def test9(self):
p = POP(**default_options)
shf = p.elements.shf
print "SHF:"
print shf
shf_values = shf.value_in(units.W / units.m**2).flatten()
print shf_values
self.assertTrue(
any(s != 0.0 for s in shf_values),
msg="Expect at least one value to be not equal to zero")
p.stop()
def test6(self):
p = POP(**default_options)
#check if we can write and again read what was written
bogus3d = numpy.random.random(p.nodes3d.shape) | units.cm / units.s
p.nodes3d.xvel = bogus3d
xvel3d = p.nodes3d.xvel
self.assertEquals(xvel3d, bogus3d)
#check if we can write and again read what was written
bogus3d = numpy.random.random(p.nodes3d.shape) | units.cm / units.s
p.nodes3d.yvel = bogus3d
yvel3d = p.nodes3d.yvel
self.assertEquals(yvel3d, bogus3d)
p.stop()
def test7(self):
p = POP(**default_options)
#test whether the getters for depth are working as expected
dzt = p.elements3d.z
dzu = p.nodes3d.z
km = p.get_number_of_vertical_levels()
for i in range(0, km - 1):
self.assertTrue(
dzu[5, 5, i] <= dzt[5, 5, i],
msg='expect dzu to be equal to or smaller than dzt')
self.assertTrue(dzt[5, 5, i] > (0.0 | units.cm),
msg='expect dzt to be larger than 0.0')
p.stop()
def test10(self):
p = POP(**default_options)
self.assertTrue(
p.parameters.windstress_monthly_file == '',
msg=
"Default value for windstress_monthly_file should be empty string")
self.assertTrue(
p.parameters.surface_heat_flux_monthly_file == '',
msg=
"Default value for surface_heat_flux_monthly_file should be empty string"
)
self.assertTrue(
p.parameters.surface_freshwater_flux_monthly_file == '',
msg=
"Default value for surface_freshwater_flux_monthly_file should be empty string"
)
self.assertTrue(p.parameters.windstress_forcing == 'none',
msg="Default for windstress forcing should be none")
self.assertTrue(
p.parameters.surface_heat_flux_forcing == 'none',
msg="Default for surface heat flux forcing should be none")
self.assertTrue(
p.parameters.surface_freshwater_flux_forcing == 'none',
msg="Default for surface freshwater flux forcing should be none")
bogus_file = '/path/to/non-existent/file'
p.set_monthly_ws_file(bogus_file)
p.set_monthly_shf_file(bogus_file)
p.set_monthly_sfwf_file(bogus_file)
self.assertTrue(
p.parameters.windstress_monthly_file == bogus_file,
msg="Error retrieving set value for windstress_monthly_file")
self.assertTrue(
p.parameters.surface_heat_flux_monthly_file == bogus_file,
msg="Error retrieving set value for surface_heat_flux_monthly_file"
)
self.assertTrue(
p.parameters.surface_freshwater_flux_monthly_file == bogus_file,
msg=
"Error retrieving set value for surface_freshwater_flux_monthly_file"
)
self.assertTrue(p.parameters.windstress_forcing == 'monthly',
msg="Setting for windstress forcing should be monthly")
self.assertTrue(
p.parameters.surface_heat_flux_forcing == 'monthly',
msg="Setting for surface heat flux forcing should be monthly")
self.assertTrue(
p.parameters.surface_freshwater_flux_forcing == 'monthly',
msg="Setting for surface freshwater flux forcing should be monthly"
)
def test5(self):
p = POP(**default_options)
temp3d = p.elements3d.temp.value_in(units.C)
self.assertTrue(
temp3d.all() < 50.,
msg='Less than 50 degrees seems reasonable for temperature')
self.assertTrue(
temp3d.all() > -10.,
msg='More than -10 degrees seems reasonable for temperature')
salt3d = p.elements3d.salt.value_in(units.g / units.kg)
