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HDF5 I/O optimizations #1129

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merged 11 commits into from
Oct 27, 2021
Merged

HDF5 I/O optimizations #1129

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04df77e
Include HDF5 optimization options
jeanbez Oct 19, 2021
d5c2232
Merge branch 'openPMD:dev' into hdf5-io-tuning
jeanbez Oct 19, 2021
b4bdc5b
Fix code style check
jeanbez Oct 19, 2021
51aa3f9
Fix validations and include checks
jeanbez Oct 20, 2021
cee8858
Fix style check
jeanbez Oct 20, 2021
ff31e04
Remove unecessary strict check
jeanbez Oct 20, 2021
e45e4b8
Update documentation with HDF5 tuning options
jeanbez Oct 20, 2021
469eb69
Update contributions
jeanbez Oct 20, 2021
983729d
Fix Guards for H5Pset_all_coll_metadata*
ax3l Oct 22, 2021
ae99116
MPI Guard: H5Pset_all_coll_metadata*
ax3l Oct 22, 2021
fa4e034
Remove duplicated variable
jeanbez Oct 23, 2021
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MPI Guard: H5Pset_all_coll_metadata*
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@ax3l
ax3l authored Oct 22, 2021
commit ae9911680840b95423a4b107c08f67a84a60efdc
20 changes: 10 additions & 10 deletions src/IO/HDF5/HDF5IOHandler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ HDF5IOHandlerImpl::HDF5IOHandlerImpl(
}
}

#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
auto const hdf5_collective_metadata = auxiliary::getEnvString( "OPENPMD_HDF5_COLLECTIVE_METADATA", "ON" );
if( hdf5_collective_metadata == "ON" )
m_hdf5_collective_metadata = 1;
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Expand Down Expand Up @@ -211,7 +211,7 @@ HDF5IOHandlerImpl::createPath(Writable* writable,
throw std::runtime_error("[HDF5] Creating a path in a file opened as read only is not possible.");

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
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#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -324,7 +324,7 @@ HDF5IOHandlerImpl::createDataset(Writable* writable,
}

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -632,7 +632,7 @@ HDF5IOHandlerImpl::openPath(
hid_t node_id, path_id;

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -683,7 +683,7 @@ HDF5IOHandlerImpl::openDataset(Writable* writable,
hid_t node_id, dataset_id;

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -1041,7 +1041,7 @@ HDF5IOHandlerImpl::writeAttribute(Writable* writable,
hid_t node_id, attribute_id;

hid_t fapl = H5Pcreate(H5P_LINK_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(fapl, true);
Expand Down Expand Up @@ -1412,7 +1412,7 @@ HDF5IOHandlerImpl::readAttribute(Writable* writable,
herr_t status;

hid_t fapl = H5Pcreate(H5P_LINK_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(fapl, true);
Expand Down Expand Up @@ -1850,7 +1850,7 @@ HDF5IOHandlerImpl::listPaths(Writable* writable,
File file = res ? res.get() : getFile( writable->parent ).get();

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -1895,7 +1895,7 @@ HDF5IOHandlerImpl::listDatasets(Writable* writable,
File file = res ? res.get() : getFile( writable->parent ).get();

hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(gapl, true);
Expand Down Expand Up @@ -1940,7 +1940,7 @@ void HDF5IOHandlerImpl::listAttributes(Writable* writable,
hid_t node_id;

hid_t fapl = H5Pcreate(H5P_LINK_ACCESS);
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#if H5_VERSION_GE(1,10,0)
#if H5_VERSION_GE(1,10,0) && openPMD_HAVE_MPI
if( m_hdf5_collective_metadata )
{
H5Pset_all_coll_metadata_ops(fapl, true);
Expand Down