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Merge pull request #1801 from pradsubedi/master
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Added support for Scalar Variable in DataSpaces
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@philip-davis
philip-davis authored Oct 15, 2019
2 parents 882bc3f + be4aacb commit d9e44ee
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Showing 4 changed files with 81 additions and 74 deletions.
26 changes: 11 additions & 15 deletions source/adios2/engine/dataspaces/DataSpacesReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -82,27 +82,24 @@ StepStatus DataSpacesReader::BeginStep(StepMode mode, const float timeout_sec)
meta_lk = new char[lk_name.length() + 1];
strcpy(meta_lk, lk_name.c_str());

MPI_Comm lock_comm = MPI_COMM_SELF;
MPI_Comm lock_comm = m_data.mpi_comm;
dspaces_lock_on_read(meta_lk, &lock_comm);

int nVars = 0;
if (!m_ProvideLatest)
{
if (rank == 0)
{
dspaces_lock_on_read(meta_lk, &lock_comm);
buffer = dspaces_get_next_meta(m_CurrentStep, fstr, &bcast_array[0],
&bcast_array[1]);
dspaces_unlock_on_read(meta_lk, &lock_comm);
}
}
else
{
if (rank == 0)
{
dspaces_lock_on_read(meta_lk, &lock_comm);
buffer = dspaces_get_latest_meta(m_CurrentStep, fstr,
&bcast_array[0], &bcast_array[1]);
dspaces_unlock_on_read(meta_lk, &lock_comm);
}
}
MPI_Bcast(bcast_array, 2, MPI_INT, 0, m_data.mpi_comm);
Expand Down Expand Up @@ -224,28 +221,27 @@ size_t DataSpacesReader::CurrentStep() const { return m_CurrentStep; }
void DataSpacesReader::EndStep()
{

MPI_Barrier(m_data.mpi_comm);
PerformGets();
char *meta_lk;
std::string lk_name = f_Name + std::to_string(m_CurrentStep);
meta_lk = new char[lk_name.length() + 1];
strcpy(meta_lk, lk_name.c_str());

MPI_Comm lock_comm = m_data.mpi_comm;
dspaces_unlock_on_read(meta_lk, &lock_comm);
}

void DataSpacesReader::DoClose(const int transportIndex)
{

if (globals_adios_is_dataspaces_connected_from_reader() &&
!globals_adios_is_dataspaces_connected_from_both())
{
// fprintf(stderr, "Disconnecting reader via finalize \n");
MPI_Barrier(m_data.mpi_comm);
dspaces_finalize();
}
globals_adios_set_dataspaces_disconnected_from_writer();
globals_adios_set_dataspaces_disconnected_from_reader();
}

void DataSpacesReader::Flush(const int transportIndex) {}

void DataSpacesReader::PerformGets()
{
if (m_DeferredStack.size() > 0 && m_CurrentStep <= latestStep)
if (m_DeferredStack.size() > 0)
{
#define declare_type(T) \
for (std::string variableName : m_DeferredStack) \
Expand Down
48 changes: 28 additions & 20 deletions source/adios2/engine/dataspaces/DataSpacesReader.tcc
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Original file line number Diff line number Diff line change
Expand Up @@ -65,28 +65,38 @@ void DataSpacesReader::ReadDsData(Variable<T> &variable, T *data, int version)
i,j --> j, i = lb[1], lb[0]
i --> i = lb[0]
*/

if (isOrderC)
if (variable.m_Shape.size() == 0)
{
for (int i = 0; i < ndims; i++)
{
gdims_in[i] =
static_cast<uint64_t>(variable.m_Shape[ndims - i - 1]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[ndims - i - 1]);
ub_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1] +
variable.m_Count[ndims - i - 1] - 1);
}
gdims_in[0] = dspaces_get_num_space_server();
lb_in[0] = 0;
ub_in[0] = 0;
ndims = 1;
}
else
{

for (int i = 0; i < ndims; i++)
if (isOrderC)
{
gdims_in[i] = static_cast<uint64_t>(variable.m_Shape[i]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[i]);
ub_in[i] = static_cast<uint64_t>(variable.m_Start[i] +
variable.m_Count[i] - 1);
for (int i = 0; i < ndims; i++)
{
gdims_in[i] =
static_cast<uint64_t>(variable.m_Shape[ndims - i - 1]);
lb_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1]);
ub_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1] +
variable.m_Count[ndims - i - 1] - 1);
}
}
else
{

for (int i = 0; i < ndims; i++)
{
gdims_in[i] = static_cast<uint64_t>(variable.m_Shape[i]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[i]);
ub_in[i] = static_cast<uint64_t>(variable.m_Start[i] +
variable.m_Count[i] - 1);
}
}
}

Expand All @@ -99,12 +109,10 @@ void DataSpacesReader::ReadDsData(Variable<T> &variable, T *data, int version)
char *cstr = new char[l_Name.length() + 1];
strcpy(cstr, l_Name.c_str());

dspaces_lock_on_read(cstr, &m_data.mpi_comm);

dspaces_define_gdim(var_str, ndims, gdims_in);
dspaces_get(var_str, version, variable.m_ElementSize, ndims, lb_in, ub_in,
(void *)data);
dspaces_unlock_on_read(cstr, &m_data.mpi_comm);

delete[] cstr;
delete[] var_str;
}
Expand Down
26 changes: 9 additions & 17 deletions source/adios2/engine/dataspaces/DataSpacesWriter.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,16 @@ size_t DataSpacesWriter::CurrentStep() const { return m_CurrentStep; }

void DataSpacesWriter::EndStep()
{
int rank;
MPI_Comm_rank(m_data.mpi_comm, &rank);
std::string local_file_var;

local_file_var = f_Name + std::to_string(m_CurrentStep);
char *meta_lk = new char[local_file_var.length() + 1];
strcpy(meta_lk, local_file_var.c_str());
MPI_Comm lock_comm = m_data.mpi_comm;

dspaces_lock_on_write(meta_lk, &lock_comm);
WriteVarInfo();
MPI_Barrier(m_data.mpi_comm);
dspaces_unlock_on_write(meta_lk, &lock_comm);
}
void DataSpacesWriter::Flush(const int transportIndex) {}