self.assertTrue(
salt3d.all() < 1.,
msg=
'Less than one gram of salt per kg of water seems reasonable for salinity'
)
self.assertTrue(salt3d.all() >= 0.,
msg='Salinity should be positive or 0')
#check if we can write and again read what was written
bogus3d = numpy.random.random(p.elements3d.shape) | units.C
p.elements3d.temp = bogus3d
temp3d = p.elements3d.temp
self.assertEquals(temp3d, bogus3d)
#check if we can write and again read what was written
bogus3d = numpy.random.random(p.elements3d.shape) | units.g / units.kg
p.elements3d.salt = bogus3d
salt3d = p.elements3d.salt
self.assertEquals(salt3d, bogus3d)
#check if we can write and again read what was written
bogus3d = numpy.random.random(
p.elements3d.shape) | units.g / units.cm**3
p.elements3d.rho = bogus3d
rho3d = p.elements3d.rho
self.assertEquals(rho3d, bogus3d)
p.stop()
def test8(self):
p = POP(**default_options)
#run for some time to ensure UVEL and VVEL contain something
time = p.get_model_time()
tend = time + (1.0 | units.day)
p.evolve_model(tend)
#test whether the getter for vertical velocity is working correctly
xvel = p.nodes3d.xvel
yvel = p.nodes3d.yvel
zvel = p.nodes3d.zvel
km = p.get_number_of_vertical_levels()
size = p.get_domain_size()
depth = p.nodes.depth.value_in(units.cm)
#look for a non-land ocean cell with some depth
for i in range(0, size[0] - 1):
for j in range(0, size[1] - 1):
if (depth[i, j] > 1000.0):
break
print "Printing info for gridpoint " + str(i) + "," + str(
j) + " with depth " + str(depth[i, j])
# i=1
# j=127
print "XVEL:"
print xvel[i, j, 0:km - 1]
print "YVEL:"
print yvel[i, j, 0:km - 1]
print "ZVEL:"
print zvel[i, j, 0:km - 1]
self.assertTrue(
any(zv != (0.0 | units.cm / units.s)
for zv in zvel[i, j, 0:km - 1]),
msg="Expect at least one value to be not equal to zero")
p.stop()
def test1(self):
instance = POP(**default_options)
self.assertEquals(instance.state_machine._current_state.name,
'UNINITIALIZED')
#a read of a parameter requires the state to be either EDIT or RUN, which means we pass through INITIALIZED
fcor = instance.forcings.coriolis_f
#check if we are in the expected state
self.assertEquals(instance.state_machine._current_state.name, 'RUN')
#check if we read a sensible value
print 'fcor[1,1] = ', fcor[1, 1]
self.assertTrue(
fcor[1, 1] != 0 | units.s**-1,
msg='Expected coriolis force to be not equal to zero for node 1,1')
#proceed to evolve
time = instance.get_model_time()
tend = time + instance.get_timestep_next()
instance.evolve_model(tend)
#check if we are in the expected state
self.assertEquals(instance.state_machine._current_state.name,
'EVOLVED')
#try to read something again, should cause a state transition to RUN
fcor = instance.forcings.coriolis_f
#check if we are in the expected state
self.assertEquals(instance.state_machine._current_state.name, 'RUN')
#check if we can write to coriolis_f
instance.forcings.coriolis_f = fcor
#check if we are in the expected state
self.assertEquals(instance.state_machine._current_state.name, 'EDIT')
instance.stop()
pilot = Pilot()
pilot.resource_name="Cartesius"
pilot.queue_name="short"
pilot.node_count=1
pilot.time= 1|units.hour
pilot.slots_per_node=24
pilot.label="CartesiusNode"
instance.pilots.add_pilot(pilot)
instance.use_for_all_workers()
from omuse.community.pop.interface import POP
p=POP(channel_type="distributed", redirection="none", number_of_workers=24)
