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Merge pull request E3SM-Project#176 from philipwjones/omega/decomp-dim
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fixes reading dimensions for Omega decomposition and unused dimensions
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@philipwjones
philipwjones authored Dec 4, 2024
2 parents 8f008c7 + b732b56 commit 399b7af
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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
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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
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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 @@ -659,15 +659,12 @@ 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 @@ -1730,10 +1727,7 @@ int IOStream::readFieldData(
} else {
Err = IO::readNDVar(DataPtr, OldFieldName, FileID, 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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