[yt-users] yt error on kraken

[Britton Smith]

Hi again everyone,

A pull request containing a fix to this bug has been accepted.  If after
updating anyone encounters errors that trace back to the get_memory_usage
function, please let us know.

Hari, can you update the yt-dev module on Kraken?

Britton

On Tue, Feb 28, 2012 at 5:30 PM, Britton Smith <brittonsmith at gmail.com>wrote:

> Hi Yuan and others,
>
> I was able to verify that the system command yt uses to get memory usage
> has an slightly non-standard return when run on the Kraken compute nodes.
> Seeing as how Kraken is a primary target for measuring memory usage, I have
> tried to implement a fix that will still return the proper number rather
> than just giving up.  I will issue a pull request and try to get this fixed
> in the code as soon as possible.
>
> Britton
>
>
> On Tue, Feb 28, 2012 at 3:41 PM, Britton Smith <brittonsmith at gmail.com>wrote:
>
>> Hi Yuan,
>>
>> Sorry for the delay in responding to your issue!  It seems that fix that
>> was put in place (by me) to get the memory usage isn't working right on
>> Kraken.  I am also seeing this behavior.  I am looking into this right
>> now.  For the time being, you should be ok loading an older yt module, like
>> yt/2.2.
>>
>> Britton
>>
>>
>> On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <yuan at astro.columbia.edu> wrote:
>>
>>> Hi all,
>>>
>>> I am trying to make a simple density projection of my data using yt on
>>> kraken. I have done this successfully many times before both on kraken
>>> and other machines, but lately I have been getting errors on kraken.
>>>
>>> I tried to run it interactively and it worked, but when I submit it as
>>> a job, I get this error:
>>>
>>> P000 yt : [INFO     ] 2012-02-24 03:40:43,722 Created plot collection
>>> with default plot-center = [0.50027465
>>> 8203125, 0.500335693359375, 0.499969482421875]
>>> Traceback (most recent call last):
>>>  File "/var/spool/alps/8952326/try1.py", line 8, in <module>
>>>    profile("Feb2012/cluster_64/",imax=20)
>>>  File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23,
>>> in profile
>>>  File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23,
>>> in profile
>>>                pc.add_projection("Density", 0)
>>>
>>>  File
>>> "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua
>>> lization/plot_collection.py", line 758, in add_projection
>>>
>>> P000 yt : [INFO     ] 2012-02-24 03:40:43,919 Starting 'Projecting
>>> level  0 /  8 '
>>>        **field_parameters)
>>> **field_parameters)
>>>              File
>>>
>>> "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.
>>> egg/yt/data_objects/data_containers.py", line 1648, in __init__
>>>
>>>  File
>>> "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_
>>> objects/data_containers.py", line 309, in _refresh_data
>>>
>>> .......
>>>
>>>
>>>   File
>>> "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs
>>> .py", line 104, in get_memory_usage
>>>    return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024
>>> ValueError: could not convert string to float: PID  Uid     VmSize Stat
>>> Command
>>>    1 root        584 S   init
>>>    2 root            SW  [migration/0]
>>>    3 root            SWN [ksoftirqd/0]
>>>    4 root            SW  [migration/1]
>>>    5 roo
>>>
>>>
>>>
>>> It seems that something went wrong at "get_memory_usage", but I had
>>> never had this error before and an interactive job does not get this
>>> error either.
>>>
>>> Sorry the error message is quite messy...
>>>
>>> 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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