[yt-users] memory error for gadget visualization
Junhwan Choi (최준환)
choi.junhwan at gmail.com
Thu Apr 9 12:54:12 PDT 2015
Hi yt users and developer,
I tried to make a simple visualization for 244/h cMpc box with 512^3
DM and gas gadget simulation with following script
==================================
import matplotlib as matplotlib
matplotlib.use('Agg')
import matplotlib.pylab as pylab
import numpy as np
import yt
import yt.units as units
index = 0
text_dict = {'color':'white', 'size':20}
fname = ('../snap_vbc_%03d.hdf5' % index)
unit_base = {'UnitLength_in_cm' : 3.08568e+21, 'UnitMass_in_g'
: 1.989e+43, 'UnitVelocity_in_cm_per_s' : 100000}
bbox_lim = 244000 #kpc
bbox = [[0,bbox_lim], [0,bbox_lim], [0,bbox_lim]]
ds = yt.load(fname,unit_base=unit_base,bounding_box=bbox)
cen_center=np.array([122000,122000,122000])
pc = yt.ProjectionPlot(ds, "z", ('deposit', 'PartType0_density'),
width = (244.0, 'Mpccm/h'))
pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift,
data_coords=False, text_args = text_dict)
pc.save("all_view_%04d" % index)
pc = yt.ProjectionPlot(ds, "z", ('deposit', 'PartType1_density'),
width = (244.0, 'Mpccm/h'))
pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift,
data_coords=False, text_args = text_dict)
pc.save("all_view_%04d" % index)
pc = yt.ProjectionPlot(ds, "z", ('deposit', 'all_density'), width =
(244.0, 'Mpccm/h'))
pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift,
data_coords=False, text_args = text_dict)
pc.save("all_view_%04d" % index)
pc = yt.ProjectionPlot(ds, "z", ('gas', 'density'), width = (244.0, 'Mpccm/h'))
pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift,
data_coords=False, text_args = text_dict)
pc.save("all_view_%04d" % index)
===================================
It initially works an make couple figures but it crash with following
error message:
.......
Traceback (most recent call last):
File "viz.py", line 56, in <module>
viz4(index)
File "viz.py", line 50, in viz4
pc = yt.ProjectionPlot(ds, "z", ('gas', 'density'), width =
(244.0, 'Mpccm/h'))
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py",
line 1228, in __init__
field_parameters = field_parameters, method = method)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/construction_data_containers.py",
line 250, in __init__
self.get_data(field)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/construction_data_containers.py",
line 295, in get_data
chunk_fields, "io", local_only = True)):
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 507, in para
llel_objects
for obj_id, obj in oiter:
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 592, in chunks
self.get_data(fields)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 693, in get_data
self._generate_fields(fields_to_generate)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 713, in _generate_fields
fd = self._generate_field(field)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 285, in _generate_field
tr = self._generate_fluid_field(field)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 303, in _generate_fluid_field
rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 319, in _generate_spatial_fluid
ind += o.select(self.selector, self[field], rv, ind)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 248, in __getitem__
self.get_data(f)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 693, in get_data
self._generate_fields(fields_to_generate)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 713, in _generate_fields
fd = self._generate_field(field)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 285, in _generate_field
tr = self._generate_fluid_field(field)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 305, in _generate_fluid_field
rv = finfo(gen_obj)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/fields/derived_field.py",
line 184, in __call__
dd = self._function(self, data)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/fields/particle_fields.py",
line 958, in _vol_weight
dens = data[ptype, density_name].in_cgs()
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/octree_subset.py",
line 77, in __getitem__
tr = super(OctreeSubset, self).__getitem__(key)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 248, in __getitem__
self.get_data(f)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
line 687, in get_data
particles, self, self._current_chunk)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/geometry/geometry_handler.py",
line 234, in _read_particle_fields
fields_to_read)
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/utilities/io_handler.py",
line 177, in _read_particle_selection
for field_r, vals in self._read_particle_fields(chunks, ptf, selector):
File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/frontends/owls/io.py",
line 97, in _read_particle_fields
coords = g["Coordinates"][:].astype("float64")
MemoryError
It looks there is a memory shortage.
I use the stampede normal node which has ~32GB and I do not think
512^3 gas and DM particles require this amount memory.
[But, I successfully made a visualization with 256^3 in 100/h cMpc run.]
Is there any my possible mistake that leaks the memory?
If so, could you inform me to overcome this memory issue.
Thank you in advance,
Junhwan Choi
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