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Overlink support 1.0 (#1249)
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* we are ready to enable overlink tests

* progress

* they all need materials

* error on no matset + overlink

* anotehr test fixed

* fixed another test

* another test fixed

* fixed last test
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@JustinPrivitera
JustinPrivitera authored Feb 5, 2024
1 parent f9f3502 commit 2aa7db4
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Showing 2 changed files with 187 additions and 84 deletions.
113 changes: 64 additions & 49 deletions src/libs/relay/conduit_relay_io_silo.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -573,14 +573,21 @@ void convert_to_double_array(const Node &n_src,
}
else
{
// if it's already a double array, we just need to compact it
if (n_src.dtype().is_double())
if (n_src.dtype().is_number())
{
conditional_compact(n_src, n_dest);
// if it's already a double array, we just need to compact it
if (n_src.dtype().is_double())
{
conditional_compact(n_src, n_dest);
}
else
{
n_src.to_double_array(n_dest);
}
}
else
{
n_src.to_double_array(n_dest);
n_dest.set_external(n_src);
}
}
}
Expand Down Expand Up @@ -3027,7 +3034,6 @@ void** prepare_mixed_field_for_write(const Node &n_var,
const DataType &vals_dtype,
const int &nvars,
bool &convert_to_double_array,
int &silo_vals_type,
Node &silo_matset,
Node &silo_mixvar_vals_compact,
std::vector<void *> &mixvars_ptrs,
Expand All @@ -3044,15 +3050,19 @@ void** prepare_mixed_field_for_write(const Node &n_var,
conduit::blueprint::mesh::field::to_silo(n_var, n_matset, silo_matset);

DataType mixvar_vals_dtype = silo_matset["field_mixvar_values"].dtype();

// if the field is mixed (has both vals and matset vals) and the types
// of vals and matset vals DO NOT match, we must convert both to
// double arrays.
convert_to_double_array = vals_dtype.id() != mixvar_vals_dtype.id();

// if we are not already converting to double array, we can do an
// additional check to see if we need to
if (! convert_to_double_array)
{
// if the field is mixed (has both vals and matset vals) and the types
// of vals and matset vals DO NOT match, we must convert both to
// double arrays.
convert_to_double_array = vals_dtype.id() != mixvar_vals_dtype.id();
}

if (convert_to_double_array)
{
silo_vals_type = DB_DOUBLE;
detail::convert_to_double_array(silo_matset["field_mixvar_values"],
silo_mixvar_vals_compact);
}
Expand Down Expand Up @@ -3238,6 +3248,12 @@ void silo_write_field(DBfile *dbfile,
// matset_values then we want to convert both to double arrays
bool convert_to_double_array = false;

// overlink requires doubles
if (write_overlink)
{
convert_to_double_array = true;
}

//
// Prepare Matset Values (if they exist)
//
Expand All @@ -3257,12 +3273,16 @@ void silo_write_field(DBfile *dbfile,
vals_dtype,
nvars,
convert_to_double_array,
silo_vals_type,
silo_matset,
silo_mixvar_vals_compact,
mixvars_ptrs,
mixlen);

if (convert_to_double_array)
{
silo_vals_type = DB_DOUBLE;
}

//
// Prepare Field Values
//
Expand Down Expand Up @@ -3605,33 +3625,6 @@ void silo_write_adjset(DBfile *dbfile,

write_dom_neighbor_nums(num_neighboring_doms, dom_neighbor_nums);

// std::vector<std::string> elem_name_strings;
// elem_name_strings.push_back("num_neighbors");
// elem_name_strings.push_back("neighbor_nums");
// // package up char ptrs for silo
// std::vector<const char *> elem_name_ptrs;
// for (size_t i = 0; i < elem_name_strings.size(); i ++)
// {
// elem_name_ptrs.push_back(elem_name_strings[i].c_str());
// }

// std::vector<int> elemlengths;
// elemlengths.push_back(1);
// elemlengths.push_back(num_neighboring_doms);

// const int nelems = 2;
// const int nvalues = num_neighboring_doms + 1;

// DBPutCompoundarray(dbfile, // dbfile
// "DOMAIN_NEIGHBOR_NUMS", // name
// elem_name_ptrs.data(), // elemnames
// elemlengths.data(), // elemlengths
// nelems, // nelems
// static_cast<void *>(dom_neighbor_nums.data()), // values
// nvalues, // nvalues
// DB_INT, // datatype
// NULL); // optlist

