Hi again everyone,<br><br>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.<br><br>Hari, can you update the yt-dev module on Kraken?<br>
<br>Britton<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 5:30 PM, Britton Smith <span dir="ltr"><<a href="mailto:brittonsmith@gmail.com">brittonsmith@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Yuan and others,<br><br>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.<span class="HOEnZb"><font color="#888888"><br>
<br>Britton</font></span><div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 3:41 PM, Britton Smith <span dir="ltr"><<a href="mailto:brittonsmith@gmail.com" target="_blank">brittonsmith@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Yuan,<br><br>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.<span><font color="#888888"><br>
<br>Britton</font></span><div><div><br><br><div class="gmail_quote">On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <span dir="ltr"><<a href="mailto:yuan@astro.columbia.edu" target="_blank">yuan@astro.columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I am trying to make a simple density projection of my data using yt on<br>
kraken. I have done this successfully many times before both on kraken<br>
and other machines, but lately I have been getting errors on kraken.<br>
<br>
I tried to run it interactively and it worked, but when I submit it as<br>
a job, I get this error:<br>
<br>
P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection<br>
with default plot-center = [0.50027465<br>
8203125, 0.500335693359375, 0.499969482421875]<br>
Traceback (most recent call last):<br>
File "/var/spool/alps/8952326/try1.py", line 8, in <module><br>
profile("Feb2012/cluster_64/",imax=20)<br>
File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23,<br>
in profile<br>
File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23,<br>
in profile<br>
pc.add_projection("Density", 0)<br>
<br>
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua<br>
lization/plot_collection.py", line 758, in add_projection<br>
<br>
P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting<br>
level 0 / 8 '<br>
**field_parameters)<br>
**field_parameters)<br>
File<br>
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.<br>
egg/yt/data_objects/data_containers.py", line 1648, in __init__<br>
<br>
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_<br>
objects/data_containers.py", line 309, in _refresh_data<br>
<br>
.......<br>
<br>
<br>
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs<br>
.py", line 104, in get_memory_usage<br>
return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024<br>
ValueError: could not convert string to float: PID Uid VmSize Stat Command<br>
1 root 584 S init<br>
2 root SW [migration/0]<br>
3 root SWN [ksoftirqd/0]<br>
4 root SW [migration/1]<br>
5 roo<br>
<br>
<br>
<br>
It seems that something went wrong at "get_memory_usage", but I had<br>
never had this error before and an interactive job does not get this<br>
error either.<br>
<br>
Sorry the error message is quite messy...<br>
<br>
Yuan<br>
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</blockquote></div><br>
</div></div></blockquote></div><br>
</div></div></blockquote></div><br>