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 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 Inventory(CitcomComponent.Inventory):
import pyre.inventory as inv
output_num_shells = inv.int("output_num_shells", default=0)
output_shell_rids = inv.list("output_shell_rids", default=[])
output_shell_num_buffered_timesteps = inv.int(
"output_shell_num_buffered_timesteps", default=5)
output_shell_every = inv.int("output_shell_every", default=4)
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 Job(Component):
name = "job"
import pyre.inventory as pyre
import pyre.util as util
from pyre.units.time import minute
task = pyre.str("name") # 'task' internally, to avoid name conflict
queue = pyre.str("queue")
mail = pyre.bool("mail", default=False)
dwalltime = pyre.dimensional("walltime", default=0 * minute)
stdin = pyre.str("stdin", default=util.devnull())
stdout = pyre.str("stdout", default="stdout.txt")
stderr = pyre.str("stderr", default="stderr.txt")
environment = pyre.list("environment")
executable = pyre.str("executable")
arguments = pyre.list("arguments")
comments = pyre.list("comments")
def __init__(self):
super(Job, self).__init__()
self.nodes = 1
self.id = None
def getStateArgs(self, stage):
state = []
if stage == 'launch':
state.append("--macros.job.name=%s" % self.task)
elif stage == 'compute':
state.append("--macros.job.id=%s" % self.id)
return state
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 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
class SchedulerSGE(BatchScheduler):
name = "sge"
import pyre.inventory as pyre
command = pyre.str("command", default="qsub")
peName = pyre.str("pe-name", default="mpi")
peNumber = pyre.str("pe-number", default="n")
qsubOptions = pyre.list("qsub-options")
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)
# Generate the main SGE 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, tempfile
filename = tempfile.mktemp()
s = open(filename, 'w')
print >>s, script
s.close()
cmd = [self.command, filename]
self._info.log("spawning: %s" % ' '.join(cmd))
status = os.spawnvp(os.P_WAIT, cmd[0], cmd)
os.remove(filename)
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
class SchedulerLSF(BatchScheduler):
name = "lsf"
import pyre.inventory as pyre
command = pyre.str("command", default="bsub")
bsubOptions = pyre.list("bsub-options")
def schedule(self, job):
import pyre.util as util
# Fix-up the job.
if not job.task:
# LSF scripts must have a job name; otherwise strange
# "/bin/sh: Event not found" errors occur (tested on
# TACC's Lonestar system).
job.task = "jobname"
job.walltime = util.hms(job.dwalltime.value)
job.arguments = ' '.join(job.arguments)
# Generate the main LSF 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:
from popen2 import Popen4
cmd = [self.command]
if self.wait:
cmd.append("-K")
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()
if self.wait:
self._info.log("Waiting for dispatch...")
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
# "[When given the -K option], bsub will exit with the same
# exit code as the job so that job scripts can take
# appropriate actions based on the exit codes. bsub exits with
# value 126 if the job was terminated while pending."
if exitStatus == 0:
pass
elif self.wait:
sys.exit(exitStatus)
else:
sys.exit("%s: %s: %s" % (sys.argv[0], cmd[0], statusStr))
return