p.change_directory('/home/ben/amuse/amuse-svn/src/omuse/community/pop/')
p.set_horiz_grid_file('data/input/grid/horiz_grid_20010402.ieeer8')
p.set_vert_grid_file('data/input/grid/in_depths.dat')
p.set_topography_file('data/input/grid/topography_20010702.ieeei4')
p.set_ts_file('data/input/restart/r.x1_SAMOC_control.00750101')
p.set_monthly_shf_file('data/input/shf_monthly/shf.normal_year+flux.mon')
p.set_monthly_sfwf_file('data/input/sfwf/sfwf_phc0-50_ncarp_r46+g8_0.5Sv_flux.mon')
p.set_monthly_ws_file('data/input/ws_monthly/ws.1958-2000.mon')
#raw_input()
z=numpy.arange(N)/(1.*(N-1))
if stretch_factor==0:
return z
else:
return 1 - numpy.tanh(stretch_factor*(1-z))/numpy.tanh(stretch_factor)
if __name__=="__main__":
#prepare the plot stuff
pyplot.ion()
pyplot.show()
#size of the modeling domain, for the benchmark it is equal in all directions
dim = 16
p=POP(number_of_workers=2, channel_type="sockets", mode='test')
cwd=os.getcwd()
depth=depth_levels(dim+1, 0.0)
dz=depth[1:]-depth[:-1]
p.parameters.topography_option='internal'
p.parameters.horiz_grid_option='amuse'
p.parameters.vert_grid_option='amuse'
p.parameters.vertical_layer_thicknesses=dz * (5000 | units.m)
#p.parameters.surface_heat_flux_forcing = 'amuse'
#p.parameters.surface_freshwater_flux_forcing = 'amuse'
p.parameters.windstress_forcing = 'analytic'
# wind forcing
instance.resources.add_resource(resource)
pilot = Pilot()
pilot.resource_name = "Cartesius"
pilot.queue_name = "short"
pilot.node_count = 50
pilot.time = 1 | units.hour
pilot.slots_per_node = 12
pilot.label = "CartesiusNode"
instance.pilots.add_pilot(pilot)
instance.use_for_all_workers()
from omuse.community.pop.interface import POP
p = POP(channel_type="distributed", redirection="none", number_of_workers=600)
p.change_directory('/home/ben/amuse/amuse-svn/src/omuse/community/pop/')
p.set_namelist_filename('pop_in_highres')
p.set_horiz_grid_file('/home/ben/pop/input/grid/grid.3600x2400.fob.da')
p.set_vert_grid_file('/home/ben/pop/input/grid/in_depths.42.dat')
p.set_topography_file(
'/home/ben/pop/input/grid/kmt_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black'
)
p.set_bottom_cell_file(
'/home/ben/pop/input/grid/dzbc_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black'
)
p.set_ts_file('/home/ben/pop/input/r.t0.1_42l_greenland.01150501')
p.set_monthly_shf_file('/home/ben/pop/input/forcing/shf.NY+H+f.mon')
p.set_monthly_sfwf_file('/home/ben/pop/input/forcing/sfwf.C+r+g8+f.mon')
x, y = m(lons, lats)
xs, ys = m(xs, ys)
m.drawmapboundary(fill_color='#99ffff')
m.fillcontinents(color='#cc9966', lake_color='#99ffff')
im1 = m.pcolormesh(xs, ys, sst_, cmap=pyplot.cm.jet, latlon=False)
pyplot.ylim(ys.min(), ys.max())
pyplot.show()
pyplot.draw()
from omuse.community.pop.interface import POP
from amuse.units import units
p = POP(channel_type="sockets", redirection="none", number_of_workers=8)
#p=POP(redirection="none",number_of_workers=8)
p.set_horiz_grid_file('data/input/grid/horiz_grid_20010402.ieeer8')
p.set_vert_grid_file('data/input/grid/in_depths.dat')
p.set_topography_file('data/input/grid/topography_20010702.ieeei4')
p.set_ts_file('data/input/restart/r.x1_SAMOC_control.00750101')
p.set_shf_monthly_file('data/input/shf_monthly/shf.normal_year+flux.mon')
p.set_sfwf_monthly_file('data/input/sfwf/sfwf_phc0-50_ncarp_r46_flux.mon')
