[yt-users] Clump finding and mpi4py

[Eve Lee]

Hello,

May I ask if the current version of yt supports parallelization of clump 
finding routine?

When I use mpirun.py -np (whatever number) python (name of my clump 
finding routine) (some arguments my routine requires) --parallel, I keep 
getting the following error:

Traceback (most recent call last):
   File "find_clumps.py", line 32, in <module>
     amods.level_sets.find_clumps(base, c_min, c_max, step)
   File 
"/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", 
line 188, in find_clumps
     elif (child._isValid()):
   File 
"/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", 
line 143, in _isValid
     self.function_value = eval(self.function)
   File "<string>", line 1, in <module>
   File 
"/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", 
line 86, in __call__
     self.func(e, *args, **kwargs)
   File 
"/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", 
line 347, in _IsBound
     bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]()
AttributeError: 'FieldDetector' object has no attribute 'quantities'

This version is updated to changeset 4457:bf868d1a8f02.

I have no problem running the same routine serially but it would be nice 
if I can run parallel to save some time.

Below is my clump finding routine if it helps:

from yt.mods import *
import sys
#Find and save clumps

#Read in the command-line-passed arguments
datadir = sys.argv[1]
pltdir = sys.argv[2]
datanum_start = int(sys.argv[3])
datanum_end = int(sys.argv[4])
datanum_step = int(sys.argv[5])

for i in range(datanum_start, datanum_end, datanum_step):
     pf = load(datadir+"DD%04i/data%04i" %(i,i))
     center = [0.5, 0.5, 0.5]
     radius = 1.0
     sp = pf.h.sphere(center, radius)

     particles = pf.h.find_particles_by_type(4)
     if type(particles) != types.NoneType:
         field = "Matter_Density" #Use both
         new_function = 
'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=False) 
 > 1.0'
     else:
         field = "Density"
         new_function = 
'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=False,include_particles=False) 
 > 1.0'

     c_min = 10**na.floor(na.log10(sp[field]).min()+1)
     c_max = 10**na.floor(na.log10(sp[field]).max()+1)
     step = 10

     #Find clumps
     base = amods.level_sets.Clump(sp, None, field, function=new_function)
     amods.level_sets.find_clumps(base, c_min, c_max, step)

     #Save clumps
     pf.h.save_object(base, "Clump")

Thanks!

Best Regards,

Eve