[yt-users] yt error on kraken

[Britton Smith]

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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