[yt-users] Problem Running yt in Parallel

[meecegre at msu.edu]

Hi,

I tried the dev module, but it still didn't work. I should note that I'm using the common install.

I also tried a script that does a few projections and profiles without slices, and it also crashed with the same error. It looks like only a few nodes are crashing, while the others run along fine for a while.

I've attached the full output, which lists the modules I have loaded near the top.

Thanks,

-- Greg

> Hi Greg,
>
> Thanks for writing.  This looks familiar to me, and I think it is
> fixed in the current development branch.  Can you use the dev module
> for yt instead of stable?
>
> One sidenote is that often slicing in parallel is not a net gain; I
> have found very few datasets where it is in fact substantially faster,
> most of them gigantic AMR runs with >1e5 grids.  I would recommend
> just doing slices in serial.
>
> Best,
>
> Matt
>
> On Fri, Jul 29, 2011 at 11:15 AM,  <meecegre at msu.edu> wrote:
>> 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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>>
>>
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