[yt-users] error when running on cluster nodes

[Tsz Ka Li]

Hi Matt,
I am afraid otool is not installed on the Turing cluster. (I got command 
not found.) Do you know of any substitute for that tool?
Actually I did not follow the whole Cray installation instructions, but 
just those in the Section "Running on a compute node". So basically I 
just copied the yt directory to the scratch disk and used the python 
there. Maybe this does not make sense to you. Anyway sorry for the 
confusion.
Thanks,
Tsz Ka


On 2/18/2011 9:26 AM, Matthew Turk wrote:
> Hi Tsz Ka,
>
> I have been thinking about it, and I am afraid I don't have any bright
> ideas.  The only thing I can think of is that we may be able to get
> more information about the dynamic loading problem by having you run:
>
> otool -L  /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so
>
> I would again caution though that if you attempted to create a
> statically linked library, this likely resulted in major breakages.
> The static linking process described on the wiki is only really
> designed for the Cray Compute Node Linux distribution, and it has a
> fundamentally different mode of linking than Darwin/OSX.
>
> Could you send the output of that to us, run on both the compute nodes
> and on the head node?  I presume loading yt still runs on the head
> node?
>
> Thanks,
>
> Matt
>
> On Thu, Feb 17, 2011 at 12:38 PM, Tsz Ka Li<tszkali2 at illinois.edu>  wrote:
>> Hi Stephen,
>> I did try to include the -V flag in the interactive mode (i.e. qsub -I -V)
>> and I saw no difference in the error outcome.
>> Thanks,
>> Tsz Ka
>>
>> On 2/17/2011 11:19 AM, Stephen Skory wrote:
>>> Tsz Ka,
>>>
>>>> I used the same python (~/yt-ppc64/bin/python) as I did in the command
>>>> line. I think I tried python2.6 but I got the same error. (Actually how
>>>> are they different?) The machine I am using is the Turing cluster in UI
>>>> (http://www.cse.illinois.edu/turing/), which is an Apple Xserve cluster
>>>> using G5 processors. You can find on the website some information about
>>>> it. Sorry I am not that familiar with cluster issues. I suppose the
>>>> nodes have full installation, though I don't know where to check. I am
>>>> using the default compilers on Turing, which are gcc for C/C++ and xlf
>>>> for Fortran.
>>> I'm going to chime in here. I noticed that on their FAQ page:
>>>
>>> http://www.cse.illinois.edu/turing/faq.html
>>>
>>> There's something about path problems on compute nodes. Your error could
>>> be due to a library problem (i.e. DYLD_LIBRARY_PATH). Have you tried
>>> submitting your job with a "#PBS -V" that keeps your environment for the
>>> job?
>>>
>>> Matt may have some other bright ideas...
>>>
>>>
>>>   Stephen Skory
>>> stephenskory at yahoo.com
>>> http://stephenskory.com/
>>> 510.621.3687 (google voice)
>>> _______________________________________________
>>> yt-users mailing list
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>>>
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