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fixes reading dimensions for Omega decomposition and unused dimension…
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…s in input

   - adds support for new dimension names during Decomp reads
   - skips reading of unused dimensions in input files
   - suppresses error/warning messages at the base IO level for missing
     variables or dimensions. The calling routine now determines
     the appropriate action when missing variables are encountered.
     This eliminates warnings for harmless situations that can cause
     confusion and unnecessary output in the log file.
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@philipwjones
philipwjones committed Dec 3, 2024
1 parent 11c9afc commit b48446b
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Showing 3 changed files with 153 additions and 67 deletions.
194 changes: 142 additions & 52 deletions components/omega/src/base/Decomp.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -131,30 +131,71 @@ int readMesh(const int MeshFileID, // file ID for open mesh file
bool IsMaster = InEnv->isMasterTask();

// Read in mesh size information - these are dimension lengths in
// the input mesh file
// the input mesh file. Check both the name under Omega name conventions
// and the older MPAS name.
std::string DimName = "NCells";
std::string DimNameOld = "nCells";
I4 NCellsID;
Err = IO::getDimFromFile(MeshFileID, "nCells", NCellsID, NCellsGlobal);
if (Err != 0 or NCellsGlobal <= 0)
LOG_CRITICAL("Decomp: error reading nCells");
Err = IO::getDimFromFile(MeshFileID, DimName, NCellsID, NCellsGlobal);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimNameOld, NCellsID, NCellsGlobal);
if (Err != 0 or NCellsGlobal <= 0)
LOG_CRITICAL("Decomp: error reading nCells");
}

DimName = "NEdges";
DimNameOld = "nEdges";
I4 NEdgesID;
Err = IO::getDimFromFile(MeshFileID, "nEdges", NEdgesID, NEdgesGlobal);
if (Err != 0 or NEdgesGlobal <= 0)
LOG_CRITICAL("Decomp: error reading NEdges");
Err = IO::getDimFromFile(MeshFileID, DimName, NEdgesID, NEdgesGlobal);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimNameOld, NEdgesID, NEdgesGlobal);
if (Err != 0 or NEdgesGlobal <= 0)
LOG_CRITICAL("Decomp: error reading NEdges");
}

DimName = "NVertices";
DimNameOld = "nVertices";
I4 NVerticesID;
Err = IO::getDimFromFile(MeshFileID, "nVertices", NVerticesID,
NVerticesGlobal);
if (Err != 0 or NVerticesGlobal <= 0)
LOG_CRITICAL("Decomp: error reading NVertices");
Err = IO::getDimFromFile(MeshFileID, DimName, NVerticesID, NVerticesGlobal);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimNameOld, NVerticesID,
NVerticesGlobal);
if (Err != 0 or NVerticesGlobal <= 0)
LOG_CRITICAL("Decomp: error reading NVertices");
}

DimName = "MaxEdges";
DimNameOld = "maxEdges";
I4 MaxEdgesID;
Err = IO::getDimFromFile(MeshFileID, "maxEdges", MaxEdgesID, MaxEdges);
if (Err != 0 or MaxEdges <= 0)
LOG_CRITICAL("Decomp: error reading MaxEdges");
Err = IO::getDimFromFile(MeshFileID, DimName, MaxEdgesID, MaxEdges);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimNameOld, MaxEdgesID, MaxEdges);
if (Err != 0 or MaxEdges <= 0)
LOG_CRITICAL("Decomp: error reading MaxEdges");
}

DimName = "VertexDegree";
DimNameOld = "vertexDegree";
I4 VertexDegreeID;
Err = IO::getDimFromFile(MeshFileID, "vertexDegree", VertexDegreeID,
VertexDegree);
if (Err != 0 or VertexDegree <= 0)
LOG_CRITICAL("Decomp: error reading VertexDegree");
MaxCellsOnEdge = 2; // currently always 2
Err = IO::getDimFromFile(MeshFileID, DimName, VertexDegreeID, VertexDegree);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimNameOld, VertexDegreeID,
VertexDegree);
if (Err != 0 or VertexDegree <= 0)
LOG_CRITICAL("Decomp: error reading VertexDegree");
}

