ImportError: dynamic module does not define module export function (PyInit__assign)

[atbogetti]

Hello,

I'm testing this out on one of my systems and cannot seem to get passed the initialization step. I get the following error:

Warning: When compiling code please add the following flags to nvcc:
-gencode arch=compute_35,code=[compute_35,sm_35]
-gencode arch=compute_61,code=[compute_61,sm_61]
-gencode arch=compute_70,code=[compute_70,sm_70]
simulation py3_test root is /bgfs/ltc1/home/atb43/qmmm/september/6_WESTPA/py3_test
Traceback (most recent call last):
File "/bgfs/ltc1/home/atb43/qmmm/py3_westpa/lib/cmds/w_init.py", line 28, in
import westpa
File "/bgfs/ltc1/home/atb43/qmmm/py3_westpa/lib/west_tools/westpa/init.py", line 1, in
from . import _rc
File "/bgfs/ltc1/home/atb43/qmmm/py3_westpa/lib/west_tools/westpa/_rc.py", line 27, in
from .yamlcfg import YAMLConfig
File "/bgfs/ltc1/home/atb43/qmmm/py3_westpa/lib/west_tools/westpa/yamlcfg.py", line 37, in
from westpa.binning import NopMapper
File "/bgfs/ltc1/home/atb43/qmmm/py3_westpa/lib/west_tools/westpa/binning/init.py", line 1, in
from . import _assign
ImportError: dynamic module does not define module export function (PyInit__assign)

This didn't happen with the python2 WESTPA. I thought this may be due to me defining my bins outside of the west.cfg (in the system.py) and so I tried doing that, but get the same error.

Here is my west.cfg file:

The master WEST configuration file for a simulation.

vi: set filetype=yaml :

---

west:
system:
driver: system.SDASystem
module_path: $WEST_SIM_ROOT
propagation:
max_total_iterations: 1000
max_run_wallclock: 72:00:00
propagator: executable
gen_istates: true
block_size: 1
data:
west_data_file: west.h5
datasets:
- name: pcoord
scaleoffset: 4
- name: solute_coords
scaleoffset: 4
- name: dihedral
scaleoffset: 4
- name: c5n34
scaleoffset: 4
- name: c7n34
scaleoffset: 4
- name: c9n34
scaleoffset: 4
- name: c12n34
scaleoffset: 4
- name: c14n34
scaleoffset: 4
- name: c16n34
scaleoffset: 4
- name: c21n34
scaleoffset: 4
- name: c25n34
scaleoffset: 4
- name: c23n34
scaleoffset: 4
data_refs:
segment: $WEST_SIM_ROOT/traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}
basis_state: $WEST_SIM_ROOT/bstates/{basis_state.auxref}
initial_state: $WEST_SIM_ROOT/istates/{initial_state.iter_created}/{initial_state.state_id}.rst
plugins:
executable:
environ:
PROPAGATION_DEBUG: 1
datasets:
- name: solute_coords
enabled: true
- name: dihedral
enabled: true
- name: c5n34
enabled: true
- name: c7n34
enabled: true
- name: c9n34
enabled: true
- name: c12n34
enabled: true
- name: c14n34
enabled: true
- name: c16n34
enabled: true
- name: c21n34
enabled: true
- name: c25n34
enabled: true
- name: c23n34
enabled: true
propagator:
executable: $WEST_SIM_ROOT/westpa_scripts/runseg.sh
stdout: $WEST_SIM_ROOT/seg_logs/{segment.n_iter:06d}-{segment.seg_id:06d}.log
stderr: $WEST_SIM_ROOT/slurm.err
stdin: null
cwd: null
environ:
SEG_DEBUG: 1
get_pcoord:
executable: $WEST_SIM_ROOT/westpa_scripts/get_pcoord.sh
stdout: $WEST_SIM_ROOT/job_logs/pcoord.log
stderr: $WEST_SIM_ROOT/job_logs/pcoord.err
gen_istate:
executable: $WEST_SIM_ROOT/westpa_scripts/gen_istate.sh
stdout: $WEST_SIM_ROOT/job_logs/istate.log
stderr: $WEST_SIM_ROOT/job_logs/istate.err
post_iteration:
enabled: true
executable: $WEST_SIM_ROOT/westpa_scripts/post_iter.sh
stdout: $WEST_SIM_ROOT/job_logs/post_iter.log
stderr: $WEST_SIM_ROOT/job_logs/post_iter.err
pre_iteration:
enabled: false
executable: $WEST_SIM_ROOT/westpa_scripts/pre_iter.sh
stderr: stdout

Settings for w_ipa, an interactive analysis program that can also automate analysis.

analysis:
directory: ANALYSIS # specify the directory all analysis files should exist in.
kinetics: # general options for both kinetics routines.
step_iter: 1
evolution: cumulative
extra: [ 'disable-correl' ]
analysis_schemes: # Analysis schemes. Required: name (TEST), states, and bins
DEFAULT:
enabled: True
bins:
- type: RectilinearBinMapper
boundaries:
- [0.0, 1.6, 'inf']
states:
- label: unbound
coords:
- [20]
- label: bound
coords:
- [1.56]

And here is my system.py file:

#!/usr/bin/env python

import numpy
import west
import os
from west import WESTSystem
from westpa.binning import RectilinearBinMapper
from westpa.binning import FuncBinMapper
from westpa.binning import RecursiveBinMapper
import logging

log = logging.getLogger(name)
log.debug('loading module %r' % name)

def radial_map(coords, mask, output):
center = numpy.array((1.6, 1.6))
coords -= center
quotients = numpy.divide(coords[:,1],coords[:,0])
angles = numpy.arctan(quotients)/(2*numpy.pi)*360
bins = numpy.arange(0,91,1)
output[mask] = numpy.digitize(angles, bins)[mask]
return output
class SDASystem(WESTSystem):
'''
Class specify binning schemes, walker counts, and other core weighted
ensemble parameters.
'''
def initialize(self):
self.pcoord_ndim = 2
self.pcoord_len = 2
self.pcoord_dtype = numpy.float32

    outer_mapper = RectilinearBinMapper(
            [[0, 1.6, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 'inf'],
             [0, 1.6, 4, 5, 'inf']]
                                        )

inner_mapper = RectilinearBinMapper(

[]

)

    radial_mapper = FuncBinMapper(radial_map, nbins=91)


    self.bin_mapper = RecursiveBinMapper(outer_mapper)
    self.bin_mapper.add_mapper(
            radial_mapper, 
            [1.6,1.6]
                               )

    self.bin_target_counts = numpy.empty((self.bin_mapper.nbins,), 
                                         dtype=numpy.int)
    self.bin_target_counts[...] = 5

Thanks,
Anthony

[astatide]

I'll go ahead and take a look into this.