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Silo improvements #478

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39 changes: 32 additions & 7 deletions src/Mesh/siloMeshDump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,25 @@ def extractFieldComponents(nodeLists, time, cycle,
metaDataTensorField, extractTensorField, dummyTensorField)
return result

#-------------------------------------------------------------------------------
# Get subdirs for the variable names. They need to be sorted s.t. parent dirs
# are created first.
#-------------------------------------------------------------------------------
def getSubDirs(fieldwad):
dirs = set()
if len(fieldwad) > 0:
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
subdirs = name.split("/")[:-1]
for i in range(len(subdirs)):
dirs.add("/".join(subdirs[:i+1]))
return sorted(dirs, key=lambda x: x.count("/"))

#-------------------------------------------------------------------------------
# Return name with / replaced by _
#-------------------------------------------------------------------------------
def unslashify(name):
return name.replace("/", "_")

#-------------------------------------------------------------------------------
# Write the master file.
#-------------------------------------------------------------------------------
Expand All @@ -154,7 +173,10 @@ def writeMasterMeshSiloFile(dirName, mesh, label, nodeLists, time, cycle, fieldw
# Make directories for variables.
assert silo.DBMkDir(db, "CELLS") == 0
assert silo.DBMkDir(db, "POINTS") == 0 # HACK

for d in getSubDirs(fieldwad):
assert silo.DBMkDir(db, "CELLS/" + d) == 0
assert silo.DBMkDir(db, "POINTS/" + d) == 0

# Pattern for constructing per domain variables.
domainNamePatterns = [("%s/domain%i.silo:" % (p1, i)) + "%s" for i in range(mpi.procs) if numZonesPerDomain[i] > 0]
numDomains = len(domainNamePatterns)
Expand Down Expand Up @@ -230,12 +252,12 @@ def writeMasterMeshSiloFile(dirName, mesh, label, nodeLists, time, cycle, fieldw
# Write the variables descriptors.
ucdTypes = vector_of_int([silo.DB_UCDVAR]*numDomains)
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
domainVarNames = vector_of_string([p % ("CELLS_" + name) for p in domainNamePatterns])
domainVarNames = vector_of_string([p % ("CELLS_" + unslashify(name)) for p in domainNamePatterns])
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "CELLS/" + name, domainVarNames, ucdTypes, optlistMV) == 0
if desc != None:
for subname, vals in subvars:
domainVarNames = vector_of_string([p % ("CELLS_" + subname) for p in domainNamePatterns])
domainVarNames = vector_of_string([p % ("CELLS_" + unslashify(subname)) for p in domainNamePatterns])
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "CELLS/" + subname, domainVarNames, ucdTypes, optlistVar) == 0

Expand All @@ -245,14 +267,14 @@ def writeMasterMeshSiloFile(dirName, mesh, label, nodeLists, time, cycle, fieldw
# for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
# domainVarNames = []
# for p in domainNamePatterns:
# domainVarNames.append(p % ("POINTS_" + name))
# domainVarNames.append(p % ("POINTS_" + unslashify(name)))
# assert len(domainVarNames) == numDomains
# assert silo.DBPutMultivar(db, "POINTS/" + name, domainVarNames, ptTypes, optlistMV) == 0
# if desc != None:
# for subname, vals in subvars:
# domainVarNames = []
# for p in domainNamePatterns:
# domainVarNames.append(p % ("POINTS_" + subname))
# domainVarNames.append(p % ("POINTS_" + unslashify(subname)))
# assert len(domainVarNames) == numDomains
# assert silo.DBPutMultivar(db, "POINTS/" + subname, domainVarNames, ptTypes, optlistVar) == 0

Expand Down Expand Up @@ -293,6 +315,9 @@ def writeDomainMeshSiloFile(dirName, mesh, index2zone, label, nodeLists, time, c
# Make directories for variables.
assert silo.DBMkDir(db, "CELLS") == 0
assert silo.DBMkDir(db, "POINTS") == 0 # HACK
for d in getSubDirs(fieldwad):
assert silo.DBMkDir(db, "CELLS/" + d) == 0
assert silo.DBMkDir(db, "POINTS/" + d) == 0

