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Merged
joewallwork merged 12 commits into from
Nov 10, 2025
Merged

XIOS: Handle CGField #951

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d9cd786
Align coords field with grid
joewallwork Oct 21, 2025
c40666f
Fix reporting of inconsistent dims and indices [skip ci]
joewallwork Oct 21, 2025
330e5c8
Handle CGFields
joewallwork Oct 14, 2025
4e9d7e6
Consider CG in XIOS write test
joewallwork Oct 13, 2025
38cdf7b
Consider CG in XIOS read test
joewallwork Oct 14, 2025
6e7df34
Mention CGField in XIOS docs
joewallwork Oct 14, 2025
e150bc0
Correct start index setting for CG
joewallwork Oct 21, 2025
536b02b
Neater error message
joewallwork Oct 21, 2025
8f40681
Switch variable names
joewallwork Oct 24, 2025
ae7c4e0
Merge branch 'issue911_xios-dgs' into issue911_xios-cg-dgs
joewallwork Nov 3, 2025
26a3c6f
Merge branch 'issue911_xios-dgs' into issue911_xios-cg-dgs
joewallwork Nov 4, 2025
0aadc1b
Merge branch 'issue911_xios-dgs' into issue911_xios-cg-dgs
joewallwork Nov 4, 2025
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4 changes: 4 additions & 0 deletions core/src/ParaGridIO_Xios.cpp
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Expand Up @@ -74,6 +74,10 @@ ModelState ParaGridIO::getModelState(const std::string& filePath)
DGSField field(ModelArray::Type::DGSTRESS);
field.resize();
state.merge(ModelState { { { fieldId, field } }, {} });
} else if (type == ModelArray::Type::CG) {
CGField field(ModelArray::Type::CG);
field.resize();
state.merge(ModelState { { { fieldId, field } }, {} });
} else {
throw std::runtime_error("ParaGridIO::getModelState: field type for field " + fieldId
+ " is not supported.");
Expand Down
55 changes: 39 additions & 16 deletions core/src/Xios.cpp
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Expand Up @@ -682,7 +682,7 @@ void Xios::affixModelMetadata()
}
auto dimName = dim.getName();
size_t localLength;
size_t start = 0;
size_t start;
if (dimType == ModelArray::Dimension::X) {
localLength = metadata.getLocalExtentX();
start = metadata.getLocalCornerX();
Expand All @@ -695,8 +695,15 @@ void Xios::affixModelMetadata()
} else if (dimType == ModelArray::Dimension::YVERTEX) {
localLength = metadata.getLocalExtentY() + 1;
start = metadata.getLocalCornerY();
} else if (dimType == ModelArray::Dimension::XCG) {
localLength = CGDEGREE * metadata.getLocalExtentX() + 1;
start = CGDEGREE * metadata.getLocalCornerX();
} else if (dimType == ModelArray::Dimension::YCG) {
localLength = CGDEGREE * metadata.getLocalExtentY() + 1;
start = CGDEGREE * metadata.getLocalCornerY();
Comment on lines +692 to +697
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@TomMelt TomMelt Oct 27, 2025

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FWIW this is also how I am currently determining the CG dims.... but I would like to hear Tim's comments on PR #969 first. I am worried we might end up in a situation where CG dims is set in several different places. I don't think you need to change this, just raising it as an FYI.

} else {
localLength = dim.getSize();
start = 0;
}

if (ModelArray::definedDimensions.at(dimType)
Expand All @@ -706,15 +713,21 @@ void Xios::affixModelMetadata()
} else {
// Otherwise, check that an attempt to modify them isn't being made
if (dim.getSize() != ModelArray::definedDimensions.at(dimType).globalLength) {
throw std::runtime_error(
"Xios: inconsistent global dimensions for " + dimName);
throw std::runtime_error("Xios: inconsistent global dimensions for "
+ dimName + ": " + std::to_string(dim.getSize()) + " vs. "
+ std::to_string(
ModelArray::definedDimensions.at(dimType).globalLength));
}
if (localLength != ModelArray::size(dimType)) {
throw std::runtime_error(
"Xios: inconsistent local dimensions for " + dimName);
if (localLength != ModelArray::definedDimensions.at(dimType).localLength) {
throw std::runtime_error("Xios: inconsistent local dimensions for "
+ dimName + ": " + std::to_string(localLength) + " vs. "
+ std::to_string(
ModelArray::definedDimensions.at(dimType).localLength));
}
if (start != ModelArray::definedDimensions.at(dimType).start) {
throw std::runtime_error("Xios: inconsistent start index for " + dimName);
throw std::runtime_error("Xios: inconsistent start index for " + dimName
+ ": " + std::to_string(start) + " vs. "
+ std::to_string(ModelArray::definedDimensions.at(dimType).start));
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@TomMelt TomMelt Oct 27, 2025

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I think this alleviates my prev. concern about different sizes for CG dims in the code. However, I might need to understand how this works a bit better. Where will this be called in NextSim? Is it only called once?

