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Merge d162be5 into 9ff9860
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@cyrush
cyrush committed Apr 7, 2020
2 parents 9ff9860 + d162be5 commit 0b29bbf
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Showing 4 changed files with 131 additions and 30 deletions.
2 changes: 1 addition & 1 deletion src/libs/conduit/conduit_utils.cpp
View file
Expand Up @@ -951,7 +951,7 @@ base64_decode(const void *src,
std::string
float64_to_string(float64 value)
{
char buffer[64];
char buffer[64] = {0};
snprintf(buffer,64,"%.15g",value);

std::string res(buffer);
Expand Down
132 changes: 104 additions & 28 deletions src/libs/relay/conduit_relay_io_hdf5.cpp
View file
Expand Up @@ -393,21 +393,26 @@ void hdf5_ref_path_with_filename(hid_t hdf5_id,
// helpers for checking if compatible
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
// if incompatible, incompat_details contains human readable details
// about why
//-----------------------------------------------------------------------------
bool check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
const std::string &ref_path,
hid_t hdf5_id);
hid_t hdf5_id,
std::string &incompat_details);

//-----------------------------------------------------------------------------
bool check_if_conduit_object_is_compatible_with_hdf5_tree(const Node &node,
const std::string &ref_path,
hid_t hdf5_id);
hid_t hdf5_id,
std::string &incompat_details);

//-----------------------------------------------------------------------------
bool check_if_conduit_node_is_compatible_with_hdf5_tree(const Node &node,
const std::string &ref_path,
hid_t hdf5_id);

hid_t hdf5_id,
std::string &incompat_details);

//-----------------------------------------------------------------------------
// helpers for writing
Expand Down Expand Up @@ -833,7 +838,8 @@ hdf5_ref_path_with_filename(hid_t hdf5_id,
bool
check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
const std::string &ref_path,
hid_t hdf5_id)
hid_t hdf5_id,
std::string &incompat_details)
{
bool res = true;
H5O_info_t h5_obj_info;
Expand All @@ -851,6 +857,15 @@ check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
if( H5Sget_simple_extent_type(h5_test_dspace) == H5S_NULL &&
!dtype.is_empty())
{
std::ostringstream oss;
oss << "Conduit Node (leaf) at path '" << ref_path << "'"
<< " is not compatible with given HDF5 Dataset at path"
<< " '" << ref_path << "'"
<< "\nHDF5 dataset has a H5S_NULL Dataspace which"
<< " only compatible with an empty Conduit Node";

incompat_details = oss.str();

res = false;
}
else
Expand Down Expand Up @@ -878,12 +893,32 @@ check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
// note: both hdf5 and conduit dtypes include null term in string size
(dtype.number_of_elements() != (index_t)H5Tget_size(h5_test_dtype) ) )
{
res = false;
std::ostringstream oss;
oss << "Conduit Node (string leaf) at path '" << ref_path << "'"
<< " is not compatible with given HDF5 Dataset at path"
<< " '" << ref_path << "'"
<< "\nConduit leaf String Node length ("
<< dtype.number_of_elements() << ")"
<< " != HDF5 Dataset size (" << H5Tget_size(h5_test_dtype) << ")";

incompat_details = oss.str();

res = false;
}
else if( ! ( (H5Tequal(h5_dtype, h5_test_dtype) > 0) &&
(dtype.number_of_elements() == h5_test_num_ele) ) )
{
res = false;
std::ostringstream oss;
oss << "Conduit Node (leaf) at path '" << ref_path << "'"
<< " is not compatible with given HDF5 Dataset at path"
<< " '" << ref_path << "'"
<< "\nConduit leaf Node number of elements ("
<< dtype.number_of_elements() << ")"
<< " != HDF5 Dataset size (" << H5Tget_size(h5_test_dtype) << ")";

incompat_details = oss.str();

res = false;
}

CONDUIT_CHECK_HDF5_ERROR_WITH_FILE_AND_REF_PATH(H5Tclose(h5_test_dtype),
Expand All @@ -903,15 +938,23 @@ check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
else
{
// bad id, or not a dataset
std::ostringstream oss;
oss << "Conduit Node (leaf) at path '" << ref_path << "'"
<< " is not compatible with given HDF5 Dataset at path"
<< "'" << ref_path << "'"
<< "\nConduit leaf vs HDF5 Dataset: Bad HDF5 Leaf ID"
<< " or HDF5 ID is not a HDF5 Group";

incompat_details = oss.str();
res = false;
}

if(res == false)
{
CONDUIT_INFO("leaf in Conduit Node at path " << ref_path <<
" is not compatible with given HDF5 tree at path "
<< ref_path);
}
//
// if(res == false)
// {
// CONDUIT_INFO("leaf in Conduit Node at path " << ref_path <<
// " is not compatible with given HDF5 tree at path "
// << ref_path);
// }

return res;
}
Expand All @@ -920,9 +963,11 @@ check_if_conduit_leaf_is_compatible_with_hdf5_obj(const DataType &dtype,
bool
check_if_conduit_object_is_compatible_with_hdf5_tree(const Node &node,
const std::string &ref_path,
hid_t hdf5_id)
hid_t hdf5_id,
std::string &incompat_details)
{
bool res = true;

// make sure we have a group ...