p.set_ws_monthly_file('data/input/ws_monthly/ws.1958-2000.mon')
#prepare the plot stuff
pyplot.ion()
lats, lons = get_lats_lons(p)
xs, ys = get_xy()
instance.resources.add_resource(resource)
pilot = Pilot()
pilot.resource_name="DAS-5"
pilot.queue_name="defq"
pilot.node_count=56
pilot.time= 24|units.hour
pilot.slots_per_node=16
pilot.label="DAS-5-Pilot"
instance.pilots.add_pilot(pilot)
instance.use_for_all_workers()
from omuse.community.pop.interface import POP
p=POP(channel_type="distributed", redirection="none", mode='3600x2400x42', number_of_workers=896, max_message_length=1000000)
#set grid info
p.set_horiz_grid_file('/var/scratch/bwn200/pop/input/grid/grid.3600x2400.fob.da')
p.set_vert_grid_file('/var/scratch/bwn200/pop/input/grid/in_depths.42.dat')
p.set_topography_file('/var/scratch/bwn200/pop/input/grid/kmt_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black')
p.set_bottom_cell_file('/var/scratch/bwn200/pop/input/grid/dzbc_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black')
p.set_ts_file('/var/scratch/bwn200/pop/input/r.t0.1_42l_greenland.01150501')
#setup forcing files
p.set_shf_monthly_file('/var/scratch/bwn200/pop/input/forcing/shf.NY+H+f.mon')
p.set_sfwf_monthly_file('/var/scratch/bwn200/pop/input/forcing/sfwf.C+r+g8+f.mon')
p.set_ws_monthly_file('/var/scratch/bwn200/pop/input/forcing/ws.o_n_avg.mon')
#setup output files
#p.set_tavg_option('nday')
def test2(self):
instance = POP(**default_options)
#proceed to evolve
#time = instance.get_model_time()
#tend = time + (1 | units.day)
#instance.evolve_model(tend)
#extract the tau_x and tau_y from POP
tau_x = instance.forcings.tau_x
tau_y = instance.forcings.tau_y
print 'tau_x='
print tau_x[range(1, 5), 1]
# print tau_x
print 'tau_y='
print tau_y[range(1, 5), 1]
# print tau_y
#check if tau_x and tau_y are not only zeroes, this also fails for things like NaN and Inf
self.assertTrue(numpy.sum(numpy.abs(tau_x)) > (0.0 | units.Pa),
msg='Expected tau_x to contain some actual values')
self.assertTrue(numpy.sum(numpy.abs(tau_y)) > (0.0 | units.Pa),
msg='Expected tau_x to contain some actual values')
#check to see if we can set and retrieve the same wind stress
size = instance.get_domain_size()
tau_x = numpy.random.random(size) | units.Pa
tau_y = numpy.random.random(size) | units.Pa
#cannot write to forcings directly unfortunately
#instance.forcings.tau_x = tau_x
#instance.forcings.tau_y = tau_y
forcings = instance.forcings.empty_copy()
forcings.tau_x = tau_x
forcings.tau_y = tau_y
forcings.new_channel_to(instance.forcings).copy_attributes(
["tau_x", "tau_y"])
self.assertEquals(instance.state_machine._current_state.name,
'EDIT_FORCINGS')
#now retrieve the wind stress from the model
tau_x_returned = instance.forcings.tau_x
tau_y_returned = instance.forcings.tau_y
self.assertEquals(instance.state_machine._current_state.name, 'RUN')
#almost equals
self.assertAlmostRelativeEqual(tau_x, tau_x_returned, places=10)
self.assertAlmostRelativeEqual(tau_y, tau_y_returned, places=10)
#check to see if the forcings we have set are not overwritten by internal routines,
#evolve the model
time = instance.get_model_time()
tend = time + instance.get_timestep_next()
instance.evolve_model(tend)
#check if wind stress is still the same
tau_x_returned = instance.forcings.tau_x
tau_y_returned = instance.forcings.tau_y
self.assertAlmostRelativeEqual(tau_x, tau_x_returned, places=10)