# Determine our dimensionality
if isinstance(mesh, polytope.Tessellation2d):
Expand Down Expand Up @@ -403,7 +428,7 @@ def writeDomainMeshSiloFile(dirName, mesh, index2zone, label, nodeLists, time, c
ctor = vector_of_double
else:
ctor = vector_of_int
assert silo.DBPutUcdvar1(db, "CELLS_" + subname, "MESH", ctor(vals), ctor([]), silo.DB_ZONECENT, varOpts) == 0
assert silo.DBPutUcdvar1(db, "CELLS_" + unslashify(subname), "MESH", ctor(vals), ctor([]), silo.DB_ZONECENT, varOpts) == 0

# print " --> %g sec to DBPutUcdvar1" % (TIME.clock() - start)
# start = TIME.clock()
Expand All @@ -419,7 +444,7 @@ def writeDomainMeshSiloFile(dirName, mesh, index2zone, label, nodeLists, time, c
# ctor = vector_of_double
# else:
# ctor = vector_of_int
# assert silo.DBPutPointvar1(db, "POINTS_" + subname, "PointMESH", ctor(vals), varOpts) == 0
# assert silo.DBPutPointvar1(db, "POINTS_" + unslashify(subname), "PointMESH", ctor(vals), varOpts) == 0

# print " --> %g sec to DBPutPointvar1" % (TIME.clock() - start)
# start = TIME.clock()
Expand Down
2 changes: 1 addition & 1 deletion src/PYB11/Silo/SiloWrappers.hh
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Original file line number Diff line number Diff line change
Expand Up @@ -1392,7 +1392,7 @@ DBPutPointmesh(DBfile& file,

// Preconditions.
const unsigned ndims = coords.size();
VERIFY(ndims == 2 or ndims == 3);
VERIFY(ndims == 1 or ndims == 2 or ndims == 3);
const unsigned npoints = coords[0].size();
for (unsigned idim = 0; idim != ndims; ++idim) VERIFY(coords[idim].size() == npoints);

Expand Down
83 changes: 59 additions & 24 deletions src/SimulationControl/siloPointmeshDump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import os, mpi
from Spheral import *
from SpheralCompiledPackages import silo
from siloMeshDump import getSubDirs, unslashify

#-------------------------------------------------------------------------------
# siloPointMeshDump -- this is the one the user should actually call!
Expand Down Expand Up @@ -45,10 +46,10 @@ def siloPointmeshDump(baseName,
os.makedirs(dire)
mpi.barrier()

# We can only pretend this is an RZ mesh if it's 2D.
# Check dimensionality.
ndim = dimension(nodeLists[0])
if not ndim in (2, 3):
raise ValueError("You need to provide 2D or 3D information for siloPointMeshDump.")
if not ndim in (1, 2, 3):
raise ValueError("You need to provide 1D, 2D or 3D information for siloPointMeshDump.")

# Characterize the fields we're going to write.
allfields = fields[:]
Expand All @@ -68,7 +69,7 @@ def siloPointmeshDump(baseName,
elif isinstance(f, eval("SymTensorField%id" % ndim)):
symTensorFields.append(f)
else:
print("siloPointmeshDump WARNING: ignoring unknown field type.")
print("siloPointmeshDump WARNING: ignoring unknown field type: %s" % type(f).__name__)

# For any tensor fields, dump the trace, determinant, min, and max eigen values.
for f in (tensorFields + symTensorFields):
Expand Down Expand Up @@ -96,9 +97,9 @@ def siloPointmeshDump(baseName,
# If we're domain 0 we write the master file.
writeMasterSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeLists, label, time, cycle, dumpGhosts, fieldwad)

# Each domain writes it's domain file.
# Each domain writes its domain file.
writeDomainSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeLists, label, time, cycle, dumpGhosts, fieldwad)

