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HDF5IOHandler: Support for float128 on ARM64/PPC64 #1364

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merged 7 commits into from
Jul 26, 2023
Merged

HDF5IOHandler: Support for float128 on ARM64/PPC64 #1364

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d9cc0d0
HDF5IOHandler: Support for float128 data types with 80bit precision o…
skalarproduktraum Jan 20, 2023
02218fa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 21, 2023
c06322f
Cleanup
franzpoeschel Jan 23, 2023
43594b5
Make this fix little-endian only
franzpoeschel May 4, 2023
7f023fe
Add comment
franzpoeschel May 4, 2023
59f1a3d
Suggestions from review
franzpoeschel Jun 27, 2023
0c53b05
Use new instead of malloc everywhere
franzpoeschel Jul 25, 2023
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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
150 changes: 146 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 +110,24 @@ HDF5IOHandlerImpl::HDF5IOHandlerImpl(
H5Tinsert(m_H5T_CLONG_DOUBLE, "r", 0, H5T_NATIVE_LDOUBLE);
H5Tinsert(m_H5T_CLONG_DOUBLE, "i", sizeof(long double), H5T_NATIVE_LDOUBLE);

H5Tset_size(m_H5T_LONG_DOUBLE_80_LE, 16);
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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 +209,14 @@ 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 @@ -1005,13 +1034,17 @@ 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 @@ -1760,6 +1793,28 @@ 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);
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if (!H5Tequal(checkDatasetTypeAgain, H5T_NATIVE_LDOUBLE))
{
dataType = m_H5T_LONG_DOUBLE_80_LE;
}
}
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;
}
}
VERIFY(
dataType >= 0,
"[HDF5] Internal error: Failed to get HDF5 datatype during dataset "
Expand Down Expand Up @@ -1951,6 +2006,14 @@ 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 @@ -2069,6 +2132,20 @@ 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 @@ -2088,7 +2165,8 @@ 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 @@ -2210,6 +2288,42 @@ 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, so allocate enough
// memory to fit 16 bytes per member
auto *tmpBuffer =
static_cast<long double *>(malloc(16 * 2 * dims[0]));
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In C++, I would use new and delete over malloc and free.

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This will need a reinterpret_cast then though, as you can't new a void pointer. But I'll push a commit.

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We found today: can be new long double 😅

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It turns out, we cannot 🙃
This branch is active when sizeof(long double) == 8, but the dataset on disk has 16-byte doubles. There is no way to allocate a correctly-sized buffer using native float types, so new char[] it is.

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]};
free(tmpBuffer);
a = Attribute(std::move(vcld));
}
else if (H5Tequal(attr_type, m_H5T_LONG_DOUBLE_80_LE))
{
// use malloc to allocate a buffer that is definitely aliased and
// big enough for 16-bit doubles
auto *tmpBuffer = static_cast<long double *>(malloc(16 * 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]};
free(tmpBuffer);
a = Attribute(std::move(vld80));
}
else if (H5Tget_class(attr_type) == H5T_STRING)
{
std::vector<std::string> vs;
Expand Down Expand Up @@ -2244,11 +2358,39 @@ 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