Folks,
I am trying to run yt halo finder with MPI, and I am encounter the following error. Could you perhaps give me a hint how to debug it further?
Here is a simple script:
---- SCRIPT -------
import yt
from yt.analysis_modules.halo_analysis.api import HaloCatalog
yt.enable_parallelism()
path = "."
aexp = "0.0802"
d = yt.load(path+"/rei10_a"+aexp +"/rei10_a"+aexp+".art")
hc = HaloCatalog(data_ds=d,finder_method='hop',output_dir=path+"/ a="+aexp+"/hop2",finder_kwargs ={"dm_only":False,"ptype":"N- BODY"})
hc.create()
-------------------
It runs just fine in a serial mode (with yt.enable_parallelism() call commented out), but with MPI it gives a type error deep inside yt:
---- SERIAL OUTPUT -------
/data/gnedin/REI/TMP >p hf.py
yt : [WARNING ] 2018-02-21 11:02:26,502 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011)
yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: current_time = 392162249.38323104 yr
yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: domain_dimensions = [64 64 64]
yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: domain_right_edge = [ 64. 64. 64.]
yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: cosmological_simulation = True
yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: current_redshift = 11.470684242933336
yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_lambda = 0.6964000165462494
yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_matter = 0.3035999834537506
yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: hubble_constant = 0.6814000010490417
yt : [INFO ] 2018-02-21 11:02:34,808 Created 256 chunks for ARTIO
yt : [INFO ] 2018-02-21 11:02:38,656 Initializing HOP
yt : [INFO ] 2018-02-21 11:02:38,658 Created 256 chunks for ARTIO
Copying arrays for 16777216 particles
Calling hop... 16777216 1.600e+02
nSmooth = 65 kd->nActive = 16777216
Building Tree...
Finding Densities...
Finding Densest Neighbors...
Grouping...
Merging Groups...
Writing Output...
All Done!Calling regroup...
No minimum group size specified. Assuming 10 particles.
ngroups = 51045
yt : [INFO ] 2018-02-21 11:07:11,099 Parsing outputs
yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: current_time = 0.0
yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: domain_dimensions = [2 2 2]
yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: domain_right_edge = [ 3.56553853e+24 3.56553853e+24 3.56553853e+24]
yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: cosmological_simulation = 0.0
yt : [INFO ] 2018-02-21 11:07:38,789 Allocating for 3.240e+02 particles (index particle type 'all')
yt : [INFO ] 2018-02-21 11:07:38,790 Identified 1.700e+01 octs
/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ units/yt_array.py:990: RuntimeWarning: divide by zero encountered in true_divide
return super(YTArray, self).__truediv__(ro)
yt : [INFO ] 2018-02-21 11:07:39,223 Saving halo catalog (324 halos) to ./a=0.0802/hop/hop.
---------------------------
------ MPI OUTPUT ---------
/data/gnedin/REI/TMP >/data/gnedin/soft/anaconda3/bin/mpirun -n 2 /data/gnedin/soft/anaconda3/bi n/python3 hf.py
yt : [INFO ] 2018-02-21 11:20:47,675 Global parallel computation enabled: 0 / 2
yt : [INFO ] 2018-02-21 11:20:47,676 Global parallel computation enabled: 1 / 2
P000 yt : [WARNING ] 2018-02-21 11:20:47,681 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011)
P001 yt : [WARNING ] 2018-02-21 11:20:47,687 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011)
P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: current_time = 392162249.38323104 yr
P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: domain_dimensions = [64 64 64]
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: domain_left_edge = [ 0. 0. 0.]
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: domain_right_edge = [ 64. 64. 64.]
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: cosmological_simulation = True
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: current_redshift = 11.470684242933336
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: omega_lambda = 0.6964000165462494
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: omega_matter = 0.3035999834537506
P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: hubble_constant = 0.6814000010490417
File "hf.py", line 15, in <module>
hc.create()
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_catalog.py", line 334, in create
self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ utilities/parallel_tools/paral lel_analysis_interface.py", line 306, in barrierize
retval = func(*args, **kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_catalog.py", line 403, in _run
self.halos_ds = self.finder_method(self.data_ds)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_finding_methods.py", line 44, in __call__
return self.function(ds, *self.args, **self.kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_finding_methods.py", line 51, in _hop_method
halo_list = HOPHaloFinder(ds, **finder_kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_finding/ halo_objects.py", line 1483, in __init__
padding=self.padding)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ utilities/parallel_tools/paral lel_analysis_interface.py", line 1191, in partition_index_3d
cx, cy, cz = np.unravel_index(mi, cc)
File "hf.py", line 15, in <module>
hc.create()
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_catalog.py", line 334, in create
self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ utilities/parallel_tools/paral lel_analysis_interface.py", line 306, in barrierize
retval = func(*args, **kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_catalog.py", line 403, in _run
self.halos_ds = self.finder_method(self.data_ds)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_finding_methods.py", line 44, in __call__
return self.function(ds, *self.args, **self.kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_analysis /halo_finding_methods.py", line 51, in _hop_method
halo_list = HOPHaloFinder(ds, **finder_kwargs)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ analysis_modules/halo_finding/ halo_objects.py", line 1483, in __init__
padding=self.padding)
File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/ utilities/parallel_tools/paral lel_analysis_interface.py", line 1191, in partition_index_3d
cx, cy, cz = np.unravel_index(mi, cc)
P000 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator operand 0 dtype could not be cast from dtype('float64') to dtype('int64') according to the rule 'same_kind'
P000 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 0.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
P001 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator operand 0 dtype could not be cast from dtype('float64') to dtype('int64') according to the rule 'same_kind'
P001 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 1.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
-------------------------------------
Any suggestion would be highly appreciated.
Nick Gnedin
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