[yt-users] yt1.6 compilation errors on Steele-Purdue

Matthew Turk matthewturk at gmail.com
Mon Feb 8 10:56:04 PST 2010 

Shankar,

Yes.

I think at this point it would be most efficient to take up any  
further installation issues with the Steele help desk. Any subsequent  
installation issues with yt that you believe are the result of issues  
with yt and not the underlying software stack (python, h5py, etc) can  
be sent to me privately, not the mailing list.

The process of installing the software stack can be tricky. The  
installation script has done its job for many users, and I'm sorry you  
were not one of them; I've used several of the problems you have  
raised to improve it. However, this level of detail coupled with this  
fine-grained of an approach to installation is not appropriate for  
this venue.

Good luck,

Matt


On Feb 8, 2010, at 10:15 AM, "Agarwal, Shankar" <sagarwal at ku.edu> wrote:

> Hi,
>
> I contacted Steele helpdesk regarding yt1.6 installation issues,  
> they say ...
>
> "We already have Python 2.5, HDF5 1.8, NumPy, MatPlotLib, and h5py  
> currently
> installed on Steele(via modules) so it might be less work to try and  
> install yt1.6
> using what is already installed instead of using the install_script.sh
> to try and install all of it locally in your home (as long as yt1.6  
> will work with
> the versions we already have installed.)"
>
>
> Is it possible that yt1.6 use the already installed dependencies ?
>
> Shankar
>
>
> -----Original Message-----
> From: yt-users-bounces at lists.spacepope.org on behalf of Agarwal,  
> Shankar
> Sent: Mon 2/8/2010 10:33 AM
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] yt1.6 compilation errors
>
> Hi, While building yt1.6 on Steele, I get 3 failure messages and a  
> lot of failed messages...
>
>
> compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ba01/ 
> u118/agarwa23/enzo/src/yt/doc/yt-x86_64/include/python2.6 -c'
> gcc: _configtest.c
> gcc _configtest.o -o _configtest
> _configtest.o: In function `main':
> /home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/src/numpy-1.3.0/ 
> _configtest.c:5: undefined reference to `exp'
> collect2: ld returned 1 exit status
> _configtest.o: In function `main':
> /home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/src/numpy-1.3.0/ 
> _configtest.c:5: undefined reference to `exp'
> collect2: ld returned 1 exit status
> failure.
> removing: _configtest.c _configtest.o
> C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall - 
> Wstrict-prototypes -fPIC
>
> compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ba01/ 
> u118/agarwa23/enzo/src/yt/doc/yt-x86_64/include/python2.6 -c'
> gcc: _configtest.c
> gcc _configtest.o -lm -o _configtest
> _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
>
>
>
> C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall - 
> Wstrict-prototypes -fPIC
>
> compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ba01/ 
> u118/agarwa23/enzo/src/yt/doc/yt-x86_64/include/python2.6 -c'
> gcc: _configtest.c
> gcc _configtest.o -o _configtest
> _configtest
> failure.
>
>
> C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall - 
> Wstrict-prototypes -fPIC
>
> compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ba01/ 
> u118/agarwa23/enzo/src/yt/doc/yt-x86_64/include/python2.6 -c'
> gcc: _configtest.c
> gcc _configtest.o -o _configtest
> _configtest
> failure.
>
>
> creating .libs/testhdf5S.c
> generating symbol list for `testhdf5'
> sort: open failed: +2: No such file or directory
> (cd .libs && gcc -c -fno-builtin "testhdf5S.c")
> rm -f .libs/testhdf5S.c .libs/testhdf5.nm .libs/testhdf5.nmS .libs/ 
> testhdf5.nmT
> gcc .libs/testhdf5S.o -ansi -O0 -fomit-frame-pointer -finline- 
> functions -o .libs/testhdf5 testhdf5.o tarray.o tattr.o tconfig.o  
> tfile.o tgenprop.o th5s.o tcoords.o theap.o titerate.o tmeta.o  
> tmisc.o trefer.o trefstr.o tselect.o tskiplist.o ttime.o ttst.o  
> tvltypes.o tvlstr.o  ./.libs/libh5test.so -L/home/ba01/u118/agarwa23/ 
> enzo/src/yt/doc/yt-x86_64/lib/ -L/home/ba01/u118/agarwa23/enzo/src/ 
> yt/doc/yt-x86_64/lib64/ ../src/.libs/libhdf5.so -lz -lm  -Wl,--rpath  
> -Wl,/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64//lib -Wl,-- 
> rpath -Wl,/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib64/ - 
> Wl,--rpath -Wl,/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib/
> creating testhdf5
>
>
>
>
>
>
> Could they be the reason for with the following...
>
> [agarwa23 at tg-steele ~]$ python
> Python 2.6.3 (r263:75183, Feb  8 2010, 10:48:42)
> [GCC 4.4.0] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from yt.mods import *
> yt.lagos   INFO       2010-02-08 11:19:35,117 No HDF4 support
> yt.lagos   WARNING    2010-02-08 11:19:35,256 No h5py. Data  
> serialization disabled.
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/autohome/u118/agarwa23/enzo/src/yt/yt/mods.py", line 32, in  
> <module>
>    import yt.lagos as lagos
>  File "/autohome/u118/agarwa23/enzo/src/yt/yt/lagos/__init__.py",  
> line 47, in <module>
>    from yt.arraytypes import *
>  File "/autohome/u118/agarwa23/enzo/src/yt/yt/arraytypes.py", line  
> 30, in <module>
>    import numpy as na
>  File "/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib/ 
> python2.6/site-packages/numpy/__init__.py", line 130, in <module>
>    import add_newdocs
>  File "/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib/ 
> python2.6/site-packages/numpy/add_newdocs.py", line 9, in <module>
>    from lib import add_newdoc
>  File "/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib/ 
> python2.6/site-packages/numpy/lib/__init__.py", line 13, in <module>
>    from polynomial import *
>  File "/home/ba01/u118/agarwa23/enzo/src/yt/doc/yt-x86_64/lib/ 
> python2.6/site-packages/numpy/lib/polynomial.py", line 11, in <module>
>    import numpy.core.numeric as NX
> AttributeError: 'module' object has no attribute 'core'
>
>
>
> Any help would be great. My python is working fine. Only when it  
> comes to importing modules, it can't find them.
>
> I had a successfully running yt1.5. Then I decided to update it. But  
> I get the above errors. I removed my older yt1.5 and checked out a  
> brand new yt1.6. But get the same errors. Thanks Matt, for helping  
> with this earlier.
>
> Shankar
>
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