Expand All @@ -85,13 +91,6 @@ void DataSpacesWriter::DoClose(const int transportIndex)
dspaces_lock_on_write(meta_lk, &(m_data.mpi_comm));
dspaces_unlock_on_write(meta_lk, &(m_data.mpi_comm));

if (globals_adios_is_dataspaces_connected_from_writer() &&
!globals_adios_is_dataspaces_connected_from_both())
{
// fprintf(stderr, "Disconnecting writer via finalize \n");
MPI_Barrier(m_data.mpi_comm);
dspaces_finalize();
}
globals_adios_set_dataspaces_disconnected_from_writer();
}

Expand Down Expand Up @@ -119,12 +118,7 @@ void DataSpacesWriter::WriteVarInfo()
char *local_str, *buffer, *name_string;
uint64_t *gdim_meta;
uint64_t gdims[MAX_DS_NDIM], lb[MAX_DS_NDIM], ub[MAX_DS_NDIM];

local_file_var = f_Name + std::to_string(m_CurrentStep);
char *meta_lk = new char[local_file_var.length() + 1];
strcpy(meta_lk, local_file_var.c_str());
MPI_Comm_rank(m_data.mpi_comm, &rank);
MPI_Comm lock_comm = MPI_COMM_SELF;

if (rank == 0)
{
Expand Down Expand Up @@ -181,13 +175,11 @@ void DataSpacesWriter::WriteVarInfo()
lb[0] = 0;
ub[0] = buf_len - 1;
gdims[0] = (ub[0] - lb[0] + 1) * dspaces_get_num_space_server();
dspaces_lock_on_write(meta_lk, &lock_comm);
dspaces_define_gdim(local_str, ndim, gdims);

dspaces_put(local_str, m_CurrentStep, elemsize, ndim, lb, ub, buffer);

dspaces_put_sync(); // wait on previous put to finish
dspaces_unlock_on_write(meta_lk, &lock_comm);
delete[] local_str;
free(dim_meta);
free(elemSize_meta);
Expand Down
55 changes: 33 additions & 22 deletions source/adios2/engine/dataspaces/DataSpacesWriter.tcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ void DataSpacesWriter::DoPutSyncCommon(Variable<T> &variable, const T *values)
unsigned int version;
version = m_CurrentStep;
int ndims = std::max(variable.m_Shape.size(), variable.m_Count.size());
ndim_vector.push_back(ndims);
bool isOrderC = helper::IsRowMajor(m_IO.m_HostLanguage);
/* Order of dimensions: in DataSpaces: fast --> slow --> slowest
For example:
Expand All @@ -47,30 +46,43 @@ void DataSpacesWriter::DoPutSyncCommon(Variable<T> &variable, const T *values)
i,j --> j, i = lb[1], lb[0]
i --> i = lb[0]
*/

if (isOrderC)
if (variable.m_SingleValue)
{
for (int i = 0; i < ndims; i++)
{
gdims_in[i] =
static_cast<uint64_t>(variable.m_Shape[ndims - i - 1]);
dims_vec.push_back(gdims_in[i]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[ndims - i - 1]);
ub_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1] +
variable.m_Count[ndims - i - 1] - 1);
}
gdims_in[0] = dspaces_get_num_space_server();
lb_in[0] = 0;
ub_in[0] = 0;
ndims = 1;
dims_vec.push_back(0);
ndim_vector.push_back(0);
}
else
{

for (int i = 0; i < ndims; i++)
ndim_vector.push_back(ndims);
if (isOrderC)
{
gdims_in[i] = static_cast<uint64_t>(variable.m_Shape[i]);
dims_vec.push_back(gdims_in[i]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[i]);
ub_in[i] = static_cast<uint64_t>(variable.m_Start[i] +
variable.m_Count[i] - 1);
for (int i = 0; i < ndims; i++)
{
gdims_in[i] =
static_cast<uint64_t>(variable.m_Shape[ndims - i - 1]);
dims_vec.push_back(gdims_in[i]);
lb_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1]);
ub_in[i] =
static_cast<uint64_t>(variable.m_Start[ndims - i - 1] +
variable.m_Count[ndims - i - 1] - 1);
}
}
else
{

for (int i = 0; i < ndims; i++)
{
gdims_in[i] = static_cast<uint64_t>(variable.m_Shape[i]);
dims_vec.push_back(gdims_in[i]);
lb_in[i] = static_cast<uint64_t>(variable.m_Start[i]);
ub_in[i] = static_cast<uint64_t>(variable.m_Start[i] +
variable.m_Count[i] - 1);
}
}
}
gdims_vector.push_back(dims_vec);
Expand Down Expand Up @@ -98,12 +110,11 @@ void DataSpacesWriter::DoPutSyncCommon(Variable<T> &variable, const T *values)
char *cstr = new char[l_Name.length() + 1];
strcpy(cstr, l_Name.c_str());

dspaces_lock_on_write(cstr, &m_data.mpi_comm);
dspaces_define_gdim(var_str, ndims, gdims_in);
dspaces_put(var_str, version, variable.m_ElementSize, ndims, lb_in, ub_in,
values);
dspaces_put_sync();
dspaces_unlock_on_write(cstr, &m_data.mpi_comm);
dspaces_put_sync();
delete[] cstr;
delete[] var_str;
}
Expand Down

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