[yt-users] yt unpacking error on Pleiades

[Clayton Strawn]

Hello,


I have a request for help.

I am trying to run some analysis code remotely through ssh in yt on NASA
Pleiades. I have been able to install yt and trident and am running in a
virtualenv, but something is having a very deeply buried error that I don't
understand and fatally kills any task I send to Pleiades.

The same code works fine on my home laptop with the same input files, so I
assume the problem is something to do with the yt distribution on Pleiades,
but I used "pip install -U yt" so it should be up-to-date. The error code
comes from the fortran_utils file, and it says "unpack requires a string
argument of length 4"


(myenv) cstrawn at pfe27:~/quasarlines/quasarlines> python quasar_scan.py
VELA_v2_08 10MpcBox_csf512_a0.330.d "[H I,H II,O IV,O V,O VI,Si II,Si
III,Si IV,C I,C II,C III,C IV,Mg II,Mg III,Mg IV]"
yt : [INFO     ] 2017-07-25 12:11:26,454 discovered
particle_data:/home1/cstrawn/quasarlines/quasarlines/PMcrs0a0.330.DAT
yt : [INFO     ] 2017-07-25 12:11:26,454 discovered
particle_header:/home1/cstrawn/quasarlines/quasarlines/PMcrda0.330.DAT
yt : [INFO     ] 2017-07-25 12:11:26,462 Using root level of 14
yt : [INFO     ] 2017-07-25 12:11:26,463 Discovered 7 species of particles
yt : [INFO     ] 2017-07-25 12:11:26,463 Particle populations:  28016640
4263936    752640    123904     19552   2089406    85309
yt : [INFO     ] 2017-07-25 12:11:26,658 Max level is 12
yt : [INFO     ] 2017-07-25 12:11:26,682 Parameters: current_time
   = 3.350407555 Gyr
yt : [INFO     ] 2017-07-25 12:11:26,682 Parameters: domain_dimensions
    = [128 128 128]
yt : [INFO     ] 2017-07-25 12:11:26,683 Parameters: domain_left_edge
   = [ 0.  0.  0.]
yt : [INFO     ] 2017-07-25 12:11:26,683 Parameters: domain_right_edge
    = [ 1.  1.  1.]
yt : [INFO     ] 2017-07-25 12:11:26,683 Parameters:
cosmological_simulation   = True
yt : [INFO     ] 2017-07-25 12:11:26,683 Parameters: current_redshift
   = 2.02694081565
yt : [INFO     ] 2017-07-25 12:11:26,683 Parameters: omega_lambda
   = 0.730000019073
yt : [INFO     ] 2017-07-25 12:11:26,684 Parameters: omega_matter
   = 0.270000010729
yt : [INFO     ] 2017-07-25 12:11:26,684 Parameters: hubble_constant
    = 0.699999988079
18426 LOSs to scan.
Is this an appropriate number? (0 for no)
1
1/18426
Traceback (most recent call last):
  File "quasar_scan.py", line 375, in <module>
    q.get_coldens(save = 10)
  File "quasar_scan.py", line 148, in get_coldens
    ftype='gas')
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/trident/ray_generator.py",
line 239, in make_simple_ray
    particle_type = _determine_particle_type_from_ftype(ds, ftype)
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/trident/ray_generator.py",
line 590, in _determine_particle_type_from_ftype
    field_list_arr = np.asarray(ds.derived_field_list)
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/data_objects/static_output.py",
line 164, in ireq
    self.index
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/data_objects/static_output.py",
line 419, in index
    self, dataset_type=self.dataset_type)
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py",
line 65, in __init__
    super(ARTIndex, self).__init__(ds, dataset_type)
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/geometry/geometry_handler.py",
line 50, in __init__
    self._setup_geometry()
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/geometry/oct_geometry_handler.py",
line 25, in _setup_geometry
    self._initialize_oct_handler()
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py",
line 91, in _initialize_oct_handler
    self.domains]
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py",
line 761, in level_count
    self.level_offsets
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py",
line 782, in level_offsets
    self.ds.min_level, self.ds.max_level)
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py",
line 820, in _count_art_octs
    ns = fpu.peek_record_size(f, endian='>')
  File
"/u/cstrawn/myenv/lib/python2.7/site-packages/yt/utilities/fortran_utils.py",
line 250, in peek_record_size
    s = struct.unpack('>i', f.read(struct.calcsize('>i')))
struct.error: unpack requires a string argument of length 4


Please let me know if this is a known problem or if you have any idea what
I should do to avoid running into it. I don't really understand fortran
enough to know what is even supposed to be happening in fortran_utils.

Thanks so much,
Clayton Strawn
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