yt install script on NICS Kraken
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@msu.edu
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
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@msu.edu
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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
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@msu.edu
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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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@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@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
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@msu.edu
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi David,
So what it's trying to do is import the WX GUI toolkit; I think this
is probably not going to work on Kraken, even if you set the
appropriate variable in the install script to 1. (On many other
systems, however, it will work.) What this will mean is that for the
most part, interactive display of plots may not work -- I will run
some tests to see if WX can be installed on Kraken, which would fix
this and allow for windows to pop up, etc etc.
What I've done for now is commit a new version of the iyt script that
will fall back on a basic matplotlib shell if wx can't be found. I've
committed this in r1301 ( http://yt.enzotools.org/changeset/1301 )
which you can get either by svn upping in the src/yt-svn-trunk
directory or simply re-running the install script (it will not
overwrite existing installations.)
Please let me know if this doesn't work!
-Matt
On Mon, May 11, 2009 at 3:52 PM, David A. Ventimiglia
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@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@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
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@msu.edu
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Hi Matt, That worked like a charm. Thanks! Best, David On Mon, 2009-05-11 at 16:04 -0700, Matthew Turk wrote:
Hi David,
So what it's trying to do is import the WX GUI toolkit; I think this is probably not going to work on Kraken, even if you set the appropriate variable in the install script to 1. (On many other systems, however, it will work.) What this will mean is that for the most part, interactive display of plots may not work -- I will run some tests to see if WX can be installed on Kraken, which would fix this and allow for windows to pop up, etc etc.
What I've done for now is commit a new version of the iyt script that will fall back on a basic matplotlib shell if wx can't be found. I've committed this in r1301 ( http://yt.enzotools.org/changeset/1301 ) which you can get either by svn upping in the src/yt-svn-trunk directory or simply re-running the install script (it will not overwrite existing installations.)
Please let me know if this doesn't work!
-Matt
On Mon, May 11, 2009 at 3:52 PM, David A. Ventimiglia
wrote: 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@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@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
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@msu.edu
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participants (2)
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David A. Ventimiglia
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Matthew Turk