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Symbol not found: _nc_close Expected in: flat namespace #171

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
Full installation of netcdf4.2 from the beginning:

rodchenko:~ $ cd /usr/local/
rodchenko:local $ cd zlib-1.2.7/
rodchenko:zlib-1.2.7 $ sudo ./configure --prefix=/usr/local
rodchenko:zlib-1.2.7 $ sudo make check install

rodchenko:zlib-1.2.7 $ cd ../hdf5-1.8.9/
rodchenko:hdf5-1.8.9 $ sudo make clean
rodchenko:hdf5-1.8.9 $ sudo ./configure --with-zlib=/usr/local 
--prefix=/usr/local --enable-hl --enable-shared
rodchenko:hdf5-1.8.9 $ sudo make check install

rodchenko:hdf5-1.8.9 $ cd ../netcdf-4.2.1.1
rodchenko:netcdf-4.2.1.1 $ sudo CPPFLAGS=-I/usr/local/include 
LDFLAGS=-L/usr/local/lib ./configure --prefix=/usr/local --enable-netcdf-4 
--enable-shared
rodchenko:netcdf-4.2.1.1 $ sudo make check install

(NB: all tests passed)

cd to netcdf4-python directory . .
rodchenko:netCDF4-1.0.4 $ USE_NCCONFIG=1 python setup.py build
rodchenko:netCDF4-1.0.4 $ sudo  USE_NCCONFIG=1 python setup.py install
rodchenko:netCDF4-1.0.4 $ cd test/
rodchenko:test $ python run_all.py

What is the expected output? What do you see instead?
Traceback (most recent call last):
  File "run_all.py", line 1, in <module>
    import glob, os, sys, unittest, netCDF4
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 7, in <module>
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 6, in __bootstrap__
ImportError: 
dlopen(/Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tm
p/netCDF4.so, 2): Symbol not found: _nc_close
  Referenced from: /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so
  Expected in: flat namespace
 in /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so

What version of the product are you using? On what operating system?
Mac OS X version 10.7.5
rodchenko:netCDF4-1.0.4 $ python
Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:06) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin

Please provide any additional information below.
I got this to install using easy_install without incident last week and then I 
ran into the problem above, in which the linker cannot find the _nc_close, 
which I believe from other tags to mean it can't find the HDF5 libraries.  The 
output from installation suggests that it can find the libraries. Perhaps 
unrelated, but the problem began after I installed MySQLdb python library, 
which required me to change a couple environmental variables in my 
.bash_profile.  

# mySQL
PATH=/usr/local/mysql/bin:$PATH
export DYLD_LIBRARY_PATH=/usr/local/mysql/lib/
export VERSIONER_PYTHON_PREFER_64_BIT=no
export VERSIONER_PYTHON_PREFER_32_BIT=yes

I tried commenting these out and resourcing the bash profile, but the _nc_close 
error was the same.  Any ideas?

Original issue reported on code.google.com by Adam.von...@gmail.com on 9 Apr 2013 at 12:44

GoogleCodeExporter commented 9 years ago 
It's not finding the netcdf libs.  Since you did not include the full output 
produced by setup.py build, it's hard to say why.  I do suspect the setting 
DYLD_LIBRARY_PATH may be a problem - in general this is a bad idea.  Try 
starting a new shell (without setting DYLD_LIBRARY_PATH) and save the entire 
output produced by 'USE_NCCONFIG=1 python setup.py build'.  If you still get 
that error, post the output here.

Original comment by whitaker.jeffrey@gmail.com on 9 Apr 2013 at 1:34

GoogleCodeExporter commented 9 years ago 
Thanks for the advice. I started a new shell and set the DYLD_LIBRARY_PATH to 
nothing; For good measure I tried it as /usr/local, and /usr/local/mysql/lib 
with the same result as before. It seems to be finding the NC and HDF libs in 
their default locs.

rodchenko:test $ echo $DYLD_LIBRARY_PATH 

rodchenko:netCDF4-1.0.4 $ USE_NCCONFIG=1 python setup.py build
using nc-config ...
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options
running build_src
build_src
building py_modules sources
building extension "netCDF4" sources
build_src: building npy-pkg config files
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running scons
running build_scripts
rodchenko:netCDF4-1.0.4 $ sudo python setup.py install

HDF5_DIR environment variable not set, checking some standard locations ..
checking /Users/adamwolf ...
checking /usr/local ...
HDF5 found in /usr/local

NETCDF4_DIR environment variable not set, checking standard locations.. 
checking /Users/adamwolf ...
checking /usr/local ...
netCDF4 found in /usr/local
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options
running build_src
build_src
building py_modules sources
building extension "netCDF4" sources
build_src: building npy-pkg config files
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running scons
running build_scripts
running install_lib
running install_scripts
changing mode of /usr/local/bin/nc3tonc4 to 755
changing mode of /usr/local/bin/nc4tonc3 to 755
running install_egg_info
Removing /Library/Python/2.7/site-packages/netCDF4-1.0.4-py2.7.egg-info
Writing /Library/Python/2.7/site-packages/netCDF4-1.0.4-py2.7.egg-info
running install_clib
customize UnixCCompiler

rodchenko:netCDF4-1.0.4 $ cd test;  python run_all.py
Traceback (most recent call last):
  File "run_all.py", line 1, in <module>
    import glob, os, sys, unittest, netCDF4
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 7, in <module>
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 6, in __bootstrap__
ImportError: 
dlopen(/Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tm
p/netCDF4.so, 2): Symbol not found: _nc_close
  Referenced from: /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so
  Expected in: flat namespace
 in /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so

For completeness' sake, here is the output of otool as you suggested in a prior 
post. It does not appear to be linked against any of zlib/hdf/netcdf:

rodchenko:test $ otool -L 
/Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCD
F4.so
/Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCD
F4.so:
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)

Original comment by Adam.von...@gmail.com on 9 Apr 2013 at 2:27

GoogleCodeExporter commented 9 years ago 
I suspect that setup.py is not finding the nc-config script, and is falling 
back on using the NETCDF4_DIR and HDF5_DIR env vars (which are not set).  Is 
nc-config in your path?  Was it installed in /usr/local/bin?