DimName = "MaxCellsOnEdge";
DimNameOld = "TWO";
I4 MaxCellsOnEdgeID;
Err = IO::getDimFromFile(MeshFileID, DimNameOld, MaxCellsOnEdgeID,
MaxCellsOnEdge);
if (Err != 0) { // dim not found, try again with older MPAS name
Err = IO::getDimFromFile(MeshFileID, DimName, MaxCellsOnEdgeID,
MaxCellsOnEdge);
if (Err != 0 or MaxCellsOnEdge <= 0)
LOG_CRITICAL("Decomp: error reading MaxCellsOnEdge");
}
I4 MaxEdgesOnEdge = 2 * MaxEdges; // 2*MaxCellsOnEdge

// Create the linear decompositions for parallel IO
Expand Down Expand Up @@ -249,7 +290,8 @@ int readMesh(const int MeshFileID, // file ID for open mesh file
if (Err != 0)
LOG_CRITICAL("Decomp: error creating Vertex IO decomposition");

// Now read the connectivity arrays
// Now read the connectivity arrays. Try reading under the new Omega
// name convention and the older MPAS mesh names.
CellsOnCellInit.resize(OnCellSize);
EdgesOnCellInit.resize(OnCellSize);
VerticesOnCellInit.resize(OnCellSize);
Expand All @@ -259,53 +301,101 @@ int readMesh(const int MeshFileID, // file ID for open mesh file
CellsOnVertexInit.resize(OnVertexSize);
EdgesOnVertexInit.resize(OnVertexSize);

std::string VarName = "CellsOnCell";
std::string VarNameOld = "cellsOnCell";
int CellsOnCellID;
Err = IO::readArray(&CellsOnCellInit[0], OnCellSize, "cellsOnCell",
MeshFileID, OnCellDecomp, CellsOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnCell");
Err = IO::readArray(&CellsOnCellInit[0], OnCellSize, VarName, MeshFileID,
OnCellDecomp, CellsOnCellID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&CellsOnCellInit[0], OnCellSize, VarNameOld,
MeshFileID, OnCellDecomp, CellsOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnCell");
}

VarName = "EdgesOnCell";
VarNameOld = "edgesOnCell";
int EdgesOnCellID;
Err = IO::readArray(&EdgesOnCellInit[0], OnCellSize, "edgesOnCell",
MeshFileID, OnCellDecomp, EdgesOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnCell");
Err = IO::readArray(&EdgesOnCellInit[0], OnCellSize, VarName, MeshFileID,
OnCellDecomp, EdgesOnCellID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&EdgesOnCellInit[0], OnCellSize, VarNameOld,
MeshFileID, OnCellDecomp, EdgesOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnCell");
}

VarName = "VerticesOnCell";
VarNameOld = "verticesOnCell";
int VerticesOnCellID;
Err = IO::readArray(&VerticesOnCellInit[0], OnCellSize, "verticesOnCell",
MeshFileID, OnCellDecomp, VerticesOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading VerticesOnCell");
Err = IO::readArray(&VerticesOnCellInit[0], OnCellSize, VarName, MeshFileID,
OnCellDecomp, VerticesOnCellID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&VerticesOnCellInit[0], OnCellSize, VarNameOld,
MeshFileID, OnCellDecomp, VerticesOnCellID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading VerticesOnCell");
}

VarName = "CellsOnEdge";
VarNameOld = "cellsOnEdge";
int CellsOnEdgeID;
Err = IO::readArray(&CellsOnEdgeInit[0], OnEdgeSize, "cellsOnEdge",
MeshFileID, OnEdgeDecomp, CellsOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnEdge");
Err = IO::readArray(&CellsOnEdgeInit[0], OnEdgeSize, VarName, MeshFileID,
OnEdgeDecomp, CellsOnEdgeID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&CellsOnEdgeInit[0], OnEdgeSize, VarNameOld,
MeshFileID, OnEdgeDecomp, CellsOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnEdge");
}

VarName = "EdgesOnEdge";
VarNameOld = "edgesOnEdge";
int EdgesOnEdgeID;
Err = IO::readArray(&EdgesOnEdgeInit[0], OnEdgeSize2, "edgesOnEdge",
MeshFileID, OnEdgeDecomp2, EdgesOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnEdge");
Err = IO::readArray(&EdgesOnEdgeInit[0], OnEdgeSize2, VarName, MeshFileID,
OnEdgeDecomp2, EdgesOnEdgeID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&EdgesOnEdgeInit[0], OnEdgeSize2, VarNameOld,
MeshFileID, OnEdgeDecomp2, EdgesOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnEdge");
}

