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

Mon Feb 8 10:15:43 PST 2010

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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