def print_log(pre,
time,
gravity,
E0=0.0 | nbody_system.energy,
cpu0=0.0,
wall0=0.0):
cpu = cputime()
wall = wallclocktime()
N = len(gravity.particles)
M = gravity.total_mass
U = gravity.potential_energy
T = gravity.kinetic_energy
Etop = T + U
E = Etop
if E0 == 0 | nbody_system.energy: E0 = E
Rvir = -0.5 * M * M / U
Q = -T / U
com = pa.center_of_mass(gravity.particles)
comv = pa.center_of_mass_velocity(gravity.particles)
if N > 15:
dcen,rcore,rhocore \
= pa.densitycentre_coreradius_coredens(gravity.particles)
else:
dcen = com
rcore = zero
rhocore = zero
cmx, cmy, cmz = dcen
lagr, mf = pa.LagrangianRadii(gravity.particles, cm=dcen) # no units!
print ''
print pre + "time=", time.number
print pre + "cpu=", cpu - cpu0
print pre + "wall=", wall - wall0
print pre + "Ntot=", N
print pre + "mass=", M.number
print pre + "Etot=", E.number
print pre + "dE/E=", E / E0 - 1
print pre + "Rvir=", Rvir.number
print pre + "Qvir=", Q
cmx, cmy, cmz = com
print pre + "cmpos[3]= %.8f %.8f %.8f" % (cmx.number, cmy.number,
cmz.number)
cmx, cmy, cmz = comv
print pre + "cmvel[3]= %.8f %.8f %.8f" % (cmx.number, cmy.number,
cmz.number)
cmx, cmy, cmz = dcen
print pre + "dcpos[3]= %.8f %.8f %.8f" % (cmx.number, cmy.number,
cmz.number)
print pre + "Rcore=", rcore.number
print pre + "Mlagr[9]=",
for m in mf:
print "%.4f" % (m),
print ''
print pre + "Rlagr[9]=",
for r in lagr.number:
print "%.8f" % (r),
print ''
sys.stdout.flush()
return E, cpu, wall
def print_log(pre, time, gravity, E0 = 0.0 | nbody_system.energy,
cpu0 = 0.0, wall0 = 0.0):
# Standard log output.
cpu = cputime()
wall = wallclocktime()
N = len(gravity.particles)
M = gravity.total_mass
U = gravity.potential_energy
T = gravity.kinetic_energy
Etop = T + U
E = Etop
if E0 == 0 | nbody_system.energy: E0 = E
Rvir = -0.5*M*M/U
Q = -T/U
com = pa.center_of_mass(gravity.particles)
comv = pa.center_of_mass_velocity(gravity.particles)
if N >= 100:
dcen,rcore,rhocore \
= pa.densitycentre_coreradius_coredens(gravity.particles)
cmx,cmy,cmz = dcen
lagr,mf = pa.LagrangianRadii(gravity.particles, cm=dcen) # no units!
print ''
print pre+"time=", time.number
print pre+"cpu=", cpu-cpu0
print pre+"wall=", wall-wall0
print pre+"Ntot=", N
print pre+"mass=", M.number
print pre+"Etot=", E.number
print pre+"dE/E=", E/E0 - 1
print pre+"Rvir=", Rvir.number
print pre+"Qvir=", Q
cmx,cmy,cmz = com
print pre+"cmpos[3]= %.8f %.8f %.8f" % (cmx.number, cmy.number, cmz.number)
cmx,cmy,cmz = comv
print pre+"cmvel[3]= %.8f %.8f %.8f" % (cmx.number, cmy.number, cmz.number)
if N >= 100:
cmx,cmy,cmz = dcen
print pre+"dcpos[3]= %.8f %.8f %.8f" \
% (cmx.number, cmy.number, cmz.number)
print pre+"Rcore=", rcore.number
print pre+"Mlagr[9]=",
for m in mf: print "%.4f" % (m),
print ''
print pre+"Rlagr[9]=",
for r in lagr.number: print "%.8f" % (r),
print ''
sys.stdout.flush()
return E,cpu,wall
def main():
global verbose
global regoldindexes
global createsysattrs
parser = _get_parser()
args = parser.parse_args()
# check arguments
if args.rng:
try:
args.rng = eval("slice(" + args.rng + ")")
except Exception:
parser.error("Error when getting the range parameter.")
