class Inventory( AbstractComponent.Inventory ):
import pyre.inventory as pinv
tofmin = pinv.float( 'tofmin', default = 0 )
tofmin.meta['tip'] = 'tof min'
tofmax = pinv.float( 'tofmax', default = 0.01 )
tofmax.meta['tip'] = 'tof max'
ntof = pinv.int( 'ntof', default = 100 )
ntof.meta['tip'] = 'number of tof channels'
xmin = pinv.float( 'xmin', default = -0.1 )
xmin.meta['tip'] = 'x min'
xmax = pinv.float( 'xmax', default = 0.1 )
xmax.meta['tip'] = 'x max'
nx = pinv.int( 'nx', default = 100 )
nx.meta['tip'] = 'number of x bins'
ymin = pinv.float( 'ymin', default = -0.1 )
ymin.meta['tip'] = 'y min'
ymax = pinv.float( 'ymax', default = 0.1 )
ymax.meta['tip'] = 'y max'
ny = pinv.int( 'ny', default = 100 )
ny.meta['tip'] = 'number of y bins'
eventsdat = pinv.str( 'eventsdat', default = 'events.dat' )
eventsdat.meta['tip'] = 'output event data file'
pass
class Launcher(Component):
import pyre.inventory as pyre
dry = pyre.bool("dry")
nodes = pyre.int("nodes", default=1); nodes.meta['tip'] = """number of machine nodes"""
nodelist = pyre.slice("nodelist");
executable = pyre.str("executable")
arguments = pyre.list("arguments")
nodelist.meta['tip'] = """a comma-separated list of machine names in square brackets (e.g., [101-103,105,107])"""
def launch(self):
raise NotImplementedError("class '%s' must override 'launch'" % self.__class__.__name__)
def argv(self):
raise NotImplementedError("class '%s' must override 'argv'" % self.__class__.__name__)
def comments(self):
return ["command: " + ' '.join(self.argv())]
class UtilTest(Script):
componentName = "UtilTest"
import pyre.inventory as pyre
answer = pyre.int("answer", default=42)
def main(self, *args, **kwds):
print "the answer is", self.answer
configuration = self.retrieveConfiguration()
print
print "the configuration is:"
print "\n".join([str(item) for item in configuration.render()])
print
utilPml = "util.pml"
print "dumping configuration to", utilPml
pml = open(utilPml, "w")
print >> pml, "\n".join(self.weaver.render(configuration))
pml.close()
dct = dictFromReg(configuration)
print
print "converted configuration to dict:", dct
print
print "converted dict back to registry:"
reg = regFromDict(dct, name=self.name, cls=OdbInventory)
print "\n".join([str(item) for item in reg.render()])
print
utilPml = "util2.pml"
print "dumping converted registry to", utilPml
pml = open(utilPml, "w")
print >> pml, "\n".join(self.weaver.render(reg))
pml.close()
class Inventory(Script.Inventory):
import pyre.inventory as inv
s = inv.str('s', default="abc")
i = inv.int('i', default=10)
f = inv.float('f', default=3.0)
func = inv.facility("func", factory=Sin)
pass
class Inventory(MultiMonitors.Inventory):
from mcni.pyre_support import facility
m1 = facility('m1', default="monitors/NDMonitor(t)")
m2 = facility('m2', default="monitors/NDMonitor(w)")
m3 = facility('m3', default="monitors/NDMonitor(t)")
m4 = facility('m4', default="monitors/NDMonitor(w)")
m5 = facility('m5', default="monitors/NDMonitor(t)")
m6 = facility('m6', default="monitors/NDMonitor(w)")
import pyre.inventory as inv
xwidth = inv.float(name='xwidth', default=0.77)
yheight = inv.float(name='yheight', default=0.385)
tmin = inv.float(name='tmin', default=0.)
tmax = inv.float(name='tmax', default=0.1)
nt = inv.int(name='nt', default=100)
wmin = inv.float(name='wmin', default=0.)