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@joewallwork joewallwork Oct 27, 2025

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My subsequent PR #968 will make it a bit clearer, but it's only called once yeah. In that follow-up PR I have it happening when the Model gets configured, which in turn calls ModelMetadata.setTime.

}
}
}
Expand All @@ -727,7 +740,7 @@ void Xios::affixModelMetadata()
{ "ydimxdimdg_comp", ModelArray::Type::DG },
{ "yxdgstress_comp", ModelArray::Type::DGSTRESS },
{ "ydimxdimdgstress_comp", ModelArray::Type::DGSTRESS },
{ "ycgxcg", ModelArray::Type::CG },
{ "y_cgx_cg", ModelArray::Type::CG },
{ "yvertexxvertexncoords", ModelArray::Type::VERTEX },
};

Expand Down Expand Up @@ -809,9 +822,15 @@ void Xios::affixModelMetadata()
if (dim == ModelArray::Dimension::X) {
cxios_set_domain_ni_glo(domain, metadata.getGlobalExtentX());
cxios_set_domain_ni(domain, metadata.getLocalExtentX());
cxios_set_domain_ibegin(domain, metadata.getLocalCornerX());
} else if (dim == ModelArray::Dimension::XVERTEX) {
cxios_set_domain_ni_glo(domain, metadata.getGlobalExtentX() + 1);
cxios_set_domain_ni(domain, metadata.getLocalExtentX() + 1);
cxios_set_domain_ibegin(domain, metadata.getLocalCornerX());
} else if (dim == ModelArray::Dimension::XCG) {
cxios_set_domain_ni_glo(domain, CGDEGREE * metadata.getGlobalExtentX() + 1);
cxios_set_domain_ni(domain, CGDEGREE * metadata.getLocalExtentX() + 1);
cxios_set_domain_ibegin(domain, CGDEGREE * metadata.getLocalCornerX());
} else {
throw std::runtime_error(
"Xios: Could not set domain extents based on dimension '"
Expand All @@ -825,7 +844,6 @@ void Xios::affixModelMetadata()
throw std::runtime_error(
"Xios: Failed to set local x-size for domain '" + domainId + "'");
}
cxios_set_domain_ibegin(domain, metadata.getLocalCornerX());
if (!cxios_is_defined_domain_ibegin(domain)) {
throw std::runtime_error(
"Xios: Failed to set local starting x-index for domain '" + domainId + "'");
Expand All @@ -844,9 +862,15 @@ void Xios::affixModelMetadata()
if (dim == ModelArray::Dimension::Y) {
cxios_set_domain_nj_glo(domain, metadata.getGlobalExtentY());
cxios_set_domain_nj(domain, metadata.getLocalExtentY());
cxios_set_domain_jbegin(domain, metadata.getLocalCornerY());
} else if (dim == ModelArray::Dimension::YVERTEX) {
cxios_set_domain_nj_glo(domain, metadata.getGlobalExtentY() + 1);
cxios_set_domain_nj(domain, metadata.getLocalExtentY() + 1);
cxios_set_domain_jbegin(domain, metadata.getLocalCornerY());
} else if (dim == ModelArray::Dimension::YCG) {
cxios_set_domain_nj_glo(domain, CGDEGREE * metadata.getGlobalExtentY() + 1);
cxios_set_domain_nj(domain, CGDEGREE * metadata.getLocalExtentY() + 1);
cxios_set_domain_jbegin(domain, CGDEGREE * metadata.getLocalCornerY());
} else {
throw std::runtime_error(
"Xios: Could not set domain extents based on dimension '"
Expand All @@ -860,7 +884,6 @@ void Xios::affixModelMetadata()
throw std::runtime_error(
"Xios: Failed to set local y-size for domain '" + domainId + "'");
}
cxios_set_domain_jbegin(domain, metadata.getLocalCornerY());
if (!cxios_is_defined_domain_jbegin(domain)) {
throw std::runtime_error(
"Xios: Failed to set local starting y-index for domain '" + domainId + "'");
Expand Down Expand Up @@ -1675,14 +1698,14 @@ void Xios::write(const std::string fieldId, ModelArray& modelarray)
std::set<std::string> fieldNames = configGetFieldNames(readAccess);
if (fieldNames.find(fieldId) == fieldNames.end()) {
throw std::runtime_error(
"Xios::write: field " + fieldId + " has not been configured for writing with XIOS.");
"Xios::write: field '" + fieldId + "' has not been configured for writing with XIOS.");
}
if (modelarray.nDimensions() != 2) {
throw std::invalid_argument("Only ModelArrays of dimension 2 are supported");
}
auto dims = modelarray.dimensions();
auto type = modelarray.getType();
if (type == ModelArray::Type::H) {
if ((type == ModelArray::Type::H) || (type == ModelArray::Type::CG)) {
cxios_write_data_k82(
fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0], dims[1], -1);
} else if (type == ModelArray::Type::VERTEX) {
Expand All @@ -1696,7 +1719,7 @@ void Xios::write(const std::string fieldId, ModelArray& modelarray)
dims[1], ModelArray::size(ModelArray::Dimension::DGSTRESS), -1);
} else {
throw std::invalid_argument(
"Only HFields, VertexFields, DGFields, and DGStressFields are supported");
"Only HFields, VertexFields, DGFields, DGStressFields, and CGFields are supported");
}
}

