[yt-users] Having trouble running yt on kraken

[Yuan Li]

Hi Matt,

I was making thin projections. Each output dataset (DD****) is about 14G.
What are "multiple root level tiles"? I have 256^3 root grids...

I just submitted another job asking for more nodes. I will let you know how
that goes (in two days).

Thanks!
Yuan

On Sat, Jul 28, 2012 at 7:24 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Yuan,
>
> On Sat, Jul 28, 2012 at 6:41 PM, Yuan Li <bear0980 at gmail.com> wrote:
> > Hi Britton,
> >
> > Thanks for your suggestion! Now the problem has been semi-solved.
> >
> > I have checked my script and I have this "module load yt/dev/", so I
> guess I
> > am using yt/dev, which is what I use on other machines.
> >
> > There is indeed a problem with "slice". I had all my functions defined
> > inside one file called profile.py (my bad: I started with profiles and
> kept
> > adding things without changing the name of it). After I changed that
> file to
> > "yuan.py", the error I got was:
> > ......
> >
> > Traceback (most recent call last):
> >   File "/var/spool/alps/2362242/try1.py", line 3, in <module>
> >     import yuan as yuan
> > ImportError: No module named yuan
> > ......
> >
> > So Kraken did not see my file. It did not complain before because there
> was
> > a built-in function in python called profile.
> >
> > Now after I added this to my script:
> > import sys
> > sys.path.append('/lustre/scratch/yuan/Thermal09/')
> >
> > Kraken could finally import my functions!
> >
> >
> > The reason why I said that it was only semi-solved is because now I am
> > getting "MemoryError". I will try to use more nodes, but it may never
> work
> > :).
>
> What operation are you doing, and how big is your dataset?  And, does
> your data have multiple root level tiles?
>
> -Matt
>
> >
> > How many nodes do you use for each job, Britton?
> >
> > Thanks!
> > Yuan
> >
> >
> > On Thu, Jul 26, 2012 at 6:39 PM, Britton Smith <brittonsmith at gmail.com>
> > wrote:
> >>
> >> Hi Yuan,
> >>
> >> This could be a result of using different version of yt on the two
> >> different platforms.  Can you check and see which version of yt you're
> using
> >> on kraken?  I believe there are modules for versions 2.2, 2.3, and the
> >> development branch on kraken.
> >>
> >> Also, the variable "slice" is already used in python for something else.
> >> If slice is apart of your script, you may want to rename that to
> something
> >> else.
> >>
> >> If your script only works on the most recent version of yt, you'll
> >> probably want to try to use the yt/dev module on Kraken.
> >>
> >> Britton
> >>
> >> On Wed, Jul 25, 2012 at 5:18 PM, Yuan Li <bear0980 at gmail.com> wrote:
> >>>
> >>> Hi all,
> >>>
> >>> I have been having trouble running yt on kraken. I am using the same
> >>> script that I use on trestles (where it sort of works). The issue I
> have on
> >>> kraken is that when I submit a non-interactive job, I get this error:
> >>> + aprun -n 12 ./try1.py --parallel
> >>> Traceback (most recent call last):
> >>>   File "/var/spool/alps/2310447/try1.py", line 3, in <module>
> >>>     slice(imin=12, imax=47, width=20)
> >>> TypeError: slice() does not take keyword arguments
> >>>
> >>>
> >>> If I run an interactive job (./try1.py --parallel), I get this error:
> >>> yuan at krakenpf2:~/scratch/Thermal09> Assertion failed in file
> >>>
> /ptmp/ulib/mpt/nightly/5.2/051011/mpich2/src/mpid/cray/src/adi/mpid_init.c
> >>> at line 115: 0
> >>> aborting job:
> >>> (null)
> >>>
> >>>
> >>> I can run a non-parallel interactive job (./try1.py) without any
> problem.
> >>>
> >>> My script looks like this:
> >>> #!/lustre/scratch/proj/sw/yt/dev/bin/python
> >>> from profile import *
> >>> slice(imin=41, imax=47, width=20)
> >>>
> >>>
> >>> Thanks!
> >>> Yuan
> >>>
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> >>>
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> >>
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