[yt-users] Problem Running yt in Parallel

[meecegre at msu.edu]

Hi everyone,

I've come across an error while trying to use yt for parallel  analysis on Kraken. Wondering if its something people have seen before.

I have my simple script that does slices of a few different quanties.  When I ran it with 12 tasks on Kraken, it worked fine for the first four  datasets, but crashed during the fifth one. I tried a simpler script  that just does a slice of density for that dataset, and it crashed again  with the same error:

IndexError: arrays used as indices must be of integer (or boolean) type

When I ran this code again with only 1 task (still on Kraken, everything else the same), it worked fine. More of the output, as well as my job script and plotting script, are below.

Since it works in serial , and works for some data sets, the problem seems to be something to do with parallelism. Is  there any sort of simple explanation or something I'm doing wrong?

Just wondering if this is something people have come across before.

--Greg

(Last few lines of output)
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File  "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py",  line 69, in find_max_cell_location
File  "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py",  line 69, in find_max_cell_location
File  "/lustre/scratch/proj/sw/yt/current/lib/python2.7/site-packages/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/object_finding_mixin.py",  line 69, in find_max_cell_location
max_grid = self.grids[mg]
IndexError: arrays used as indices must be of integer (or boolean) type
max_grid = self.grids[mg]
max_grid = self.grids[mg]
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type

(Job script)
#!/bin/bash
#PBS -A TG-AST090040
#PBS -l size=12,walltime=2:00:00
#PBS -j oe
#PBS -N slicer

cd /lustre/scratch/oshea/nested_ics_real1/analysis

ls
pwd

export MPLCONFIGDIR=${PBS_O_WORKDIR}/.matplotlib/
[ ! -d ${MPLCONFIGDIR} ] && mkdir ${MPLCONFIGDIR}

module unload PrgEnv-pgi
module load PrgEnv-gnu
module load yt

aprun -n 12 python ./simple_slice.py --parallel

(simple_slice.py)
from yt.mods import *

DD = 40

fileName = "../DD%s/DD%s" % ((str(DD)).zfill(4),  (str(DD)).zfill(4))

pf = load(fileName)
pc = PlotCollection(pf)

pc.add_slice("Density", 0)

pc.save("./%s" % str(DD).zfill(4))
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