self.assertAlmostRelativeEqual(tau_y, tau_y_returned, places=10)
instance.stop()
def test3(self):
p = POP(**default_options)
mystr = ''
mynum = 0
bogus_file = '/fake/path/to/file'
mystr = p.get_ts_option()
self.assertEquals(mystr, 'internal')
p.set_ts_option('restart')
mystr = p.get_ts_option()
self.assertEquals(mystr, 'restart')
mystr = p.get_ts_file()
self.assertEquals(mystr, '')
p.set_ts_file(bogus_file)
mystr = p.get_ts_file()
self.assertEquals(mystr, bogus_file)
mystr = p.get_ts_file_format()
self.assertEquals(mystr, 'bin')
p.set_ts_file_format('nc')
mystr = p.get_ts_file_format()
self.assertEquals(mystr, 'nc')
mystr = p.get_distribution()
self.assertEquals(mystr, 'cartesian')
p.set_distribution('predefined')
mystr = p.get_distribution()
self.assertEquals(mystr, 'predefined')
mystr = p.get_distribution_file()
self.assertEquals(mystr, '')
p.set_distribution_file(bogus_file)
mystr = p.get_distribution_file()
self.assertEquals(mystr, bogus_file)
mystr = p.get_ew_boundary_type()
self.assertEquals(mystr, 'cyclic')
p.set_ew_boundary_type('closed')
mystr = p.get_ew_boundary_type()
self.assertEquals(mystr, 'closed')
mystr = p.get_ns_boundary_type()
self.assertEquals(mystr, 'closed')
p.set_ns_boundary_type('tripole')
mystr = p.get_ns_boundary_type()
self.assertEquals(mystr, 'tripole')
mystr = p.get_restart_option()
self.assertEquals(mystr, 'never')
p.set_restart_option('nday')
mystr = p.get_restart_option()
self.assertEquals(mystr, 'nday')
mynum = p.get_restart_freq_option()
self.assertEquals(mynum, 1)
p.set_restart_freq_option(5)
mynum = p.get_restart_freq_option()
self.assertEquals(mynum, 5)
mystr = p.get_restart_file()
self.assertEquals(mystr, '')
p.set_restart_file(bogus_file)
mystr = p.get_restart_file()
self.assertEquals(mystr, bogus_file)
mystr = p.get_tavg_option()
self.assertEquals(mystr, 'never')
p.set_tavg_option('nday')
mystr = p.get_tavg_option()
self.assertEquals(mystr, 'nday')
mynum = p.get_tavg_freq_option()
self.assertEquals(mynum, 1)
p.set_tavg_freq_option(5)
mynum = p.get_tavg_freq_option()
self.assertEquals(mynum, 5)
mystr = p.get_tavg_file()
self.assertEquals(mystr, '')
p.set_tavg_file(bogus_file)
mystr = p.get_tavg_file()
self.assertEquals(mystr, bogus_file)
mystr = p.get_movie_option()
self.assertEquals(mystr, 'never')
p.set_movie_option('nday')
mystr = p.get_movie_option()
self.assertEquals(mystr, 'nday')
mynum = p.get_movie_freq_option()
self.assertEquals(mynum, 1)
p.set_movie_freq_option(5)
mynum = p.get_movie_freq_option()
self.assertEquals(mynum, 5)
mystr = p.get_movie_file()
self.assertEquals(mystr, '')
p.set_movie_file(bogus_file)
mystr = p.get_movie_file()
self.assertEquals(mystr, bogus_file)
mystr = p.get_runid()
self.assertEquals(mystr, 'AMUSE')
p.set_runid('MYRUNID')
mystr = p.get_runid()
self.assertEquals(mystr, 'MYRUNID')
mystr = p.get_dt_option()
self.assertEquals(mystr, 'steps_per_day')
p.set_dt_option('seconds')
mystr = p.get_dt_option()
self.assertEquals(mystr, 'seconds')
p.set_dt_option('steps_per_year')
mystr = p.get_dt_option()
self.assertEquals(mystr, 'steps_per_year')
mynum = p.get_dt_count()
self.assertEquals(mynum, 45)
p.set_dt_count(5)
mynum = p.get_dt_count()
self.assertEquals(mynum, 5)
def test4(self):
p = POP(**default_options)
mystr = ''
mynum = 0
bogus_file = '/fake/path/to/file'
mystr = p.parameters.ts_option
self.assertEquals(mystr, 'internal')
