[yt-users] yt install script on NICS Kraken
David A. Ventimiglia
ventimig at msu.edu
Mon May 11 15:52:47 PDT 2009
Hi Matt,
Ok, I'm getting slap-happy. The previous error message I posted was due
to me screwing up my PATH variable. Now, I get:
ventimig at kraken-pwd4(XT5):~> iyt
yt.lagos WARNING 2009-05-11 18:50:56,844 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
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
5 del require
6 __file__ = '/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt'
----> 7 execfile(__file__)
8
9
/nics/b/home/ventimig/scratch/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
19 sys.exit()
20
---> 21 ip_shell = IPython.Shell.IPShellMatplotlibWX(user_ns=namespace)
22
23 # The rest is a modified version of the IPython default profile code
/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Shell.pyc in __init__(self, argv, user_ns, user_global_ns, debug)
1116 def __init__(self,argv=None,user_ns=None,user_global_ns=None,debug=1):
1117 IPShellWX.__init__(self,argv,user_ns,user_global_ns,debug,
-> 1118 shell_class=MatplotlibMTShell)
1119 _load_pylab(self.IP.user_ns)
1120
/nics/b/home/ventimig/scratch/yt-x86_64/lib/python2.6/site-packages/IPython/Shell.pyc in __init__(self, argv, user_ns, user_global_ns, debug, shell_class)
876 wantedwxversion)
877
--> 878 import wx
879
880 threading.Thread.__init__(self)
ImportError: No module named wx
On Mon, 2009-05-11 at 15:40 -0700, David A. Ventimiglia wrote:
> 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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> > >
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