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Merge pull request ornladios#1577 from germasch/pr/fix_hdf5_msvc
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fix HDF5Reader build with MSVC
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Chuck Atkins committed Jun 30, 2019
2 parents 2a95dbf + 6fe4dbf commit 00ca539
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Showing 4 changed files with 41 additions and 37 deletions.
10 changes: 6 additions & 4 deletions source/adios2/engine/hdf5/HDF5ReaderP.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@
#include "adios2/common/ADIOSMPI.h"
#include "adios2/helper/adiosFunctions.h" //CSVToVector

#include <vector>

namespace adios2
{
namespace core
Expand Down Expand Up @@ -146,7 +148,7 @@ size_t HDF5ReaderP::ReadDataset(hid_t dataSetId, hid_t h5Type,
}
else
{
hsize_t start[ndims], count[ndims], stride[ndims];
std::vector<hsize_t> start(ndims), count(ndims), stride(ndims);
bool isOrderC = helper::IsRowMajor(m_IO.m_HostLanguage);

for (int i = 0; i < ndims; i++)
Expand All @@ -164,12 +166,12 @@ size_t HDF5ReaderP::ReadDataset(hid_t dataSetId, hid_t h5Type,
slabsize *= count[i];
stride[i] = 1;
}
hid_t ret = H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, start,
stride, count, NULL);
hid_t ret = H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, start.data(),
stride.data(), count.data(), NULL);
if (ret < 0)
return 0;

hid_t memDataSpace = H5Screate_simple(ndims, count, NULL);
hid_t memDataSpace = H5Screate_simple(ndims, count.data(), NULL);
interop::HDF5TypeGuard g_mds(memDataSpace, interop::E_H5_SPACE);

int elementsRead = 1;
Expand Down
27 changes: 13 additions & 14 deletions source/adios2/toolkit/interop/hdf5/HDF5Common.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
#include <ios>
#include <iostream>
#include <stdexcept>
#include <vector>

#include "adios2/common/ADIOSMPI.h"
#include "adios2/helper/adiosFunctions.h" // IsRowMajor
Expand Down Expand Up @@ -189,7 +190,7 @@ void HDF5Common::WriteAdiosSteps()
hid_t attr =
H5Acreate(m_FileId, ATTRNAME_NUM_STEPS.c_str(),
/*"NumSteps",*/ H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
uint totalAdiosSteps = m_CurrentAdiosStep + 1;
unsigned int totalAdiosSteps = m_CurrentAdiosStep + 1;

if (m_GroupId < 0)
{
Expand Down Expand Up @@ -295,18 +296,16 @@ void HDF5Common::FindVarsFromH5(core::IO &io, hid_t top_id, const char *gname,
hid_t datasetId = H5Dopen(gid, name, H5P_DEFAULT);
HDF5TypeGuard d(datasetId, E_H5_DATASET);

char longName[std::strlen(heritage) +
std::strlen(gname) + std::strlen(name) +
10];
std::string longName;

if (strcmp(gname, "/") == 0)
{
sprintf(longName, "/%s", name);
longName = std::string("/") + name;
}
else
{
sprintf(longName, "%s/%s/%s", heritage, gname,
name);
longName = std::string(heritage) + "/" + gname +
"/" + name;
}
// CreateVar(io, datasetId, name);
ReadNativeAttrToIO(io, datasetId, longName);
Expand Down Expand Up @@ -419,8 +418,8 @@ void HDF5Common::AddVar(core::IO &io, std::string const &name, hid_t datasetId,
{
hid_t dspace = H5Dget_space(datasetId);
const int ndims = H5Sget_simple_extent_ndims(dspace);
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dspace, dims, NULL);
std::vector<hsize_t> dims(ndims);
H5Sget_simple_extent_dims(dspace, dims.data(), NULL);
H5Sclose(dspace);

Dims shape;
Expand Down Expand Up @@ -934,9 +933,9 @@ void HDF5Common::AddNonStringAttribute(core::IO &io,
}
else
{
T val[arraySize];
H5Aread(attrId, h5Type, val);
io.DefineAttribute(attrName, val, arraySize);
std::vector<T> val(arraySize);
H5Aread(attrId, h5Type, val.data());
io.DefineAttribute(attrName, val.data(), arraySize);
}
}

Expand Down Expand Up @@ -1245,7 +1244,7 @@ void HDF5Common::ReadAttrToIO(core::IO &io)
{
numAttrs = oinfo.num_attrs;
int k = 0;
int MAX_ATTR_NAME_SIZE = 100;
const int MAX_ATTR_NAME_SIZE = 100;
for (k = 0; k < numAttrs; k++)
{
char attrName[MAX_ATTR_NAME_SIZE];
Expand Down Expand Up @@ -1303,7 +1302,7 @@ void HDF5Common::ReadNativeAttrToIO(core::IO &io, hid_t datasetId,
// consuimg
}
int k = 0;
int MAX_ATTR_NAME_SIZE = 100;
const int MAX_ATTR_NAME_SIZE = 100;
for (k = 0; k < numAttrs; k++)
{
char attrName[MAX_ATTR_NAME_SIZE];
Expand Down
4 changes: 2 additions & 2 deletions source/adios2/toolkit/interop/hdf5/HDF5Common.tcc
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Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,7 @@ void HDF5Common::AddBlockInfo(const core::Variable<T> &variable, hid_t parentId)
H5Dcreate(parentId, blockInfo_name.c_str(), H5T_NATIVE_HSIZE,
metaSpace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

size_t blocks[dimSize * 2];
std::vector<size_t> blocks(dimSize * 2);
for (int i = 0; i < dimSize; i++)
{
blocks[i + dimSize] = variable.m_Count[i];
Expand All @@ -223,7 +223,7 @@ void HDF5Common::AddBlockInfo(const core::Variable<T> &variable, hid_t parentId)
metaCount, NULL);