wmax = inv.float(name='wmax', default=10)
nw = inv.int(name='nw', default=100)
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as inv
tracer = inv.bool("tracer", default=False)
# tracer_ic_method=0 (random generated array)
# tracer_ic_method=1 (all proc read the same file)
# tracer_ic_method=2 (each proc reads its own file)
tracer_ic_method = inv.int("tracer_ic_method", default=0)
# (tracer_ic_method == 0)
tracers_per_element = inv.int("tracers_per_element", default=10)
# (tracer_ic_method == 1)
tracer_file = inv.str("tracer_file", default="tracer.dat")
# How many flavors of tracers
# If tracer_flavors > 0, each element will report the number of
# tracers of each flavor inside it. This information can be used
# later for many purposes. One of it is to compute composition,
# either using absolute method or ratio method.
tracer_flavors = inv.int("tracer_flavors", default=0)
# How to initialize tracer flavors
ic_method_for_flavors = inv.int("ic_method_for_flavors", default=0)
z_interface = inv.list("z_interface", default=[0.7])
ictracer_grd_file = inv.str("ictracer_grd_file", default="")
ictracer_grd_layers = inv.int("ictracer_grd_layers", default=2)
# Warning level
itracer_warnings = inv.bool("itracer_warnings", default=True)
# Enriched internal heat production
tracer_enriched = inv.bool("tracer_enriched", default=False)
Q0_enriched = inv.float("Q0_enriched", default=0.0)
# Regular grid parameters
regular_grid_deltheta = inv.float("regular_grid_deltheta", default=1.0)
regular_grid_delphi = inv.float("regular_grid_delphi", default=1.0)
# Analytical Test Function
#analytical_tracer_test = inv.int("analytical_tracer_test", default=0)
chemical_buoyancy = inv.bool("chemical_buoyancy", default=True)
# ibuoy_type=0 (absolute method, not implemented)
# ibuoy_type=1 (ratio method)
buoy_type = inv.int("buoy_type", default=1)
buoyancy_ratio = inv.list("buoyancy_ratio", default=[1.0])
# DJB
hybrid_method = inv.int("hybrid_method", default=0)
# This is not used anymore and is left here for backward compatibility
reset_initial_composition = inv.bool("reset_initial_composition",
default=False)
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as prop
ADV = prop.bool("ADV", default=True)
filter_temp = prop.bool("filter_temp", default=False)
monitor_max_T = prop.bool("monitor_max_T", default=True)
fixed_timestep = prop.float("fixed_timestep", default=0.0)
finetunedt = prop.float("finetunedt", default=0.9)
adv_gamma = prop.float("adv_gamma", default=0.5)
adv_sub_iterations = prop.int("adv_sub_iterations", default=2)
inputdiffusivity = prop.float("inputdiffusivity", default=1)
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as prop
Solver = prop.str("Solver", default="cgrad",
validator=prop.choice(["cgrad",
"multigrid"]))
node_assemble = prop.bool("node_assemble", default=True)
precond = prop.bool("precond", default=True)
accuracy = prop.float("accuracy", default=1.0e-4)
inner_accuracy_scale = prop.float("inner_accuracy_scale", default=1.0)
check_continuity_convergence = prop.bool("check_continuity_convergence", default=True)
check_pressure_convergence = prop.bool("check_pressure_convergence", default=True)
mg_cycle = prop.int("mg_cycle", default=1)
down_heavy = prop.int("down_heavy", default=3)
up_heavy = prop.int("up_heavy", default=3)
vlowstep = prop.int("vlowstep", default=1000)
vhighstep = prop.int("vhighstep", default=3)
max_mg_cycles = prop.int("max_mg_cycles", default=50)
piterations = prop.int("piterations", default=1000)
aug_lagr = prop.bool("aug_lagr", default=True)
aug_number = prop.float("aug_number", default=2.0e3)
uzawa = prop.str("uzawa", default="cg",
validator=prop.choice(["cg", "bicg"]))
compress_iter_maxstep = prop.int("compress_iter_maxstep", default=100)
inner_remove_rigid_rotation = prop.bool("inner_remove_rigid_rotation", default=False)
remove_rigid_rotation = prop.bool("remove_rigid_rotation", default=True)
remove_angular_momentum = prop.bool("remove_angular_momentum", default=True)
only_check_vel_convergence = prop.bool("only_check_vel_convergence", default=False)