Expand All @@ -1712,14 +1735,14 @@ void Xios::read(const std::string fieldId, ModelArray& modelarray)
std::set<std::string> fieldNames = configGetFieldNames(readAccess);
if (fieldNames.find(fieldId) == fieldNames.end()) {
throw std::runtime_error(
"Xios::read: field " + fieldId + " has not been configured for reading with XIOS.");
"Xios::read: field '" + fieldId + "' has not been configured for reading with XIOS.");
}
if (modelarray.nDimensions() != 2) {
throw std::invalid_argument("Only ModelArrays of dimension 2 are supported");
}
auto dims = modelarray.dimensions();
auto type = modelarray.getType();
if (type == ModelArray::Type::H) {
if ((type == ModelArray::Type::H) || (type == ModelArray::Type::CG)) {
cxios_read_data_k82(
fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0], dims[1]);
} else if (type == ModelArray::Type::VERTEX) {
Expand All @@ -1733,7 +1756,7 @@ void Xios::read(const std::string fieldId, ModelArray& modelarray)
dims[1], ModelArray::size(ModelArray::Dimension::DGSTRESS));
} else {
throw std::invalid_argument(
"Only HFields, VertexFields, DGFields, and DGStressFields are supported");
"Only HFields, VertexFields, DGFields, DGStressFields, and CGFields are supported");
}
}
}
Expand Down
2 changes: 2 additions & 0 deletions core/src/include/Xios.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -199,6 +199,7 @@ class Xios : public Configured<Xios> {
{ ModelArray::Type::VERTEX, "VertexDomain" },
{ ModelArray::Type::DG, "HDomain" },
{ ModelArray::Type::DGSTRESS, "HDomain" },
{ ModelArray::Type::CG, "CGDomain" },
};
xios::CDomainGroup* getDomainGroup();
xios::CDomain* getDomain(std::string domainId);
Expand All @@ -224,6 +225,7 @@ class Xios : public Configured<Xios> {
{ ModelArray::Type::VERTEX, "VertexGrid" },
{ ModelArray::Type::DG, "DGGrid" },
{ ModelArray::Type::DGSTRESS, "DGSGrid" },
{ ModelArray::Type::CG, "CGGrid" },
};

/* File */
Expand Down
44 changes: 36 additions & 8 deletions core/test/XiosRead_test.cpp
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Expand Up @@ -25,6 +25,7 @@ const std::string forcingFilename = testFilesDir + "/xios_test_forcing.nc";

static const int DG = 3;
static const int DGSTRESSCOMP = 8;
static const int CGDEGREE = 2;