if args.chunkshape.isdigit() or args.chunkshape.startswith('('):
args.chunkshape = eval(args.chunkshape)
if args.complevel < 0 or args.complevel > 9:
parser.error(
'invalid "complevel" value, it sould be in te range [0, 9]')
# Catch the files passed as the last arguments
src = args.src.rsplit(':', 1)
dst = args.dst.rsplit(':', 1)
if len(src) == 1:
srcfile, srcnode = src[0], "/"
else:
srcfile, srcnode = src
if len(dst) == 1:
dstfile, dstnode = dst[0], "/"
else:
dstfile, dstnode = dst
if srcnode == "":
# case where filename == "filename:" instead of "filename:/"
srcnode = "/"
if dstnode == "":
# case where filename == "filename:" instead of "filename:/"
dstnode = "/"
# Ignore the warnings for tables that contains oldindexes
# (these will be handled by the copying routines)
warnings.filterwarnings("ignore", category=OldIndexWarning)
# Ignore the flavors warnings during upgrading flavor operations
if args.upgradeflavors:
warnings.filterwarnings("ignore", category=FlavorWarning)
# Build the Filters instance
filter_params = (
args.complevel,
args.complib,
args.shuffle,
args.bitshuffle,
args.fletcher32,
)
if (filter_params == (None, ) * 4 or args.keepfilters):
filters = None
else:
if args.complevel is None:
args.complevel = 0
if args.shuffle is None:
if args.complevel > 0:
args.shuffle = True
else:
args.shuffle = False
if args.bitshuffle is None:
args.bitshuffle = False
if args.bitshuffle:
# Shuffle and bitshuffle are mutually exclusive
args.shuffle = False
if args.complib is None:
args.complib = "zlib"
if args.fletcher32 is None:
args.fletcher32 = False
filters = Filters(complevel=args.complevel,
complib=args.complib,
shuffle=args.shuffle,
bitshuffle=args.bitshuffle,
fletcher32=args.fletcher32)
# The start, stop and step params:
start, stop, step = None, None, 1 # Defaults
if args.rng:
start, stop, step = args.rng.start, args.rng.stop, args.rng.step
# Set globals
verbose = args.verbose
regoldindexes = args.regoldindexes
createsysattrs = args.createsysattrs
# Some timing
t1 = time.time()
cpu1 = cputime()
# Copy the file
if verbose:
print("+=+" * 20)
print("Recursive copy:", args.recursive)
print("Applying filters:", filters)
if args.sortby is not None:
print("Sorting table(s) by column:", args.sortby)
print("Forcing a CSI creation:", args.checkCSI)
if args.propindexes:
print("Recreating indexes in copied table(s)")
print("Start copying %s:%s to %s:%s" %
(srcfile, srcnode, dstfile, dstnode))
print("+=+" * 20)
# Check whether the specified source node is a group or a leaf
h5srcfile = open_file(srcfile, 'r')
srcnodeobject = h5srcfile.get_node(srcnode)
# Close the file again
h5srcfile.close()
stats = {'groups': 0, 'leaves': 0, 'links': 0, 'bytes': 0, 'hardlinks': 0}
if isinstance(srcnodeobject, Group):
copy_children(srcfile,
dstfile,
srcnode,
dstnode,
title=args.title,
recursive=args.recursive,
filters=filters,
copyuserattrs=args.copyuserattrs,
overwritefile=args.overwritefile,
overwrtnodes=args.overwrtnodes,
stats=stats,
start=start,
stop=stop,
step=step,
chunkshape=args.chunkshape,
sortby=args.sortby,
check_CSI=args.checkCSI,
propindexes=args.propindexes,
upgradeflavors=args.upgradeflavors,
use_hardlinks=True)
else:
# If not a Group, it should be a Leaf
copy_leaf(srcfile,
dstfile,
srcnode,
dstnode,
title=args.title,
filters=filters,
copyuserattrs=args.copyuserattrs,
overwritefile=args.overwritefile,
overwrtnodes=args.overwrtnodes,
stats=stats,
start=start,
stop=stop,
step=step,
chunkshape=args.chunkshape,
sortby=args.sortby,
check_CSI=args.checkCSI,
propindexes=args.propindexes,
upgradeflavors=args.upgradeflavors)
# Gather some statistics
t2 = time.time()
cpu2 = cputime()
tcopy = round(t2 - t1, 3)
cpucopy = round(cpu2 - cpu1, 3)
try:
tpercent = int(round(cpucopy / tcopy, 2) * 100)
except ZeroDivisionError:
tpercent = 'NaN'
if verbose:
ngroups = stats['groups']
nleaves = stats['leaves']
nlinks = stats['links']
nhardlinks = stats['hardlinks']
nbytescopied = stats['bytes']
nnodes = ngroups + nleaves + nlinks + nhardlinks
print(
"Groups copied:",
ngroups,
", Leaves copied:",
nleaves,
", Links copied:",
nlinks,
", Hard links copied:",
nhardlinks,
)
if args.copyuserattrs:
print("User attrs copied")
else:
print("User attrs not copied")
print("KBytes copied:", round(nbytescopied / 1024., 3))
print("Time copying: %s s (real) %s s (cpu) %s%%" %
(tcopy, cpucopy, tpercent))
print("Copied nodes/sec: ", round((nnodes) / float(tcopy), 1))
print("Copied KB/s :", int(nbytescopied / (tcopy * 1024)))
date = dates[0]
for hour in range(24):
data = get_data(tiles, date, hour)
hmap.plot_frame((data, date, hour))
hmap.save_frame()
else:
thm = movietools.ThreadedHorizMap(720, 12)
thm.check()
thm.setup_colorbar((vmin, vmax, cmap))
time_read = 0.