#-------------------------------------------------------------------------------
# Extract the fields we're going to write. This requires exploding vector and
# tensor fields into their components.
Expand Down Expand Up @@ -178,6 +179,10 @@ def writeMasterSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeList
assert optlist.addOption(silo.DBOPT_MATNOS, silo.DBOPT_NMATNOS, vector_of_int(matnos)) == 0
assert silo.DBPutMultimat(db, "MATERIAL", vector_of_string(material_names), optlist) == 0

# Create directories for any fields that have slashes in their names
for d in getSubDirs(fieldwad):
silo.DBMkDir(db, d)

# Write the variable descriptions for non-scalar variables (vector and tensors).
writeDefvars(db, fieldwad)

Expand All @@ -190,7 +195,7 @@ def writeMasterSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeList
for iproc, p in enumerate(domainNamePatterns):
nvals = mpi.bcast(nlocalvals, root=iproc)
if nvals > 0:
domainVarNames.append(p % name)
domainVarNames.append(p % unslashify(name))
else:
domainVarNames.append("EMPTY")
assert len(domainVarNames) == ndoms
Expand All @@ -202,7 +207,7 @@ def writeMasterSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeList
for iproc, p in enumerate(domainNamePatterns):
nvals = mpi.bcast(nlocalvals, root=iproc)
if nvals > 0:
domainVarNames.append(p % subname)
domainVarNames.append(p % unslashify(subname))
else:
domainVarNames.append("EMPTY")
assert len(domainVarNames) == ndoms
Expand Down Expand Up @@ -285,6 +290,10 @@ def writeDomainSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeList
# Write the variable descriptions for non-scalar variables (vector and tensors).
writeDefvars(db, fieldwad)

# Create directories for any fields that have slashes in their names
for d in getSubDirs(fieldwad):
silo.DBMkDir(db, d)

# Write the field components.
varOpts = silo.DBoptlist(1024)
assert varOpts.addOption(silo.DBOPT_CYCLE, cycle) == 0
Expand All @@ -296,7 +305,7 @@ def writeDomainSiloFile(ndim, baseDirectory, baseName, procDirBaseName, nodeList
ctor = vector_of_double
else:
ctor = vector_of_int
assert silo.DBPutPointvar1(db, subname, "mesh", ctor(vals), varOpts) == 0
assert silo.DBPutPointvar1(db, unslashify(subname), "mesh", ctor(vals), varOpts) == 0

# That's it.
assert silo.DBClose(db) == 0
Expand Down Expand Up @@ -418,9 +427,15 @@ def metaDataScalarField(name, time, cycle, dim):
#-------------------------------------------------------------------------------
def extractVectorField(name, field, vals, dim):
assert len(vals) == dim or len(vals) == 0
assert dim in (2,3)
assert dim in (1,2,3)

if dim == 2:
if dim == 1:
if vals == []:
vals = [["%s_x" % name, vector_of_double()]]
for v in field:
vals[0][1].append(v.x)

elif dim == 2:
if vals == []:
vals = [["%s_x" % name, vector_of_double()],
["%s_y" % name, vector_of_double()]]
Expand All @@ -442,9 +457,11 @@ def extractVectorField(name, field, vals, dim):

def dummyVectorField(name, n, vals, dim):
assert len(vals) == dim or len(vals) == 0
assert dim in (2,3)
assert dim in (1,2,3)
if vals == []:
if dim == 2:
if dim == 1:
vals = [["%s_x" % name, vector_of_double([0.0]*n)]]
elif dim == 2:
vals = [["%s_x" % name, vector_of_double([0.0]*n)],
["%s_y" % name, vector_of_double([0.0]*n)]]
else:
Expand All @@ -457,18 +474,23 @@ def dummyVectorField(name, n, vals, dim):
return vals

