[yt-users] yt error on kraken

[Yuan Li]

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