time_video = 0.
time_total = 0.
nframes = 0
for date, hour in itertools.product(mydates, range(24)):
t0 = cputime()
assert ds.is_datetiles_online(tiles, date), comm.Abort()
data = get_data(tiles, date, hour)
t1 = cputime()
thm.do_frame((axis, lons, lats), (data, date, hour))
t2 = cputime()
time_read += t1 - t0
time_video += t2 - t1
time_total += t2 - t0
nframes += 1
if True:
print(
f"myrank: {myrank} io:{time_read:.1f} video:{time_video:.1f} total:{time_total:.1f} nframes:{nframes} timeperframe:{time_total/nframes:.2f}"
)
thm.close()
# pool.close()
def run_ph4(infile = None, number_of_stars = 40,
end_time = 10 | nbody_system.time,
delta_t = 1 | nbody_system.time,
n_workers = 1, use_gpu = 1, gpu_worker = 1, gpu_id = -1,
accuracy_parameter = 0.1,
softening_length = -1 | nbody_system.length,
manage_encounters = 1):
if infile != None: print "input file =", infile
print "end_time =", end_time.number
print "delta_t =", delta_t.number
print "n_workers =", n_workers
print "use_gpu =", use_gpu
print "manage_encounters =", manage_encounters
print "initializing the gravity module"
sys.stdout.flush()
# Note that there are actually really three GPU options to test:
#
# 1. use the GPU code and allow GPU use (default)
# 2. use the GPU code but disable GPU use (-g)
# 3. use the non-GPU code (-G)
#print "1"; sys.stdout.flush()
gpu = 0
if gpu_worker == 1:
try:
gravity = grav(number_of_workers = n_workers,
redirection = "none", mode = "gpu")
# debugger='valgrind')
gpu = 1
except Exception as ex:
print \
'*** GPU worker code not found. Reverting to non-GPU code. ***'
gpu = 0
if gpu == 0:
gravity = grav(number_of_workers = n_workers,
redirection = "none")
# debugger='valgrind')
#print "2"; sys.stdout.flush()
gravity.initialize_code()
#print "3"; sys.stdout.flush()
gravity.parameters.set_defaults()
gravity.parameters.gpu_id = gpu_id
#-----------------------------------------------------------------
#print "4"; sys.stdout.flush()
print "making a Plummer model"
stars = new_plummer_model(number_of_stars)
id = numpy.arange(number_of_stars)
stars.id = id+1
print "setting particle masses and radii"
stars.mass = (1.0 / number_of_stars) | nbody_system.mass
if 0:
scaled_mass = new_salpeter_mass_distribution_nbody(number_of_stars)
stars.mass = scaled_mass
stars.radius = 0.0 | nbody_system.length
print "centering stars"
stars.move_to_center()
if 0:
print "scaling stars to virial equilibrium"
stars.scale_to_standard(smoothing_length_squared
= gravity.parameters.epsilon_squared)
time = 0.0 | nbody_system.time
sys.stdout.flush()
#-----------------------------------------------------------------
#print "5"; sys.stdout.flush()
if softening_length == -1 | nbody_system.length:
eps2 = 0.25*(float(number_of_stars))**(-0.666667) \
| nbody_system.length**2
else:
eps2 = softening_length*softening_length
#print "6"; sys.stdout.flush()
gravity.parameters.timestep_parameter = accuracy_parameter
gravity.parameters.epsilon_squared = eps2
gravity.parameters.use_gpu = use_gpu
gravity.parameters.manage_encounters = manage_encounters
print "adding particles"
# print stars
sys.stdout.flush()
gravity.particles.add_particles(stars)
gravity.commit_particles()
print ''
print "number_of_stars =", number_of_stars
sys.stdout.flush()
E0,cpu0,wall0 = print_log('', time, gravity)