Also, you did not delete the build directory before re-running setup.py build, 
so it didn't actually rebuild anything.

Original comment by whitaker.jeffrey@gmail.com on 9 Apr 2013 at 4:03

GoogleCodeExporter commented 9 years ago 
I tried a couple variants . . nc-config is easy enough to find:
rodchenko:~ $ which nc-config
/usr/local/bin/nc-config

I get similar messages if I use nc-config or define the NC and HDF directories 
in setup.cfg.  Here is the output.  Most intriguing is the linker warning for 
incorrect architecture; I'm not sure why that is because those libraries are 
built for X86_64, and the compile options here also for X86_64. Is the arch 
-i386 flag causing the warning?

rodchenko:netCDF4-1.0.4 $ rm -rf build/
rodchenko:netCDF4-1.0.4 $ python setup.py build
reading from setup.cfg...
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options
running build_src
build_src
building py_modules sources
building extension "netCDF4" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.macosx-10.7-intel-2.7
copying netcdftime.py -> build/lib.macosx-10.7-intel-2.7
copying netCDF4_utils.py -> build/lib.macosx-10.7-intel-2.7
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'netCDF4' extension
compiling C sources
C compiler: llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe 
-fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE 
-DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g 
-fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 
-pipe

creating build/temp.macosx-10.7-intel-2.7
compile options: '-I/usr/local/include -I/usr/local/include 
-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/num
py/core/include 
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c'
llvm-gcc-4.2: netCDF4.c
netCDF4.c: In function '__pyx_f_7netCDF4__set_att':
netCDF4.c:15677: warning: implicit conversion shortens 64-bit value into a 
32-bit value
netCDF4.c:15866: warning: implicit conversion shortens 64-bit value into a 
32-bit value
netCDF4.c: In function '__pyx_pf_7netCDF4_8Variable___init__':
netCDF4.c:26874: warning: implicit conversion shortens 64-bit value into a 
32-bit value
netCDF4.c: In function '__pyx_pf_7netCDF4_8Variable_52_put':
netCDF4.c:36814: warning: implicit conversion shortens 64-bit value into a 
32-bit value
netCDF4.c: In function '__pyx_pf_7netCDF4_8Variable_54_get':
netCDF4.c:38099: warning: implicit conversion shortens 64-bit value into a 
32-bit value
netCDF4.c: In function '__pyx_f_7netCDF4__def_compound':
netCDF4.c:41439: warning: implicit conversion shortens 64-bit value into a 
32-bit value
llvm-gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch 
x86_64 build/temp.macosx-10.7-intel-2.7/netCDF4.o -L/usr/local/lib 
-L/usr/local/lib -L/usr/local/lib -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 
-lz -o build/lib.macosx-10.7-intel-2.7/netCDF4.so
ld: warning: in /usr/local/lib/libnetcdf.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libhdf5_hl.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libhdf5.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libz.dylib, file is not of required architecture
running scons
running build_scripts
creating build/scripts.macosx-10.7-intel-2.7
copying utils/nc3tonc4 -> build/scripts.macosx-10.7-intel-2.7
copying and adjusting utils/nc4tonc3 -> build/scripts.macosx-10.7-intel-2.7
changing mode of build/scripts.macosx-10.7-intel-2.7/nc4tonc3 from 644 to 755
rodchenko:netCDF4-1.0.4 $ cd test; python run_all.py
Traceback (most recent call last):
  File "run_all.py", line 1, in <module>
    import glob, os, sys, unittest, netCDF4
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 7, in <module>
  File "build/bdist.macosx-10.7-intel/egg/netCDF4.py", line 6, in __bootstrap__
ImportError: 
dlopen(/Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tm
p/netCDF4.so, 2): Symbol not found: _nc_close
  Referenced from: /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so
  Expected in: flat namespace
 in /Users/adamwolf/.python-eggs/netCDF4-1.0.4-py2.7-macosx-10.7-intel.egg-tmp/netCDF4.so

rodchenko:test $ file /usr/local/lib/libnetcdf.dylib
/usr/local/lib/libnetcdf.dylib: Mach-O 64-bit dynamically linked shared library 
x86_64

Original comment by Adam.von...@gmail.com on 9 Apr 2013 at 12:45

GoogleCodeExporter commented 9 years ago 
This is your problem

ld: warning: in /usr/local/lib/libnetcdf.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libhdf5_hl.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libhdf5.dylib, file is not of required 
architecture
ld: warning: in /usr/local/lib/libz.dylib, file is not of required architecture

I'm not a macos expert, so I don't know what to tell you other than to install 
hdf5 and netcdf via macports (that's always worked fine for me).

Original comment by whitaker.jeffrey@gmail.com on 9 Apr 2013 at 2:15

GoogleCodeExporter commented 9 years ago 
BTW:  It looks like the libs were built 64 bit (x86_64) but your python is 32 
bit (i386). I think you can tell by doing 'file /usr/local/lib/libnetcdf.dylib'.

Original comment by whitaker.jeffrey@gmail.com on 9 Apr 2013 at 2:25

GoogleCodeExporter commented 9 years ago

Original comment by whitaker.jeffrey@gmail.com on 26 Feb 2014 at 2:04