namespace Nextsim {

Expand All @@ -47,7 +48,7 @@ MPI_TEST_CASE("TestXiosRead", 2)
config << "restart_period = P0-0T01:30:00" << std::endl;
config << "[XiosInput]" << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << ","
<< ticeName << std::endl;
<< ticeName << "," << ciceName << std::endl;
config << "[XiosForcing]" << std::endl;
config << "filename = " << forcingFilename << std::endl;
config << "field_names = " << uName << std::endl;
Expand Down Expand Up @@ -107,26 +108,53 @@ MPI_TEST_CASE("TestXiosRead", 2)
metadata.setTime(xiosHandler.getCalendarStart());
REQUIRE(xiosHandler.getCalendarStep() == 0);
ModelState restarts = grid.getModelState(restartFilename);
const int rank = xiosHandler.getClientMPIRank();
for (auto& entry : restarts.data) {
for (size_t j = 0; j < ny; ++j) {
for (size_t i = 0; i < nx; ++i) {
if (entry.first == maskName) {
if (entry.first == maskName) {
for (size_t j = 0; j < ny; ++j) {
for (size_t i = 0; i < nx; ++i) {
REQUIRE(entry.second(i, j) == doctest::Approx(j >= 1 ? 1.0 : 0.0));
} else if (entry.first == coordsName) {
REQUIRE(entry.second.components({ i, j })[0] == doctest::Approx(i));
}
}
} else if (entry.first == coordsName) {
for (size_t j = 0; j < ny + 1; ++j) {
for (size_t i = 0; i < nx + 1; ++i) {
if (rank == 0) {
REQUIRE(entry.second.components({ i, j })[0] == doctest::Approx(i));
} else {
REQUIRE(entry.second.components({ i, j })[0] == doctest::Approx(i + 2));
}
REQUIRE(entry.second.components({ i, j })[1] == doctest::Approx(j));
} else if (entry.first == hiceName) {
}
}
} else if (entry.first == hiceName) {
for (size_t j = 0; j < ny; ++j) {
for (size_t i = 0; i < nx; ++i) {
for (size_t d = 0; d < DG; ++d) {
float expected = 1.0 * (d + DG * (i + nx * j));
REQUIRE(entry.second.components({ i, j })[d] == doctest::Approx(expected));
}
} else if (entry.first == ticeName) {
}
}
} else if (entry.first == ticeName) {
for (size_t j = 0; j < ny; ++j) {
for (size_t i = 0; i < nx; ++i) {
for (size_t d = 0; d < DGSTRESSCOMP; ++d) {
REQUIRE(entry.second.components({ i, j })[d]
== doctest::Approx(2.0 * (d + DGSTRESSCOMP * (i + nx * j))));
}
}
}
} else if (entry.first == ciceName) {
for (size_t j = 0; j < CGDEGREE * ny + 1; ++j) {
for (size_t i = 0; i < CGDEGREE * nx + 1; ++i) {
if (rank == 0) {
REQUIRE(entry.second(i, j) == doctest::Approx((i + 1) * (j + 1)));
} else {
REQUIRE(entry.second(i, j) == doctest::Approx((i + 5) * (j + 1)));
}
}
}
}
}

Expand Down
48 changes: 40 additions & 8 deletions core/test/XiosWrite_test.cpp
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Expand Up @@ -25,6 +25,7 @@ const std::string diagnosticFilename = testFilesDir + "/xios_test_diagnostic.nc"

static const int DG = 3;
static const int DGSTRESSCOMP = 8;
static const int CGDEGREE = 2;