p.parameters.ts_option = 'restart'
mystr = p.parameters.ts_option
self.assertEquals(mystr, 'restart')
mystr = p.parameters.ts_file
self.assertEquals(mystr, '')
p.parameters.ts_file = bogus_file
mystr = p.parameters.ts_file
self.assertEquals(mystr, bogus_file)
mystr = p.parameters.ts_file_format
self.assertEquals(mystr, 'bin')
p.parameters.ts_file_format = 'nc'
mystr = p.parameters.ts_file_format
self.assertEquals(mystr, 'nc')
mystr = p.parameters.distribution
self.assertEquals(mystr, 'cartesian')
p.parameters.distribution = 'predefined'
mystr = p.parameters.distribution
self.assertEquals(mystr, 'predefined')
mystr = p.parameters.distribution_file
self.assertEquals(mystr, '')
p.parameters.distribution_file = bogus_file
mystr = p.parameters.distribution_file
self.assertEquals(mystr, bogus_file)
mystr = p.parameters.ew_boundary_type
self.assertEquals(mystr, 'cyclic')
p.parameters.ew_boundary_type = 'closed'
mystr = p.parameters.ew_boundary_type
self.assertEquals(mystr, 'closed')
mystr = p.parameters.ns_boundary_type
self.assertEquals(mystr, 'closed')
p.parameters.ns_boundary_type = 'tripole'
mystr = p.parameters.ns_boundary_type
self.assertEquals(mystr, 'tripole')
mystr = p.parameters.restart_option
self.assertEquals(mystr, 'never')
p.parameters.restart_option = 'nday'
mystr = p.parameters.restart_option
self.assertEquals(mystr, 'nday')
mynum = p.parameters.restart_freq_option
self.assertEquals(mynum, 1)
p.parameters.restart_freq_option = 5
mynum = p.parameters.restart_freq_option
self.assertEquals(mynum, 5)
mystr = p.parameters.restart_file
self.assertEquals(mystr, '')
p.parameters.restart_file = bogus_file
mystr = p.parameters.restart_file
self.assertEquals(mystr, bogus_file)
mystr = p.parameters.tavg_option
self.assertEquals(mystr, 'never')
p.parameters.tavg_option = 'nday'
mystr = p.parameters.tavg_option
self.assertEquals(mystr, 'nday')
mynum = p.parameters.tavg_freq_option
self.assertEquals(mynum, 1)
p.parameters.tavg_freq_option = 5
mynum = p.parameters.tavg_freq_option
self.assertEquals(mynum, 5)
mystr = p.parameters.tavg_file
self.assertEquals(mystr, '')
p.parameters.tavg_file = bogus_file
mystr = p.parameters.tavg_file
self.assertEquals(mystr, bogus_file)
mystr = p.parameters.movie_option
self.assertEquals(mystr, 'never')
p.parameters.movie_option = 'nday'
mystr = p.parameters.movie_option
self.assertEquals(mystr, 'nday')
mynum = p.parameters.movie_freq_option
self.assertEquals(mynum, 1)
p.parameters.movie_freq_option = 5
mynum = p.parameters.movie_freq_option
self.assertEquals(mynum, 5)
mystr = p.parameters.movie_file
self.assertEquals(mystr, '')
p.parameters.movie_file = bogus_file
mystr = p.parameters.movie_file
self.assertEquals(mystr, bogus_file)
mystr = p.parameters.runid
self.assertEquals(mystr, 'AMUSE')
p.parameters.runid = 'MYRUNID'
mystr = p.parameters.runid
self.assertEquals(mystr, 'MYRUNID')
mystr = p.parameters.dt_option
self.assertEquals(mystr, 'steps_per_day')
p.parameters.dt_option = 'seconds'
mystr = p.parameters.dt_option
self.assertEquals(mystr, 'seconds')
p.parameters.dt_option = 'steps_per_year'
mystr = p.parameters.dt_option
self.assertEquals(mystr, 'steps_per_year')
mynum = p.parameters.dt_count
self.assertEquals(mynum, 45)
p.parameters.dt_count = 5
mynum = p.parameters.dt_count
self.assertEquals(mynum, 5)
def initialize_pop(self):