//
// COMMUNICATIONS LISTS FOR NEIGHBORING DOMAINS
//
Expand Down Expand Up @@ -4176,7 +4169,7 @@ void silo_write_topo(const Node &mesh_domain,
<< " mesh " << topo_name)

// compact arrays
Node n_coords_compact, new_coords;
Node n_coords_compact, n_coords_compact_final, new_coords;

// here we handle the unstructured points case:
if (unstructured_points)
Expand Down Expand Up @@ -4219,15 +4212,25 @@ void silo_write_topo(const Node &mesh_domain,
detail::conditional_compact(n_coords["values"], n_coords_compact);
}

// overlink requires doubles
if (write_overlink)
{
detail::convert_to_double_array(n_coords_compact, n_coords_compact_final);
}
else
{
n_coords_compact_final.set_external(n_coords_compact);
}

// get num pts
const int num_pts = get_explicit_num_pts(n_coords_compact);
const int num_pts = get_explicit_num_pts(n_coords_compact_final);
n_mesh_info[topo_name]["num_pts"].set(num_pts);

// get coords ptrs
void *coords_ptrs[3] = {NULL, NULL, NULL};
int coords_dtype = assign_coords_ptrs(coords_ptrs,
ndims,
n_coords_compact,
n_coords_compact_final,
silo_coordset_axis_labels.data());

if (topo_type == "unstructured")
Expand Down Expand Up @@ -4321,12 +4324,22 @@ void silo_write_matset(DBfile *dbfile,
Node &n_mesh_info)
{
// use to_silo utility to create the needed silo arrays
Node silo_matset, silo_matset_compact;
Node silo_matset, silo_matset_compact, silo_mix_vfs_final;
conduit::blueprint::mesh::matset::to_silo(n_matset, silo_matset);

// compact the arrays if necessary
detail::conditional_compact(silo_matset, silo_matset_compact);

// mix vfs must be doubles for overlink
if (write_overlink)
{
detail::convert_to_double_array(silo_matset_compact["mix_vf"], silo_mix_vfs_final);
}
else
{
silo_mix_vfs_final.set_external(silo_matset_compact["mix_vf"]);
}

if (!n_matset.has_path("topology"))
{
CONDUIT_INFO("Skipping this matset because we are "
Expand Down Expand Up @@ -4380,9 +4393,9 @@ void silo_write_matset(DBfile *dbfile,
const int mixlen = silo_matset_compact["mix_mat"].dtype().number_of_elements();

// get the datatype of the volume fractions
const int mat_type = detail::dtype_to_silo_type(silo_matset_compact["mix_vf"].dtype());
const int mat_type = detail::dtype_to_silo_type(silo_mix_vfs_final.dtype());
CONDUIT_ASSERT(mat_type == DB_FLOAT || mat_type == DB_DOUBLE,
"Invalid matset volume fraction type: " << silo_matset_compact["mix_vf"].dtype().to_string());
"Invalid matset volume fraction type: " << silo_mix_vfs_final.dtype().to_string());

// create optlist and add to it
detail::SiloObjectWrapperCheckError<DBoptlist, decltype(&DBFreeOptlist)> optlist{
Expand Down Expand Up @@ -4426,7 +4439,7 @@ void silo_write_matset(DBfile *dbfile,
int_arrays["mix_next"].value(),
int_arrays["mix_mat"].value(),
NULL, // mix zone is optional
silo_matset_compact["mix_vf"].data_ptr(), // volume fractions
silo_mix_vfs_final.data_ptr(), // volume fractions
mixlen, // length of mixed data arrays
mat_type, // data type of volume fractions
optlist.getSiloObject()); // optlist
Expand Down Expand Up @@ -4513,6 +4526,11 @@ void silo_mesh_write(const Node &mesh_domain,
}
}

// either we are not writing overlink, or there is a matset present
// overlink requires a matset
CONDUIT_ASSERT(! write_overlink || mesh_domain.has_path("matsets"),
"Writing to Overlink requires a matset.");

if (mesh_domain.has_path("matsets"))
{
// We want to enforce that there is only one matset per topo
Expand Down Expand Up @@ -5394,9 +5412,6 @@ void CONDUIT_RELAY_API write_mesh(const Node &mesh,
// more will happen for this case later
if (write_overlink)
{
CONDUIT_INFO("Overlink is not yet fully supported. Outputted files "
"with this option will be missing several components "
"that Overlink requires.")
opts_suffix = "none"; // force no suffix for overlink case
opts_root_file_ext = "silo"; // force .silo file extension for root file
}
Expand Down
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