# Channel to copy values from the code to the set in memory.
channel = gravity.particles.new_channel_to(stars)
stopping_condition = gravity.stopping_conditions.collision_detection
stopping_condition.enable()
#-----------------------------------------------------------------
cpu0 = cputime()
t0 = 0.
pi = math.pi
times = [1., 2., pi, 4*pi/3, 5., 2*pi, 2*pi + pi/100,
2*pi + pi/5, 7., 8., 3*pi, 10.]
gravity.parameters.force_sync = 1 # stays set until explicitly unset
for t in times:
time = t|nbody_system.time
print "\nEvolving to time", time
sys.stdout.flush()
gravity.parameters.block_steps = 0
gravity.parameters.total_steps = 0
gravity.evolve_model(time)
dt = t - t0
t0 = t
cpu = cputime()
dcpu = cpu - cpu0
cpu0 = cpu
# Ensure that the stars list is consistent with the internal
# data in the module.
ls = len(stars)
# Update the bookkeeping: synchronize stars with the module data.
try:
gravity.update_particle_set()
gravity.particles.synchronize_to(stars)
except:
pass
# Copy values from the module to the set in memory.
channel.copy()
# Copy the index (ID) as used in the module to the id field in
# memory. The index is not copied by default, as different
# codes may have different indices for the same particle and
# we don't want to overwrite silently.
channel.copy_attribute("index_in_code", "id")
if stopping_condition.is_set():
star1 = stopping_condition.particles(0)[0]
star2 = stopping_condition.particles(1)[0]
print '\nstopping condition set at time', \
gravity.get_time().number,'for:\n'
print star1
print ''
print star2
print ''
raise Exception("no encounter handling")
if len(stars) != ls:
if 0:
print "stars:"
for s in stars:
print " ", s.id.number, s.mass.number, \
s.x.number, s.y.number, s.z.number
else:
print "number of stars =", len(stars)
sys.stdout.flush()
print_log('', time, gravity, E0, cpu0, wall0)
print '@@@'
print '@@@ t =', time.number, ' dt =', dt
print '@@@ sync_time =', gravity.parameters.sync_time.number
print '@@@ dcpu/dt =', dcpu/dt
nb = gravity.parameters.block_steps
ns = gravity.parameters.total_steps
print '@@@ d(block_steps) =', nb, ' #/dt =', nb/dt
print '@@@ d(total steps) =', ns, ' #/dt =', ns/dt
#print stars
sys.stdout.flush()
#-----------------------------------------------------------------
print ''
gravity.stop()
def main():
global verbose
global regoldindexes
global createsysattrs
parser = _get_parser()
args = parser.parse_args()
# check arguments
if args.rng:
try:
args.rng = eval("slice(" + args.rng + ")")
except Exception:
parser.error("Error when getting the range parameter.")