p=POP(redirection="file", number_of_workers=8,redirect_stdout_file="pop.out")
cwd=os.getcwd()
p.change_directory(cwd)
popdatadir="/home/inti/code/amuse/trunk/sandbox/pelupes/pop/"
#set the grid we want to use
p.set_horiz_grid_file(popdatadir+'data/input/grid/horiz_grid_20010402.ieeer8')
p.set_vert_grid_file(popdatadir+'data/input/grid/in_depths.dat')
p.set_topography_file(popdatadir+'data/input/grid/topography_20010702.ieeei4')
#set the restart file
p.set_ts_file(popdatadir+'data/input/restart/r.x1_SAMOC_control.00750101')
#setup the forcing
p.set_shf_monthly_file(popdatadir+'data/input/shf_monthly/shf.normal_year+flux.mon')
p.set_sfwf_monthly_file(popdatadir+'data/input/sfwf/sfwf_phc0-50_ncarp_r46_flux.mon')
p.set_ws_monthly_file(popdatadir+'data/input/ws_monthly/ws.1958-2000.mon')
self.pop_grid=p.get_grid()
self.pop_forcings_grid=StaggeredGrid(p.elements, p.forcings, p._compute_cell_corners)
self.pop=p
self.timestep=self.timestep or self.pop.timestep/2
def init_pop_highres():
#machine settings
popdatadir = '/var/scratch/bwn200/pop/input/'
username = '******'
# distribution files have been provided for the following settings:
# 16 cores: [19, 23, 28, 37, 56] nodes
# 24 cores: [15, 19, 25, 37] nodes
# if you want a different number of cores and/or nodes generate
# a distribution file yourself using: github.com/nlesc/esalsa-tools
num_nodes = 37
num_cores = 16
num_workers = num_nodes * num_cores
distributed_amuse = init_das5_only(username, num_nodes, num_cores)
distributed_amuse.use_for_all_workers()
p = POP(channel_type="distributed",
redirection="none",
mode='3600x2400x42',
number_of_workers=num_workers,
max_message_length=1000000)
p.change_directory(os.getcwd())
#setup distribution file
p.parameters.distribution_file = 'distribution_files/dist-60x60-' + str(
num_nodes) + '-' + str(num_cores)
#set grid info
p.set_horiz_grid_file(popdatadir + 'grid/grid.3600x2400.fob.da')
p.set_vert_grid_file(popdatadir + 'grid/in_depths.42.dat')
p.set_topography_file(
popdatadir +
'grid/kmt_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black')
p.set_bottom_cell_file(
popdatadir +
'grid/dzbc_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black')
p.set_ts_file(popdatadir + 'r.t0.1_42l_greenland.01150501')
#setup forcing files
p.set_shf_monthly_file(popdatadir + 'forcing/shf.NY+H+f.mon')
p.set_sfwf_monthly_file(popdatadir + 'forcing/sfwf.C+r+g8+f.mon')
p.set_ws_monthly_file(popdatadir + 'forcing/ws.o_n_avg.mon')
return p
pilot = Pilot()
pilot.resource_name = "DAS-5"
pilot.queue_name = "defq"
pilot.node_count = 56
pilot.time = 1 | units.hour
pilot.slots_per_node = 16
pilot.label = "DAS-5-Pilot"
instance.pilots.add_pilot(pilot)
instance.use_for_all_workers()
from omuse.community.pop.interface import POP
p = POP(channel_type="distributed",
redirection="none",
mode='3600x2400x42',
number_of_workers=896,
max_message_length=1000000)
#set grid info
p.set_horiz_grid_file(
'/var/scratch/bwn200/pop/input/grid/grid.3600x2400.fob.da')
p.set_vert_grid_file('/var/scratch/bwn200/pop/input/grid/in_depths.42.dat')
p.set_topography_file(
'/var/scratch/bwn200/pop/input/grid/kmt_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black'
)
p.set_bottom_cell_file(
'/var/scratch/bwn200/pop/input/grid/dzbc_pbc.p1_tripole.s2.0-og.20060315.no_caspian_or_black'
)
p.set_ts_file('/var/scratch/bwn200/pop/input/r.t0.1_42l_greenland.01150501')
