[yt-users] Having trouble running yt on kraken

[Matthew Turk]

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
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
>>
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