[yt-users] yt error on kraken

Harinarayan Krishnan hkrishnan at lbl.gov
Tue Feb 28 18:41:02 PST 2012


Hi all,

The Kraken yt-dev module just finished updating. Let me know if anyone
has any issues with the installation. Also, if the changes did not
get updated for some reason.

Best regards,
Hari


On Tue, Feb 28, 2012 at 5:31 PM, Britton Smith <brittonsmith at gmail.com> wrote:
> 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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