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adding Adios2 io support #113

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adding Adios2 io support #113

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c786f61
support for Omega_h_USE_ADIOS2 added
seegyoung Aug 25, 2024
788e45c
checking in adios2 dev
seegyoung Aug 26, 2024
906c8bc
adding osh2bp and bp2osh to utils
seegyoung Sep 7, 2024
dcdfe09
minor changes
seegyoung Sep 9, 2024
a3fe049
adding missing header file and sanity check
seegyoung Sep 12, 2024
ad95f00
adding adios2 impl (cpp) and config.sh for romulus
seegyoung Sep 17, 2024
a76e37a
config.sh removed
seegyoung Sep 17, 2024
cb35d7f
resolve conflicts
seegyoung Dec 17, 2024
5627b34
adding prefix option in adios2 read/write
seegyoung Dec 28, 2024
1971fe0
writing multiple meshes with prefix
seegyoung Dec 30, 2024
aae867b
writing multiple meshes added to adios2_io test
seegyoung Dec 31, 2024
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4 changes: 2 additions & 2 deletions src/Omega_h_adios2.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -462,7 +462,7 @@ void read_parents(adios2::IO &io, adios2::Engine &reader, Mesh* mesh, std::strin
}
}

void write_adios2(adios2::IO &io, adios2::Engine & writer,
void _write_adios2(adios2::IO &io, adios2::Engine & writer,
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Why is this named _write_adios2? We generally avoid having names that start with underscore or double underscore in C++ because depending on the second symbol it could be undefined behavior.

see: https://en.cppreference.com/w/cpp/language/identifiers

Mesh* mesh, std::string pref)
{
comm_size = mesh->comm()->size();
Expand Down Expand Up @@ -506,7 +506,7 @@ void write_adios2(filesystem::path const& path,
adios2::Engine writer = io.Open(filename, adios2::Mode::Write);
writer.BeginStep();
for (; it!=mesh_map.end(); ++it)
write_adios2(io, writer, it->first, it->second);
_write_adios2(io, writer, it->first, it->second);
writer.EndStep();
writer.Close();
}
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2 changes: 2 additions & 0 deletions src/Omega_h_adios2.hpp
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Expand Up @@ -18,6 +18,8 @@ template <typename T>
void read_value(adios2::IO &, adios2::Engine &reader,
T *val, std::string &name, bool global=false);

void write_adios2(filesystem::path const& path,
std::map<Mesh*, std::string>& mesh_map);
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Why is this stored as a map? Instead of a list of pairs or struct that holds a name and a omega_h mesh pointer?

void write_adios2(filesystem::path const& path, Mesh *mesh, std::string pref="");

Mesh read_adios2(filesystem::path const& path, Library* lib, std::string pref="");
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55 changes: 37 additions & 18 deletions src/adios2_io.cpp
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Expand Up @@ -76,39 +76,58 @@ int main(int argc, char *argv[])

Omega_h::CmdLine cmdline;

cmdline.add_arg<std::string>("input.osh");
cmdline.add_arg<std::string>("input1.osh");
cmdline.add_arg<std::string>("input2.osh");
cmdline.add_arg<std::string>("output.bp");
if (!cmdline.parse_final(world, &argc, argv)) return -1;
Omega_h::filesystem::path inpath = cmdline.get<std::string>("input.osh");
Omega_h::filesystem::path inpath1 = cmdline.get<std::string>("input1.osh");
Omega_h::filesystem::path inpath2 = cmdline.get<std::string>("input2.osh");
Omega_h::filesystem::path outpath=cmdline.get<std::string>("output.bp");

Omega_h::Mesh mesh(&lib);
Omega_h::binary::read(inpath, world, &mesh);
cout<<"\n--- Mesh loaded from \""<<inpath<<"\" ---\n";
print_info(&lib, mesh);
Omega_h::Mesh mesh1(&lib);
Omega_h::binary::read(inpath1, world, &mesh1);
Omega_h::Mesh mesh2(&lib);
Omega_h::binary::read(inpath2, world, &mesh2);

cout<<"\n--- Mesh loaded from \""<<inpath1<<"\" ---\n";
print_info(&lib, mesh1);
cout<<"\n--- Mesh loaded from \""<<inpath2<<"\" ---\n";
print_info(&lib, mesh2);

// Omega_h::Mesh mesh = build_box(world, OMEGA_H_SIMPLEX, 1., 1., 0., 2, 2, 0);
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Remove commented code.

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Got it.

Omega_h::binary::write("omegah.osh", &mesh);
Omega_h::vtk::write_parallel("omegah.vtk", &mesh);
Omega_h::binary::write("omegah1.osh", &mesh1);
Omega_h::binary::write("omegah2.osh", &mesh2);
// Omega_h::vtk::write_parallel("omegah.vtk", &mesh);

try
{
write_adios2(outpath, &mesh, std::string("test"));
Omega_h::Mesh mesh2 = read_adios2(outpath, &lib, std::string("test"));
Omega_h::vtk::write_parallel("adios2.vtk", &mesh2);

cout<<"\n\n--- Mesh loaded back from \""<<outpath<<"\" ---\n";
print_info(&lib, mesh2);
map<Mesh*, std::string> mmap;
mmap[&mesh1]="m1";
mmap[&mesh2]="m2";
write_adios2(outpath, mmap);
Omega_h::Mesh mesh3 = read_adios2(outpath, &lib, std::string("m1"));
Omega_h::Mesh mesh4 = read_adios2(outpath, &lib, std::string("m2"));
//Omega_h::vtk::write_parallel("adios2.vtk", &mesh2);

cout<<"\n\n--- Two meshes loaded back from \""<<outpath<<"\" ---\n";
print_info(&lib, mesh3);
print_info(&lib, mesh4);

double tol = 1e-6, floor = 0.0;
bool allow_superset = false;
auto opts = MeshCompareOpts::init(
&mesh, VarCompareOpts{VarCompareOpts::RELATIVE, tol, floor});
auto res = compare_meshes(&mesh, &mesh2, opts, true);
&mesh1, VarCompareOpts{VarCompareOpts::RELATIVE, tol, floor});
auto res = compare_meshes(&mesh1, &mesh3, opts, true);
if (res == OMEGA_H_SAME || (allow_superset && res == OMEGA_H_MORE))
{
cout << "\nSUCCESS! Two meshes (.osh and .bp) are the same\n";
return 0;
opts = MeshCompareOpts::init(
&mesh2, VarCompareOpts{VarCompareOpts::RELATIVE, tol, floor});
res = compare_meshes(&mesh2, &mesh4, opts, true);
if (res == OMEGA_H_SAME || (allow_superset && res == OMEGA_H_MORE))
{
cout << "\nSUCCESS! Meshes loaded from .osh and .bp are the same\n";
return 0;
}
}
cout << "\nFAIL! Two meshes (.osh and .bp) are NOT the same\n";
return 2;
Expand Down