H5Dwrite(metaId, H5T_NATIVE_HSIZE, metaLocal_id, metaSpace_id,
m_PropertyTxfID, blocks);
m_PropertyTxfID, blocks.data());

H5Sclose(metaLocal_id);
H5Sclose(metaSpace_id);
Expand Down
37 changes: 20 additions & 17 deletions source/utils/adios_iotest/hdf5Stream.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
#include <math.h>
#include <stdexcept>
#include <string>
#include <vector>

hdf5Stream::hdf5Stream(const std::string &streamName, const adios2::Mode mode,
MPI_Comm comm)
Expand Down Expand Up @@ -80,9 +81,9 @@ hid_t hdf5Stream::hdf5Type(std::string &type)
void hdf5Stream::defineHDF5Array(const std::shared_ptr<VariableInfo> ov)
{
const int ndim = ov->ndim + 1;
hsize_t maxdims[ndim];
hsize_t dims[ndim];
hsize_t count[ndim];
std::vector<hsize_t> maxdims(ndim);
std::vector<hsize_t> dims(ndim);
std::vector<hsize_t> count(ndim);

maxdims[0] = H5S_UNLIMITED;
dims[0] = 1;
Expand All @@ -94,14 +95,14 @@ void hdf5Stream::defineHDF5Array(const std::shared_ptr<VariableInfo> ov)
count[d] = ov->count[d - 1];
}

hid_t dataspace = H5Screate_simple(ndim, dims, maxdims);
hid_t dataspace = H5Screate_simple(ndim, dims.data(), maxdims.data());

hid_t cparms;
/*
* Set chunking, the only way to have extendible arrays
*/
cparms = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparms, ndim, count);
H5Pset_chunk(cparms, ndim, count.data());

hid_t dataset;
dataset = H5Dcreate2(h5file, ov->name.c_str(), hdf5Type(ov->type),
Expand All @@ -117,9 +118,9 @@ void hdf5Stream::putHDF5Array(const std::shared_ptr<VariableInfo> ov,
const auto it = varmap.find(ov->name);
hdf5VarInfo &vi = it->second;
int ndim = ov->ndim + 1;
hsize_t start[ndim];
hsize_t count[ndim];
hsize_t dims[ndim];
std::vector<hsize_t> start(ndim);
std::vector<hsize_t> count(ndim);
std::vector<hsize_t> dims(ndim);
start[0] = step - 1;
count[0] = 1;
dims[0] = step;
Expand All @@ -130,12 +131,13 @@ void hdf5Stream::putHDF5Array(const std::shared_ptr<VariableInfo> ov,
dims[d] = ov->shape[d - 1];
}

H5Dset_extent(vi.dataset, dims);
H5Dset_extent(vi.dataset, dims.data());
hid_t filespace = H5Dget_space(vi.dataset);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, NULL, count, NULL);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start.data(), NULL,
count.data(), NULL);
hid_t dxpl_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
hid_t memspace = H5Screate_simple(ndim, count, NULL);
hid_t memspace = H5Screate_simple(ndim, count.data(), NULL);
H5Dwrite(vi.dataset, hdf5Type(ov->type), memspace, filespace, dxpl_id,
ov->data.data());
H5Pclose(dxpl_id);
Expand Down Expand Up @@ -256,8 +258,8 @@ void hdf5Stream::getHDF5Array(std::shared_ptr<VariableInfo> ov, size_t step)
}
int ndim = ov->ndim + 1;

hsize_t start[ndim];
hsize_t count[ndim];
std::vector<hsize_t> start(ndim);
std::vector<hsize_t> count(ndim);
start[0] = step - 1;
count[0] = 1;
for (int d = 1; d < ndim; ++d)
Expand All @@ -272,10 +274,11 @@ void hdf5Stream::getHDF5Array(std::shared_ptr<VariableInfo> ov, size_t step)
ov->data.resize(ov->datasize);
}

hid_t memspace = H5Screate_simple(ndim, count, NULL);
hid_t memspace = H5Screate_simple(ndim, count.data(), NULL);
hid_t dxpl_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, NULL, count, NULL);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start.data(), NULL,
count.data(), NULL);
void *buf = reinterpret_cast<void *>(ov->data.data());
H5Dread(dataset, hdf5Type(ov->type), memspace, filespace, dxpl_id, buf);

Expand Down Expand Up @@ -317,9 +320,9 @@ adios2::StepStatus hdf5Stream::Read(CommandRead *cmdR, Config &cfg,
std::shared_ptr<VariableInfo> var = cmdR->variables.front();
hid_t dataset = H5Dopen2(h5file, var->name.c_str(), H5P_DEFAULT);
hid_t filespace = H5Dget_space(dataset);
hsize_t dims[var->ndim + 1];
std::vector<hsize_t> dims(var->ndim + 1);
int ndim = H5Sget_simple_extent_ndims(filespace);
H5Sget_simple_extent_dims(filespace, dims, NULL);
H5Sget_simple_extent_dims(filespace, dims.data(), NULL);
/* ndim == var->ndim+1 */
nSteps = dims[0];
if (!settings.myRank && settings.verbose)
Expand Down

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