribute(reinterpret_cast<long double *>(bfr)[0]);
}
else if (H5Tget_class(attr_type) == H5T_STRING)
{
if (H5Tis_variable_str(attr_type))
Expand Down Expand Up @@ -2070,6 +2147,20 @@ void HDF5IOHandlerImpl::readAttribute(
status = H5Aread(attr_id, attr_type, &cld);
a = Attribute(cld);
}
else if (complexSize == 16)
{
char bfr[2 * 16];
status = H5Aread(attr_id, attr_type, bfr);
H5Tconvert(
attr_type,
m_H5T_CLONG_DOUBLE,
1,
bfr,
nullptr,
H5P_DEFAULT);
a = Attribute(
reinterpret_cast<std::complex<long double> *>(bfr)[0]);
}
else
throw error::ReadError(
error::AffectedObject::Attribute,
Expand All @@ -2089,7 +2180,8 @@ void HDF5IOHandlerImpl::readAttribute(
error::AffectedObject::Attribute,
error::Reason::UnexpectedContent,
"HDF5",
"[HDF5] Unsupported scalar attribute type");
"[HDF5] Unsupported scalar attribute type for '" + attr_name +
"'.");
}
else if (attr_class == H5S_SIMPLE)
{
Expand Down Expand Up @@ -2211,6 +2303,49 @@ void HDF5IOHandlerImpl::readAttribute(
status = H5Aread(attr_id, attr_type, vcld.data());
a = Attribute(vcld);
}
else if (H5Tequal(attr_type, m_H5T_CLONG_DOUBLE_80_LE))
{
// worst case:
// sizeof(long double) is only 8, but the dataset on disk has
// 16-byte long doubles
// --> do NOT use `new long double[]` as the buffer would be too
// small
auto *tmpBuffer =
reinterpret_cast<long double *>(new char[16lu * 2lu * dims[0]]);
status = H5Aread(attr_id, attr_type, tmpBuffer);
H5Tconvert(
attr_type,
m_H5T_CLONG_DOUBLE,
dims[0],
tmpBuffer,
nullptr,
H5P_DEFAULT);
std::vector<std::complex<long double> > vcld{
tmpBuffer, tmpBuffer + dims[0]};
delete[] tmpBuffer;
a = Attribute(std::move(vcld));
}
else if (H5Tequal(attr_type, m_H5T_LONG_DOUBLE_80_LE))
{
// worst case:
// sizeof(long double) is only 8, but the dataset on disk has
// 16-byte long doubles
// --> do NOT use `new long double[]` as the buffer would be too
// small
auto *tmpBuffer =
reinterpret_cast<long double *>(new char[16lu * dims[0]]);
status = H5Aread(attr_id, attr_type, tmpBuffer);
H5Tconvert(
attr_type,
H5T_NATIVE_LDOUBLE,
dims[0],
tmpBuffer,
nullptr,
H5P_DEFAULT);
std::vector<long double> vld80{tmpBuffer, tmpBuffer + dims[0]};
delete[] tmpBuffer;
a = Attribute(std::move(vld80));
}
else if (H5Tget_class(attr_type) == H5T_STRING)
{
std::vector<std::string> vs;
Expand Down Expand Up @@ -2245,11 +2380,39 @@ void HDF5IOHandlerImpl::readAttribute(
a = Attribute(vs);
}
else
{
auto order = H5Tget_order(attr_type);
auto prec = H5Tget_precision(attr_type);
auto ebias = H5Tget_ebias(attr_type);
size_t spos, epos, esize, mpos, msize;
H5Tget_fields(attr_type, &spos, &epos, &esize, &mpos, &msize);

auto norm = H5Tget_norm(attr_type);
auto cset = H5Tget_cset(attr_type);
auto sign = H5Tget_sign(attr_type);

std::stringstream detailed_info;
detailed_info << "order " << std::to_string(order) << std::endl
<< "prec " << std::to_string(prec) << std::endl
<< "ebias " << std::to_string(ebias) << std::endl
<< "fields " << std::to_string(spos) << " "
<< std::to_string(epos) << " "
<< std::to_string(esize) << " "
<< std::to_string(mpos) << " "
<< std::to_string(msize) << "norm "
<< std::to_string(norm) << std::endl
<< "cset " << std::to_string(cset) << std::endl
<< "sign " << std::to_string(sign) << std::endl
<< std::endl;

throw error::ReadError(
error::AffectedObject::Attribute,
error::Reason::UnexpectedContent,
"HDF5",
"[HDF5] Unsupported simple attribute type");
"[HDF5] Unsupported simple attribute type " +
std::to_string(attr_type) + " for " + attr_name +
".\n(Info for debugging: " + detailed_info.str() + ")");
}
}
else
throw std::runtime_error("[HDF5] Unsupported attribute class");
Expand Down

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