[yt-users] yt install script on NICS Kraken

[David A. Ventimiglia]

Hi Matt,

Thanks for the quick and detailed reply.  After swapping the PrgEnv-pgi
environment in favor of the PrgEnv-gnu env, and running the yt
install_script.sh file from the development trunk, I get a different
error on Kraken:

========================================================================
ventimig at kraken-pwd3(XT5):~/scratch> iyt
yt.lagos   WARNING    2009-05-11 18:32:13,681 No HDF4 support
/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
  from sets import Set
Traceback (most recent call last):
  File "/nics/b/home/ventimig/scratch/yt-x86_64/bin/iyt", line 7, in <module>
    execfile(__file__)
  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3, in <module>
    from yt.mods import *
  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 33, in <module>
    import yt.raven as raven
  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/raven/__init__.py", line 44, in <module>
    import matplotlib.image
  File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/image.py", line 13, in <module>
    from matplotlib import artist as martist
  File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/artist.py", line 5, in <module>
    from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath
  File "/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module>
    from matplotlib._path import affine_transform
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/matplotlib/_path.so)

Any ideas?  Thanks in advance!
Best,
David



On Mon, 2009-05-11 at 12:37 -0700, Matthew Turk wrote:
> Hi David,
> 
> Unfortunately, compiling with the PGI compilers on Kraken (unless you
> are doing a static-linking, which Stephen Skory has documented here:
> http://yt.enzotools.org/wiki/CrayXT5Installation ) is a bit of a pain.
>  I would recommend that you use gcc.  I'm afraid I don't know how to
> get the PGI compilers to work properly -- but you might be able to do
> some modification of the LD_LIBRARY_PATH to make them work.
> 
> I'd recommend that you run the install script, unmodified, after
> module swapping the PGI for GNU environments:
> 
> $ module swap PrgEnv-pgi PrgEnv-gnu
> $ bash install_script.sh
> 
> In a fresh environment, this works for me.  If you already have run
> the install script, you may have to remove your existing yt
> installation directory and run it again.  I apologize that this is a
> bit of a time-consuming task, but I believe it should work.
> 
> Good luck, and please let us know if this works!
> 
> -Matt
> 
> On Mon, May 11, 2009 at 12:34 PM, David A. Ventimiglia <ventimig at msu.edu> wrote:
> > Hello,
> >
> > I'm new to yt, so I apologize if I'm doing something dumb.  But, I'm
> > trying to install yt on Kraken and am having a little trouble.
> > install_script.sh appeared to run fine, but when I run iyt I get these
> > errors:
> >
> > yt.lagos   WARNING    2009-05-11 15:09:47,175 No HDF4 support
> > yt.lagos   WARNING    2009-05-11 15:09:47,185 No h5py. Data serialization will fail.
> > Traceback (most recent call last):
> >  File "/nics/b/home/ventimig/scratch/yt-x86_64/bin/iyt", line 7, in <module>
> >    execfile(__file__)
> >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3, in <module>
> >    from yt.mods import *
> >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 32, in <module>
> >    import yt.lagos as lagos
> >  File "/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/yt/lagos/__init__.py", line 74, in <module>
> >    import HDF5LightReader
> > ImportError: libpgc.so: cannot open shared object file: No such file or directory
> >
> > Evidently it can't find one of the Portland Group libraries, but I
> > thought all that'd be taken care of by having the PrgEnv-pgi module
> > loaded.  What am I doing wrong?  Thanks!
> >
> > Best,
> > David Ventimiglia
> > ventimig at msu.edu
> >
> >
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