Hi Matt,<br><br>I was making thin projections. Each output dataset (DD****) is about 14G. What are "multiple root level tiles"? I have 256^3 root grids...<br><br>I just submitted another job asking for more nodes. I will let you know how that goes (in two days).<br>
<br>Thanks!<br>Yuan<br><br><div class="gmail_quote">On Sat, Jul 28, 2012 at 7:24 PM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@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>
<div class="im"><br>
On Sat, Jul 28, 2012 at 6:41 PM, Yuan Li <<a href="mailto:bear0980@gmail.com">bear0980@gmail.com</a>> wrote:<br>
> Hi Britton,<br>
><br>
> Thanks for your suggestion! Now the problem has been semi-solved.<br>
><br>
> I have checked my script and I have this "module load yt/dev/", so I guess I<br>
> am using yt/dev, which is what I use on other machines.<br>
><br>
> There is indeed a problem with "slice". I had all my functions defined<br>
> inside one file called profile.py (my bad: I started with profiles and kept<br>
> adding things without changing the name of it). After I changed that file to<br>
> "yuan.py", the error I got was:<br>
> ......<br>
><br>
> Traceback (most recent call last):<br>
> File "/var/spool/alps/2362242/try1.py", line 3, in <module><br>
> import yuan as yuan<br>
> ImportError: No module named yuan<br>
> ......<br>
><br>
> So Kraken did not see my file. It did not complain before because there was<br>
> a built-in function in python called profile.<br>
><br>
> Now after I added this to my script:<br>
> import sys<br>
> sys.path.append('/lustre/scratch/yuan/Thermal09/')<br>
><br>
> Kraken could finally import my functions!<br>
><br>
><br>
> The reason why I said that it was only semi-solved is because now I am<br>
> getting "MemoryError". I will try to use more nodes, but it may never work<br>
> :).<br>
<br>
</div>What operation are you doing, and how big is your dataset? And, does<br>
your data have multiple root level tiles?<br>
<br>
-Matt<br>
<div class="HOEnZb"><div class="h5"><br>
><br>
> How many nodes do you use for each job, Britton?<br>
><br>
> Thanks!<br>
> Yuan<br>
><br>
><br>
> On Thu, Jul 26, 2012 at 6:39 PM, Britton Smith <<a href="mailto:brittonsmith@gmail.com">brittonsmith@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Hi Yuan,<br>
>><br>
>> This could be a result of using different version of yt on the two<br>
>> different platforms. Can you check and see which version of yt you're using<br>
>> on kraken? I believe there are modules for versions 2.2, 2.3, and the<br>
>> development branch on kraken.<br>
>><br>
>> Also, the variable "slice" is already used in python for something else.<br>
>> If slice is apart of your script, you may want to rename that to something<br>
>> else.<br>
>><br>
>> If your script only works on the most recent version of yt, you'll<br>
>> probably want to try to use the yt/dev module on Kraken.<br>
>><br>
>> Britton<br>
>><br>
>> On Wed, Jul 25, 2012 at 5:18 PM, Yuan Li <<a href="mailto:bear0980@gmail.com">bear0980@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi all,<br>
>>><br>
>>> I have been having trouble running yt on kraken. I am using the same<br>
>>> script that I use on trestles (where it sort of works). The issue I have on<br>
>>> kraken is that when I submit a non-interactive job, I get this error:<br>
>>> + aprun -n 12 ./try1.py --parallel<br>
>>> Traceback (most recent call last):<br>
>>> File "/var/spool/alps/2310447/try1.py", line 3, in <module><br>
>>> slice(imin=12, imax=47, width=20)<br>
>>> TypeError: slice() does not take keyword arguments<br>
>>><br>
>>><br>
>>> If I run an interactive job (./try1.py --parallel), I get this error:<br>
>>> yuan@krakenpf2:~/scratch/Thermal09> Assertion failed in file<br>
>>> /ptmp/ulib/mpt/nightly/5.2/051011/mpich2/src/mpid/cray/src/adi/mpid_init.c<br>
>>> at line 115: 0<br>
>>> aborting job:<br>
>>> (null)<br>
>>><br>
>>><br>
>>> I can run a non-parallel interactive job (./try1.py) without any problem.<br>
>>><br>
>>> My script looks like this:<br>
>>> #!/lustre/scratch/proj/sw/yt/dev/bin/python<br>
>>> from profile import *<br>
>>> slice(imin=41, imax=47, width=20)<br>
>>><br>
>>><br>
>>> Thanks!<br>
>>> Yuan<br>
>>><br>
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>><br>
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</div></div></blockquote></div><br>