VarName = "VerticesOnEdge";
VarNameOld = "verticesOnEdge";
int VerticesOnEdgeID;
Err = IO::readArray(&VerticesOnEdgeInit[0], OnEdgeSize, "verticesOnEdge",
MeshFileID, OnEdgeDecomp, VerticesOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading VerticesOnEdge");
Err = IO::readArray(&VerticesOnEdgeInit[0], OnEdgeSize, VarName, MeshFileID,
OnEdgeDecomp, VerticesOnEdgeID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&VerticesOnEdgeInit[0], OnEdgeSize, VarNameOld,
MeshFileID, OnEdgeDecomp, VerticesOnEdgeID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading VerticesOnEdge");
}

VarName = "CellsOnVertex";
VarNameOld = "cellsOnVertex";
int CellsOnVertexID;
Err = IO::readArray(&CellsOnVertexInit[0], OnVertexSize, "cellsOnVertex",
MeshFileID, OnVertexDecomp, CellsOnVertexID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnVertex");
Err = IO::readArray(&CellsOnVertexInit[0], OnVertexSize, VarName, MeshFileID,
OnVertexDecomp, CellsOnVertexID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&CellsOnVertexInit[0], OnVertexSize, VarNameOld,
MeshFileID, OnVertexDecomp, CellsOnVertexID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading CellsOnVertex");
}

VarName = "EdgesOnVertex";
VarNameOld = "edgesOnVertex";
int EdgesOnVertexID;
Err = IO::readArray(&EdgesOnVertexInit[0], OnVertexSize, "edgesOnVertex",
MeshFileID, OnVertexDecomp, EdgesOnVertexID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnVertex");
Err = IO::readArray(&EdgesOnVertexInit[0], OnVertexSize, VarName, MeshFileID,
OnVertexDecomp, EdgesOnVertexID);
if (Err != 0) { // not found, try again under older name
Err = IO::readArray(&EdgesOnVertexInit[0], OnVertexSize, VarNameOld,
MeshFileID, OnVertexDecomp, EdgesOnVertexID);
if (Err != 0)
LOG_CRITICAL("Decomp: error reading EdgesOnVertex");
}

// Initial decompositions are no longer needed so remove them now
Err = IO::destroyDecomp(OnCellDecomp);
Expand Down
6 changes: 4 additions & 2 deletions components/omega/src/base/IO.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -331,7 +331,8 @@ int getDimFromFile(int FileID, // [in] ID of the file containing dim
// First get the dimension ID
Err = PIOc_inq_dimid(FileID, DimName.c_str(), &DimID);
if (Err != PIO_NOERR) {
LOG_ERROR("PIO error while reading dimension {} ", DimName);
// Dimension missing in file - return error but let calling routine
// decide how to respond
return Err;
}

Expand Down Expand Up @@ -701,7 +702,8 @@ int readArray(void *Array, // [out] array to be read
// Find variable ID from file
Err = PIOc_inq_varid(FileID, VarName.c_str(), &VarID);
if (Err != PIO_NOERR) {
LOG_ERROR("IO::readArray: Error finding varid for variable {}", VarName);
// Variable not in file. Return error but let calling routine decide
// how to respond
return Err;
}

Expand Down
20 changes: 7 additions & 13 deletions components/omega/src/infra/IOStream.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -650,15 +650,12 @@ int IOStream::defineAllDims(
if (Err != 0) { // can't find dim in file
// Try again using old name for back compatibility to MPAS
Err = IO::getDimFromFile(FileID, OldDimName, DimID, InLength);
if (Err == 0) {
LOG_INFO("Ignore PIO Error for Dimension {}: ", DimName);
LOG_INFO("Found under old dimension name {}: ", OldDimName);
} else {
if (Err != 0)
LOG_WARN("Dimension {} not found in input stream {}", DimName,
Name);
}
continue;
// If still not found, we skip this dimension, assuming it
// is not used for any variables to be read from the file. A later
// error check will catch any case where the dimension is actually
// needed but missing.
if (Err != 0)
continue;
}
// Check dimension length in input file matches what is expected
if (InLength != Length) {
Expand Down Expand Up @@ -1629,10 +1626,7 @@ int IOStream::readFieldData(
// For back compatibility, try to read again with old field name
Err = IO::readArray(DataPtr, LocSize, OldFieldName, FileID, DecompID,
FieldID);
if (Err == 0) {
LOG_INFO("Ignore PIO error for field {} ", FieldName);
LOG_INFO("Found field under old name {} ", OldFieldName);
} else {
if (Err != 0) { // still not found - return error
LOG_ERROR("Error reading data array for {} in stream {}", FieldName,
Name);
return Err;
Expand Down

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