error when running on cluster nodes
Hi all, I run into an error which occurs when I submit a yt script to run on cluster nodes. The script runs successfully from the command line though, and I am NOT running MPI here. The error is as follows: /Traceback (most recent call last): File "MergerTree.py", line 1, in <module> from yt.mods import * File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/mods.py", line 92, in <module> from yt.visualization.api import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in <module> import artist File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in <module> from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module> from matplotlib._path import affine_transform ImportError: /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZZN2Py15PythonExtensionINS_22ExtensionModuleBasePtrEE9behaviorsEvE1p/ Apparently it is related to matplotlib. I tried to do something similar to the instructions on the wiki for CrayXT5 Installation (http://yt.enzotools.org/wiki/CrayXT5Installation) in the section 'Running on a compute node', but I still got the same error. Does anyone have ideas on what this means? I appreciate any help from you. Thanks, Tsz Ka
Hi Tsz Ka, Usually these problems are seen when you're running the wrong version of Python, or you're using some combination of C++ compilers. I think unless you're running on Compute Node Linux, following the suggestions on the XT5 Installation page may not be necessary, and I am afraid I don't recognize the machine (ppc64) you're running on. Which machine is it -- can you tell me a little more about it? And do you know if the compute nodes have a full installation stack? And can you verify you're using the correct python executable? Best, Matt On Wed, Feb 16, 2011 at 6:54 PM, Tsz Ka Li <tszkali2@illinois.edu> wrote:
Hi all, I run into an error which occurs when I submit a yt script to run on cluster nodes. The script runs successfully from the command line though, and I am NOT running MPI here. The error is as follows:
Traceback (most recent call last): File "MergerTree.py", line 1, in <module> from yt.mods import * File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/mods.py", line 92, in <module> from yt.visualization.api import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in <module> import artist File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in <module> from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module> from matplotlib._path import affine_transform ImportError: /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZZN2Py15PythonExtensionINS_22ExtensionModuleBasePtrEE9behaviorsEvE1p
Apparently it is related to matplotlib. I tried to do something similar to the instructions on the wiki for CrayXT5 Installation (http://yt.enzotools.org/wiki/CrayXT5Installation) in the section 'Running on a compute node', but I still got the same error.
Does anyone have ideas on what this means? I appreciate any help from you.
Thanks, Tsz Ka
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Hi Matt, I used the same python (~/yt-ppc64/bin/python) as I did in the command line. I think I tried python2.6 but I got the same error. (Actually how are they different?) The machine I am using is the Turing cluster in UI (http://www.cse.illinois.edu/turing/), which is an Apple Xserve cluster using G5 processors. You can find on the website some information about it. Sorry I am not that familiar with cluster issues. I suppose the nodes have full installation, though I don't know where to check. I am using the default compilers on Turing, which are gcc for C/C++ and xlf for Fortran. Thank you very much for looking into this issue for me. Cheers, Tsz Ka On 2/16/2011 10:22 PM, Matthew Turk wrote:
Hi Tsz Ka,
Usually these problems are seen when you're running the wrong version of Python, or you're using some combination of C++ compilers. I think unless you're running on Compute Node Linux, following the suggestions on the XT5 Installation page may not be necessary, and I am afraid I don't recognize the machine (ppc64) you're running on. Which machine is it -- can you tell me a little more about it? And do you know if the compute nodes have a full installation stack? And can you verify you're using the correct python executable?
Best,
Matt
On Wed, Feb 16, 2011 at 6:54 PM, Tsz Ka Li<tszkali2@illinois.edu> wrote:
Hi all, I run into an error which occurs when I submit a yt script to run on cluster nodes. The script runs successfully from the command line though, and I am NOT running MPI here. The error is as follows:
Traceback (most recent call last): File "MergerTree.py", line 1, in<module> from yt.mods import * File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/mods.py", line 92, in <module> from yt.visualization.api import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/api.py", line 34, in<module> from plot_collection import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/plot_collection.py", line 26, in<module> from matplotlib import figure File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in<module> import artist File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in<module> from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in<module> from matplotlib._path import affine_transform ImportError: /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZZN2Py15PythonExtensionINS_22ExtensionModuleBasePtrEE9behaviorsEvE1p
Apparently it is related to matplotlib. I tried to do something similar to the instructions on the wiki for CrayXT5 Installation (http://yt.enzotools.org/wiki/CrayXT5Installation) in the section 'Running on a compute node', but I still got the same error.
Does anyone have ideas on what this means? I appreciate any help from you.
Thanks, Tsz Ka
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participants (2)
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Matthew Turk -
Tsz Ka Li