if args.chunkshape.isdigit() or args.chunkshape.startswith('('):
args.chunkshape = eval(args.chunkshape)
if args.complevel < 0 or args.complevel > 9:
parser.error(
'invalid "complevel" value, it sould be in te range [0, 9]'
)
# Catch the files passed as the last arguments
src = args.src.rsplit(':', 1)
dst = args.dst.rsplit(':', 1)
if len(src) == 1:
srcfile, srcnode = src[0], "/"
else:
srcfile, srcnode = src
if len(dst) == 1:
dstfile, dstnode = dst[0], "/"
else:
dstfile, dstnode = dst
if srcnode == "":
# case where filename == "filename:" instead of "filename:/"
srcnode = "/"
if dstnode == "":
# case where filename == "filename:" instead of "filename:/"
dstnode = "/"
# Ignore the warnings for tables that contains oldindexes
# (these will be handled by the copying routines)
warnings.filterwarnings("ignore", category=OldIndexWarning)
# Ignore the flavors warnings during upgrading flavor operations
if args.upgradeflavors:
warnings.filterwarnings("ignore", category=FlavorWarning)
# Build the Filters instance
filter_params = (
args.complevel,
args.complib,
args.shuffle,
args.bitshuffle,
args.fletcher32,
)
if (filter_params == (None,) * 4 or args.keepfilters):
filters = None
else:
if args.complevel is None:
args.complevel = 0
if args.shuffle is None:
if args.complevel > 0:
args.shuffle = True
else:
args.shuffle = False
if args.bitshuffle is None:
args.bitshuffle = False
if args.bitshuffle:
# Shuffle and bitshuffle are mutually exclusive
args.shuffle = False
if args.complib is None:
args.complib = "zlib"
if args.fletcher32 is None:
args.fletcher32 = False
filters = Filters(complevel=args.complevel, complib=args.complib,
shuffle=args.shuffle, bitshuffle=args.bitshuffle,
fletcher32=args.fletcher32)
# The start, stop and step params:
start, stop, step = None, None, 1 # Defaults
if args.rng:
start, stop, step = args.rng.start, args.rng.stop, args.rng.step
# Set globals
verbose = args.verbose
regoldindexes = args.regoldindexes
createsysattrs = args.createsysattrs
# Some timing
t1 = time.time()
cpu1 = cputime()
# Copy the file
if verbose:
print("+=+" * 20)
print("Recursive copy:", args.recursive)
print("Applying filters:", filters)
if args.sortby is not None:
print("Sorting table(s) by column:", args.sortby)
print("Forcing a CSI creation:", args.checkCSI)
if args.propindexes:
print("Recreating indexes in copied table(s)")
print("Start copying %s:%s to %s:%s" % (srcfile, srcnode,
dstfile, dstnode))
print("+=+" * 20)
allow_padding = not args.dont_allow_padding
# Check whether the specified source node is a group or a leaf
h5srcfile = open_file(srcfile, 'r', allow_padding=allow_padding)
srcnodeobject = h5srcfile.get_node(srcnode)
# Close the file again
h5srcfile.close()
stats = {'groups': 0, 'leaves': 0, 'links': 0, 'bytes': 0, 'hardlinks': 0}
if isinstance(srcnodeobject, Group):
copy_children(
srcfile, dstfile, srcnode, dstnode,
title=args.title, recursive=args.recursive, filters=filters,
copyuserattrs=args.copyuserattrs, overwritefile=args.overwritefile,
overwrtnodes=args.overwrtnodes, stats=stats,
start=start, stop=stop, step=step, chunkshape=args.chunkshape,
sortby=args.sortby, check_CSI=args.checkCSI,
propindexes=args.propindexes,
upgradeflavors=args.upgradeflavors,
allow_padding=allow_padding,
use_hardlinks=True)
else:
# If not a Group, it should be a Leaf
copy_leaf(
srcfile, dstfile, srcnode, dstnode,
title=args.title, filters=filters,
copyuserattrs=args.copyuserattrs,
overwritefile=args.overwritefile, overwrtnodes=args.overwrtnodes,
stats=stats, start=start, stop=stop, step=step,
chunkshape=args.chunkshape,
sortby=args.sortby, check_CSI=args.checkCSI,
propindexes=args.propindexes,
upgradeflavors=args.upgradeflavors,
allow_padding=allow_padding,
)
# Gather some statistics
t2 = time.time()
cpu2 = cputime ()
tcopy = round(t2 - t1, 3)
cpucopy = round(cpu2 - cpu1, 3)
try:
tpercent = int(round(cpucopy / tcopy, 2) * 100)
except ZeroDivisionError:
tpercent = 'NaN'
if verbose:
ngroups = stats['groups']
nleaves = stats['leaves']
nlinks = stats['links']
nhardlinks = stats['hardlinks']
nbytescopied = stats['bytes']
nnodes = ngroups + nleaves + nlinks + nhardlinks
print(
"Groups copied:", ngroups,
", Leaves copied:", nleaves,
", Links copied:", nlinks,
", Hard links copied:", nhardlinks,
)
if args.copyuserattrs:
print("User attrs copied")
else:
print("User attrs not copied")
print("KBytes copied:", round(nbytescopied / 1024., 3))
print("Time copying: %s s (real) %s s (cpu) %s%%" % (
tcopy, cpucopy, tpercent))
print("Copied nodes/sec: ", round((nnodes) / float(tcopy), 1))
print("Copied KB/s :", int(nbytescopied / (tcopy * 1024)))