def metaDataVectorField(name, time, cycle, dim):
assert dim in (2,3)
assert dim in (1,2,3)
optlistDef = silo.DBoptlist()
optlistMV = silo.DBoptlist()
optlistVar = silo.DBoptlist()
for optlist in (optlistDef, optlistMV, optlistVar):
assert optlist.addOption(silo.DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(silo.DBOPT_DTIME, time) == 0
assert optlistMV.addOption(silo.DBOPT_TENSOR_RANK, silo.DB_VARTYPE_VECTOR) == 0
assert optlistVar.addOption(silo.DBOPT_HIDE_FROM_GUI, 1) == 0
# For 1D, don't hide components
if dim > 1:
assert optlistVar.addOption(silo.DBOPT_HIDE_FROM_GUI, 1) == 0
assert optlistVar.addOption(silo.DBOPT_TENSOR_RANK, silo.DB_VARTYPE_SCALAR) == 0

if dim == 2:
if dim == 1:
return ("{%s_x}" % name, silo.DB_VARTYPE_VECTOR,
optlistDef, optlistMV, optlistVar)
elif dim == 2:
return ("{%s_x, %s_y}" % (name, name), silo.DB_VARTYPE_VECTOR,
optlistDef, optlistMV, optlistVar)
else:
Expand All @@ -480,8 +502,14 @@ def metaDataVectorField(name, time, cycle, dim):
#-------------------------------------------------------------------------------
def extractTensorField(name, field, vals, dim):
assert len(vals) == dim*dim or len(vals) == 0
assert dim in (2,3)
if dim == 2:
assert dim in (1,2,3)
if dim == 1:
if vals == []:
vals = [["%s_xx" % name, vector_of_double()]]
for t in field:
vals[0][1].append(t.xx)

elif dim == 2:
if vals == []:
vals = [["%s_xx" % name, vector_of_double()],
["%s_xy" % name, vector_of_double()],
Expand Down Expand Up @@ -511,9 +539,11 @@ def extractTensorField(name, field, vals, dim):

def dummyTensorField(name, n, vals, dim):
assert len(vals) == dim*dim or len(vals) == 0
assert dim in (2,3)
assert dim in (1,2,3)
if vals == []:
if dim == 2:
if dim == 1:
vals = [["%s_xx" % name, vector_of_double([0.0]*n)]]
elif dim == 2:
vals = [["%s_xx" % name, vector_of_double([0.0]*n)],
["%s_xy" % name, vector_of_double([0.0]*n)],
["%s_yx" % name, vector_of_double([0.0]*n)],
Expand All @@ -534,18 +564,23 @@ def dummyTensorField(name, n, vals, dim):
return vals

def metaDataTensorField(name, time, cycle, dim):
assert dim in (2,3)
assert dim in (1,2,3)
optlistDef = silo.DBoptlist()
optlistMV = silo.DBoptlist()
optlistVar = silo.DBoptlist()
for optlist in (optlistDef, optlistMV, optlistVar):
assert optlist.addOption(silo.DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(silo.DBOPT_DTIME, time) == 0
assert optlistMV.addOption(silo.DBOPT_TENSOR_RANK, silo.DB_VARTYPE_TENSOR) == 0
assert optlistVar.addOption(silo.DBOPT_HIDE_FROM_GUI, 1) == 0
# For 1D, don't hide components
if dim > 1:
assert optlistVar.addOption(silo.DBOPT_HIDE_FROM_GUI, 1) == 0
assert optlistVar.addOption(silo.DBOPT_TENSOR_RANK, silo.DB_VARTYPE_SCALAR) == 0

if dim == 2:
if dim == 1:
return ("{%s_xx}" % name, silo.DB_VARTYPE_TENSOR,
optlistDef, optlistMV, optlistVar)
elif dim == 2:
return ("{{%s_xx, %s_xy}, {%s_yx, %s_yy}}" % (name, name, name, name), silo.DB_VARTYPE_TENSOR,
optlistDef, optlistMV, optlistVar)
else:
Expand All @@ -562,7 +597,7 @@ def writeDefvars(db, fieldwad):
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
if desc != None:
assert optlistDef != None
assert len(subvars) > 1
assert len(subvars) > 0
names.append(name)
defs.append(desc)
types.append(type)
Expand Down