# Not used. Retained here for backward compatibility.
tole_compressibility = prop.float("tole_compressibility", default=1.0e-7)
relative_err_accuracy = prop.float("relative_err_accuracy", default=0.001)
class SchedulerTACCRanger(SchedulerSGE):
name = "tacc-ranger"
import pyre.inventory as pyre
command = pyre.str("command", default="qsub")
tpn = pyre.int("tpn",
default=16,
validator=pyre.choice([1, 2, 4, 8, 12, 15, 16]))
tpn.meta['tip'] = 'Task per node'
qsubOptions = pyre.list("qsub-options")
def schedule(self, job):
from math import ceil
# round up to multiple of 16
nodes = ceil(job.nodes / float(self.tpn))
self.cores = int(nodes * 16)
SchedulerSGE.schedule(self, job)
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as inv
output_format = inv.str("output_format", default="ascii",
validator=inv.choice(["ascii",
"ascii-gz",
"vtk",
"hdf5"]))
output_optional = inv.str("output_optional",
default="surf,botm,tracer")
# experimental vtk output
gzdir_vtkio = inv.int("gzdir_vtkio", default=0)
# remove net rotation
gzdir_rnr = inv.bool("gzdir_rnr", default=False)
# write additional heat flux files? if yes, how frequent?
write_q_files = inv.int("write_q_files", default=0)
# max. degree for spherical harmonics output
output_ll_max = inv.int("output_ll_max", default=20)
# self-gravitation, for geoid only
self_gravitation = inv.bool("self_gravitation", default=False)
# compute stress/topography by consistent-boundary-flux method
use_cbf_topo = inv.bool("use_cbf_topo", default=False)
mega1 = 1024*1024
#megaq = 256*1024
# size of collective buffer used by MPI-IO
cb_block_size = inv.int("cb_block_size", default=mega1)
cb_buffer_size = inv.int("cb_buffer_size", default=mega1*4)
# size of data sieve buffer used by HDF5
sieve_buf_size = inv.int("sieve_buf_size", default=mega1)
# memory alignment used by HDF5
output_alignment = inv.int("output_alignment", default=mega1/4)
output_alignment_threshold = inv.int("output_alignment_threshold",
default=mega1/2)
# cache for chunked dataset used by HDF5
cache_mdc_nelmts = inv.int("cache_mdc_nelmts", default=10330)
cache_rdcc_nelmts = inv.int("cache_rdcc_nelmts", default=521)
cache_rdcc_nbytes = inv.int("cache_rdcc_nbytes", default=mega1)
class SchedulerPBS(BatchScheduler):
name = "pbs"
import pyre.inventory as pyre
command = pyre.str("command", default="qsub")
qsubOptions = pyre.list("qsub-options")
resourceList = pyre.list("resource-list")
ppn = pyre.int("ppn", default=1)
def schedule(self, job):
import pyre.util as util
# Fix-up the job.
if not job.task:
job.task = "jobname"
job.walltime = util.hms(job.dwalltime.value)
job.arguments = ' '.join(job.arguments)
job.resourceList = self.buildResourceList(job)
# Generate the main PBS batch script.
script = self.retrieveTemplate('batch.sh', ['schedulers', 'scripts', self.name])
if script is None:
self._error.log("could not locate batch script template for '%s'" % self.name)
sys.exit(1)
script.scheduler = self
script.job = job
if self.dry:
print script
return
try:
import os
from popen2 import Popen4
cmd = [self.command]
self._info.log("spawning: %s" % ' '.join(cmd))
child = Popen4(cmd)
self._info.log("spawned process %d" % child.pid)
print >> child.tochild, script
child.tochild.close()
for line in child.fromchild:
self._info.line(" " + line.rstrip())
status = child.wait()
self._info.log()
exitStatus = None
if (os.WIFSIGNALED(status)):
statusStr = "signal %d" % os.WTERMSIG(status)
elif (os.WIFEXITED(status)):
exitStatus = os.WEXITSTATUS(status)
statusStr = "exit %d" % exitStatus
else:
statusStr = "status %d" % status
self._info.log("%s: %s" % (cmd[0], statusStr))
except IOError, e:
self._error.log("%s: %s" % (self.command, e))
return
if exitStatus == 0:
pass
else:
sys.exit("%s: %s: %s" % (sys.argv[0], cmd[0], statusStr))
return