[yt-users] Cluster Compile Issue

[Chenchong Zhu]

Hi,

I've tried a fresh install with install_script.sh with only gcc loaded; my
LD_LIBRARY_PATH only contains

/scinet/gpc/compilers/gcc-4.6.1/requiredlibs/lib:/scinet/gpc/compilers/gcc-4.6.1/lib:/scinet/gpc/compilers/gcc-4.6.1/lib64


After building, I still get the same missing libimf.so error.  An ls of the
directory you specified shows that it actually doesn't exist.  My suspicion
is the associated python module somehow compiled incorrectly, but the only
error I encountered during installation was that ZeroMQ didn't build
properly, which was solved by fixing a line in the ZeroMQ source, then
restarting install_script.bash.  This doesn't have anything to do with my
current problem, right?

Running ipython with intel loaded has its own issues, but if that's
actually easier than debugging this I can give it a go.

I've posted the output of env to past.yt-project.org.

Best,

Charles

On Fri, Jul 26, 2013 at 2:49 AM, Kacper Kowalik <xarthisius.kk at gmail.com>wrote:

> On 26.07.2013 01:25, Chenchong Zhu wrote:
> > Hi Kacper (and yt-users),
> >
> > Thanks for your response!
> >
> > I should have been more clear and said that I've only been using the yt
> > install script to do everything, and was surprised that libimf.so wasn't
> > compiled.  The full text of my error is:
> >
> > (yt-x86_64)gpc-f101n084-$ ipython
> > Traceback (most recent call last):
> >   File "/home/m/mhvk/czhu/yt-x86_64/bin/ipython", line 5, in <module>
> >     from IPython.frontend.terminal.ipapp import launch_new_instance
> >   File
> >
> "/home/m/mhvk/czhu/yt-x86_64/lib/python2.7/site-packages/IPython/__init__.py",
> > line 43, in <module>
> >     from .config.loader import Config
> >   File
> >
> "/home/m/mhvk/czhu/yt-x86_64/lib/python2.7/site-packages/IPython/config/__init__.py",
> > line 16, in <module>
> >     from .application import *
> >   File
> >
> "/home/m/mhvk/czhu/yt-x86_64/lib/python2.7/site-packages/IPython/config/application.py",
> > line 22, in <module>
> >     import logging
> >   File "/home/m/mhvk/czhu/yt-x86_64/lib/python2.7/logging/__init__.py",
> > line 26, in <module>
> >     import sys, os, time, cStringIO, traceback, warnings, weakref
> > ImportError: libimf.so: cannot open shared object file: No such file or
> > directory
>
> Hi,
> it looks like the python itself was compiled with intel. You could
> verify that by running:
>
>   cd /home/m/mhvk/czhu/yt-x86_64/lib/python2.7/lib-dynload
>   readelf -d cStringIO.so -d | grep NEEDED
>
> See if libimf.so pops there. If that's the case I think you should
> remove the python2.7* in /home/m/mhvk/czhu/yt-x86_64/src and try
> installing it again via install_script.sh. Make sure you do *not* have
> any references to intel in LD_LIBRARY_PATH.
>
> Alternatively, you could try running ipython with intel module loaded.
>
> If you could paste output 'env' on http://paste.yt-project.org/ we could
> try to find out where the intel compiler lurks ;)
>
> Cheers,
> Kacper
>
> > Best,
> >
> > Charles
> >
> > P.S. I wrote a meaningless "(though )" in my last e-mail, which was
> > supposed to report that installing ZeroMQ using install_script.bash gives
> > the error
> >
> > "stream_engine.hpp(97): error #82: storage class is not first
> >           const static size_t greeting_size = 12"
> >
> >
> > which I had to manually fix in the source to "static const", and then
> rerun
> > install_script.bash.
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
>
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