namespace Nextsim {

Expand All @@ -47,7 +48,8 @@ MPI_TEST_CASE("TestXiosWrite", 2)
config << "restart_period = P0-0T01:30:00" << std::endl;
config << "[XiosOutput]" << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << ","
<< ticeName << std::endl;
<< ticeName << "," << ciceName << std::endl;
config << "period = P0-0T01:30:00" << std::endl;
config << "[XiosDiagnostic]" << std::endl;
config << "filename = " << diagnosticFilename << std::endl;
config << "field_names = " << uName << std::endl;
Expand Down Expand Up @@ -79,10 +81,22 @@ MPI_TEST_CASE("TestXiosWrite", 2)
const size_t ny_glo = 2;
const size_t nx = 2;
const size_t ny = 2;
ModelArray::setDimension(ModelArray::Dimension::X, nx_glo, nx, 0);
ModelArray::setDimension(ModelArray::Dimension::Y, ny_glo, ny, 0);
ModelArray::setDimension(ModelArray::Dimension::XVERTEX, nx_glo + 1, nx + 1, 0);
ModelArray::setDimension(ModelArray::Dimension::YVERTEX, ny_glo + 1, ny + 1, 0);
size_t nx_start;
const size_t ny_start = 0;
const int rank = xiosHandler.getClientMPIRank();
if (rank == 0) {
nx_start = 0;
} else {
nx_start = nx_glo - nx;
}
ModelArray::setDimension(ModelArray::Dimension::X, nx_glo, nx, nx_start);
ModelArray::setDimension(ModelArray::Dimension::XVERTEX, nx_glo + 1, nx + 1, nx_start);
ModelArray::setDimension(
ModelArray::Dimension::XCG, CGDEGREE * nx_glo + 1, CGDEGREE * nx + 1, CGDEGREE * nx_start);
ModelArray::setDimension(ModelArray::Dimension::Y, ny_glo, ny, ny_start);
ModelArray::setDimension(ModelArray::Dimension::YVERTEX, ny_glo + 1, ny + 1, ny_start);
ModelArray::setDimension(
ModelArray::Dimension::YCG, CGDEGREE * ny_glo + 1, CGDEGREE * ny + 1, ny_start);
ModelArray::setNComponents(ModelArray::Type::DG, DG);
ModelArray::setNComponents(ModelArray::Type::DGSTRESS, DGSTRESSCOMP);
ModelArray::setNComponents(ModelArray::Type::VERTEX, ModelArray::nCoords);
Expand All @@ -99,6 +113,7 @@ MPI_TEST_CASE("TestXiosWrite", 2)
xiosHandler.setFieldType(coordsName, ModelArray::Type::VERTEX);
xiosHandler.setFieldType(hiceName, ModelArray::Type::DG);
xiosHandler.setFieldType(ticeName, ModelArray::Type::DGSTRESS);
xiosHandler.setFieldType(ciceName, ModelArray::Type::CG);
xiosHandler.setFieldType(uName, ModelArray::Type::H);

// Set file split frequency for restarts (but not diagnostics)
Expand All @@ -120,8 +135,13 @@ MPI_TEST_CASE("TestXiosWrite", 2)
coordinates.resize();
for (size_t j = 0; j < ny + 1; ++j) {
for (size_t i = 0; i < nx + 1; ++i) {
coordinates.components({ i, j })[0] = (double)i;
coordinates.components({ i, j })[1] = (double)j;
if (rank == 0) {
coordinates.components({ i, j })[0] = (double)i;
coordinates.components({ i, j })[1] = (double)j;
} else {
coordinates.components({ i, j })[0] = (double)(i + 2);
coordinates.components({ i, j })[1] = (double)j;
}
}
}
DGField hice(ModelArray::Type::DG);
Expand All @@ -142,6 +162,17 @@ MPI_TEST_CASE("TestXiosWrite", 2)
}
}
}
CGField cice(ModelArray::Type::CG);
cice.resize();
for (size_t j = 0; j < CGDEGREE * ny + 1; ++j) {
for (size_t i = 0; i < CGDEGREE * nx + 1; ++i) {
if (rank == 0) {
cice(i, j) = (double)((i + 1) * (j + 1));
} else {
cice(i, j) = (double)((i + 5) * (j + 1));
}
}
}
HField u(ModelArray::Type::H);
u.resize();

Expand Down Expand Up @@ -172,6 +203,7 @@ MPI_TEST_CASE("TestXiosWrite", 2)
{ coordsName, coordinates },
{ hiceName, hice },
{ ticeName, tice },
{ ciceName, cice },
},
{} };
ModelState diagnostics = { {
Expand All @@ -188,7 +220,7 @@ MPI_TEST_CASE("TestXiosWrite", 2)
REQUIRE(std::filesystem::exists("xios_test_output_20230317171100-20230317201059.nc"));
REQUIRE(std::filesystem::exists("xios_test_output_20230317201100-20230317231059.nc"));
REQUIRE(std::filesystem::exists("xios_test_diagnostic.nc"));
if (xiosHandler.getClientMPIRank() == 0) {
if (rank == 0) {
std::filesystem::remove("xios_test_output_20230317171100-20230317201059.nc");
std::filesystem::remove("xios_test_output_20230317201100-20230317231059.nc");
std::filesystem::remove("xios_test_diagnostic.nc");
Expand Down
4 changes: 2 additions & 2 deletions core/test/xios_test_forcing.cdl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ dimensions:
y = 2 ;
xvertex = 5 ;
yvertex = 3 ;
x_cg = 2 ;
y_cg = 2 ;
x_cg = 9 ;
y_cg = 5 ;
dg_comp = 3 ;
dgstress_comp = 8 ;
ncoords = 2 ;
Expand Down
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