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@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,