H5O_info_t h5_obj_info;
Expand Down Expand Up @@ -953,7 +998,8 @@ check_if_conduit_object_is_compatible_with_hdf5_tree(const Node &node,
// compatible with the conduit node
res = check_if_conduit_node_is_compatible_with_hdf5_tree(child,
chld_ref_path,
h5_child_obj);
h5_child_obj,
incompat_details);

CONDUIT_CHECK_HDF5_ERROR_WITH_FILE_AND_REF_PATH(H5Oclose(h5_child_obj),
hdf5_id,
Expand All @@ -966,9 +1012,15 @@ check_if_conduit_object_is_compatible_with_hdf5_tree(const Node &node,
}
else // bad id or not a group
{
CONDUIT_INFO("object in Conduit Node at path " << ref_path <<
" is not compatible with given HDF5 tree at path "
<< ref_path );
std::ostringstream oss;
oss << "Conduit Node (object) at path '" << ref_path << "'"
<< " is not compatible with given HDF5 tree at path"
<< "'" << ref_path << "'"
<< "\nConduit Object vs HDF5 Group: Bad HDF5 Group ID "
<< "or HDF5 ID is not a HDF5 Group";

incompat_details = oss.str();

res = false;
}

Expand All @@ -980,29 +1032,46 @@ check_if_conduit_object_is_compatible_with_hdf5_tree(const Node &node,
bool
check_if_conduit_node_is_compatible_with_hdf5_tree(const Node &node,
const std::string &ref_path,
hid_t hdf5_id)
hid_t hdf5_id,
std::string &incompat_details)
{
bool res = true;

DataType dt = node.dtype();
// check for leaf or group
if(dt.is_number() || dt.is_string())
{
res = check_if_conduit_leaf_is_compatible_with_hdf5_obj(dt,
ref_path,
hdf5_id);
hdf5_id,
incompat_details);
}
else if(dt.is_object())
{
res = check_if_conduit_object_is_compatible_with_hdf5_tree(node,
ref_path,
hdf5_id);
hdf5_id,
incompat_details);
}
else // not supported
{
std::ostringstream oss;
oss << "Conduit Node at path '" << ref_path << "'"
<< " has an unsupported dtype (" << dt.name() << ")"
<< " for HDF5 i/o and cannot be written to HDF5 path"
<< " '" << ref_path << "'";

if(dt.is_list()) // let them know there is hope for lists in the future
{
// we don't support lists yet, but provide helpful
// info when passed a list
oss << "\nA future conduit release will add"
<< " list read/write support for HDF5.";
}
incompat_details = oss.str();
res = false;
}

return res;
}

Expand Down Expand Up @@ -2262,10 +2331,12 @@ hdf5_write(const Node &node,
n.set_external(const_cast<Node&>(node));
}

std::string incompat_details;
// check compat
if(check_if_conduit_node_is_compatible_with_hdf5_tree(n,
"",
hdf5_id))
hdf5_id,
incompat_details))
{
// write if we are compat
write_conduit_node_to_hdf5_tree(n,"",hdf5_id);
Expand All @@ -2280,7 +2351,8 @@ hdf5_write(const Node &node,
CONDUIT_ERROR("Failed to write node to "
<< "\"" << hdf5_error_ref_path << "\", "
<< "existing HDF5 tree is "
<< "incompatible with the Conduit Node.");
<< "incompatible with the Conduit Node."
<< "\nDetails:\n" << incompat_details);
}

// restore hdf5 error stack
Expand All @@ -2297,10 +2369,13 @@ hdf5_write(const Node &node,
// of check_if_conduit_node_is_compatible_with_hdf5_tree
HDF5ErrorStackSupressor supress_hdf5_errors;

std::string incompat_details;

// check compat
if(check_if_conduit_node_is_compatible_with_hdf5_tree(node,
"",
hdf5_id))
hdf5_id,
incompat_details))
{
// write if we are compat
write_conduit_node_to_hdf5_tree(node,
Expand All @@ -2315,7 +2390,8 @@ hdf5_write(const Node &node,
CONDUIT_ERROR("Failed to write node to "
<< "\"" << hdf5_fname << "\", "
<< "existing HDF5 tree is "
<< "incompatible with the Conduit Node.");
<< "incompatible with the Conduit Node."
<< " Details: " << incompat_details);
}
// restore hdf5 error stack
}
Expand Down
2 changes: 1 addition & 1 deletion src/tests/blueprint/t_blueprint_mpi_relay.cpp
View file
Expand Up @@ -90,7 +90,7 @@ void mesh_blueprint_save(const Node &data,
int par_size = mpi::size(MPI_COMM_WORLD);

// setup the directory
char fmt_buff[64];
char fmt_buff[64] = {0};
int cycle = data["state/cycle"].to_int32();
snprintf(fmt_buff, sizeof(fmt_buff), "%06d",cycle);

Expand Down
25 changes: 25 additions & 0 deletions src/tests/relay/t_relay_io_hdf5.cpp
View file
Expand Up @@ -1344,4 +1344,29 @@ TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_string_compress)

}

//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_list_incompat_error_message)
{
std::string tout_std = "tout_hdf5_w_list_error.hdf5";

Node n;
n.append() = "42";
n.append() = "42";
n.append() = "42";
n.append() = "42";

bool excpt_occured = false;
try
{
io::save(n,tout_std, "hdf5");
}
catch(Error &e)
{
excpt_occured = true;
CONDUIT_INFO(e.message());
}

EXPECT_TRUE(excpt_occured);
}


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