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Allocate memory for variables at first use instead of in processConfi… #1413

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merged 1 commit into from
May 14, 2019
Merged

Allocate memory for variables at first use instead of in processConfi… #1413

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10 changes: 10 additions & 0 deletions source/utils/adios_iotest/adiosStream.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,11 @@ void adiosStream::putADIOSArray(const std::shared_ptr<VariableInfo> ov)

void adiosStream::getADIOSArray(std::shared_ptr<VariableInfo> ov)
{
// Allocate memory on first access
if (!ov->data.size())
{
ov->data.resize(ov->datasize);
}
if (ov->type == "double")
{
adios2::Variable<double> v = io.InquireVariable<double>(ov->name);
Expand Down Expand Up @@ -258,6 +263,11 @@ void adiosStream::writeADIOS(CommandWrite *cmdW, Config &cfg,
std::map<std::string, adios2::Params> definedVars = io.AvailableVariables();
for (auto ov : cmdW->variables)
{
// Allocate memory on first access
if (!ov->data.size())
{
ov->data.resize(ov->datasize);
}
// if the variable is not in the IO group it means
// we have not defined it yet (e.g. a write-only variable or a linked
// variable defined in another read group)
Expand Down
11 changes: 11 additions & 0 deletions source/utils/adios_iotest/hdf5Stream.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -167,6 +167,11 @@ void hdf5Stream::Write(CommandWrite *cmdW, Config &cfg,

for (auto ov : cmdW->variables)
{
// Allocate memory on first access
if (!ov->data.size())
{
ov->data.resize(ov->datasize);
}
if (step == 1)
{
if (!settings.myRank && settings.verbose)
Expand Down Expand Up @@ -261,6 +266,12 @@ void hdf5Stream::getHDF5Array(std::shared_ptr<VariableInfo> ov, size_t step)
count[d] = ov->count[d - 1];
}

// Allocate memory on first access
if (!ov->data.size())
{
ov->data.resize(ov->datasize);
}

hid_t memspace = H5Screate_simple(ndim, count, NULL);
hid_t dxpl_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
Expand Down
69 changes: 34 additions & 35 deletions source/utils/adios_iotest/processConfig.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -749,61 +749,60 @@ Config processConfig(const Settings &settings, size_t *currentConfigLineNumber)
else if (key == "array")
{
// process config line and get global array info
VariableInfo ov = processArray(words, settings);
ov.datasize = ov.elemsize;
std::vector<size_t> pos(
ov.ndim); // Position of rank in N-dim space

std::shared_ptr<VariableInfo> ovp =
std::make_shared<VariableInfo>(
processArray(words, settings));
ovp->datasize = ovp->elemsize;
// Position of rank in N-dim space
std::vector<size_t> pos(ovp->ndim);
// Calculate rank's position in N-dim space
decompRowMajor(ov.ndim, settings.myRank, ov.decomp.data(),
decompRowMajor(ovp->ndim, settings.myRank, ovp->decomp.data(),
pos.data());

if (settings.isStrongScaling)
{
// Calculate the local size and offsets based on the
// definition
for (size_t i = 0; i < ov.ndim; ++i)
for (size_t i = 0; i < ovp->ndim; ++i)
{
size_t count = ov.shape[i] / ov.decomp[i];
size_t count = ovp->shape[i] / ovp->decomp[i];
size_t offs = count * pos[i];
if (pos[i] == ov.decomp[i] - 1 && pos[i] != 0)
if (pos[i] == ovp->decomp[i] - 1 && pos[i] != 0)
{
// last process in dim(i) need to write all the rest
// of dimension
count = ov.shape[i] - offs;
count = ovp->shape[i] - offs;
}
ov.start.push_back(offs);
ov.count.push_back(count);
ov.datasize *= count;
ovp->start.push_back(offs);
ovp->count.push_back(count);
ovp->datasize *= count;
}
}
else
{
// Calculate the local size and offsets based on the
// definition
for (size_t i = 0; i < ov.ndim; ++i)
for (size_t i = 0; i < ovp->ndim; ++i)
{
size_t shape = ov.count[i] * ov.decomp[i];
size_t offs = ov.count[i] * pos[i];
ov.start.push_back(offs);
ov.shape.push_back(shape);
ov.datasize *= ov.count[i];
size_t shape = ovp->count[i] * ovp->decomp[i];
size_t offs = ovp->count[i] * pos[i];
ovp->start.push_back(offs);
ovp->shape.push_back(shape);
ovp->datasize *= ovp->count[i];
}
}

// Allocate data array
ov.data.resize(ov.datasize);
// Postpone Allocating the data array until first use
// ovp->data.resize(ovp->datasize);

std::shared_ptr<VariableInfo> ovp =
std::make_shared<VariableInfo>(ov);
currentVarList->push_back(ovp);
currentVarMap->emplace(ov.name, ovp);
currentVarMap->emplace(ovp->name, ovp);

/* DEBUG */
if (verbose0)
{
auto grpIt = cfg.groupVariablesMap.find(currentGroup);
auto vIt = grpIt->second.find(ov.name);
auto vIt = grpIt->second.find(ovp->name);
std::cout << " DEBUG variable = " << vIt->second->name
<< " type = " << vIt->second->type << " varmap = "
<< static_cast<void *>(vIt->second.get())
Expand All @@ -812,20 +811,20 @@ Config processConfig(const Settings &settings, size_t *currentConfigLineNumber)
if (settings.verbose > 2)
{
std::cout << "--> rank = " << settings.myRank
<< ": Variable array name = " << ov.name
<< " type = " << ov.type
<< " elemsize = " << ov.elemsize
<< " local datasize = " << ov.datasize
<< " shape = " << DimsToString(ov.shape)
<< " start = " << DimsToString(ov.start)
<< " count = " << DimsToString(ov.count)
<< ": Variable array name = " << ovp->name
<< " type = " << ovp->type
<< " elemsize = " << ovp->elemsize
<< " local datasize = " << ovp->datasize
<< " shape = " << DimsToString(ovp->shape)
<< " start = " << DimsToString(ovp->start)
<< " count = " << DimsToString(ovp->count)
<< std::endl;
}
else if (verbose0)
{
std::cout << "--> Variable array name = " << ov.name
<< " type = " << ov.type
<< " elemsize = " << ov.elemsize << std::endl;
std::cout << "--> Variable array name = " << ovp->name
<< " type = " << ovp->type
<< " elemsize = " << ovp->elemsize << std::endl;
}
}
else if (key == "link")
Expand Down