Re: [yt-users] yt error on kraken

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 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 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org