Hi,
I used the -I option to specify the location of the header fiels, which I
didn't know existed for the setup.py script, but now I have a new error:
login1% setenv HDF5_DIR $TACC_HDF5_DIR
login1% python setup.py build_ext -I/${MPICH_HOME}/include --inplace
* Found numpy 1.4.1 package installed.
* Found HDF5 headers at
``/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include``, library at
``/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib``.
.. WARNING:: Could not find the HDF5 runtime.
The HDF5 shared library was *not* found in the default library
paths. In case of runtime problems, please remember to install it.
* Could not find LZO 2 headers and library; disabling support for it.
* Could not find LZO 1 headers and library; disabling support for it.
* Found bzip2 headers at ``/usr/include``, library at ``/usr/lib64``.
running build_ext
building 'tables.utilsExtension' extension
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1
-I/home/01225/bbelson/local/Python-2.6.5/lib/python2.6/site-packages/numpy/core/include
-I/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include
-I//opt/apps/intel11_1/mvapich2/1.4/include
-I/home/01225/bbelson/local/Python-2.6.5/include/python2.6 -c'
extra options: '-Isrc -DH5_USE_16_API'
gcc: src/H5ATTR.c
gcc: src/utils.c
/home/01225/bbelson/local/Python-2.6.5/lib/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:
warning: '_import_array' defined but not used
gcc: src/H5ARRAY.c
/home/01225/bbelson/local/Python-2.6.5/lib/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1187:
warning: '_import_array' defined but not used
gcc: tables/utilsExtension.c
tables/utilsExtension.c: In function
'__pyx_f_6tables_14utilsExtension_loadEnum':
tables/utilsExtension.c:2699: warning: '__pyx_exc_lineno' may be used
uninitialized in this function
tables/utilsExtension.c:2653: warning: '__pyx_r' may be used uninitialized
in this function
tables/utilsExtension.c: In function
'__pyx_f_6tables_14utilsExtension_enumToHDF5':
tables/utilsExtension.c:2310: warning: '__pyx_exc_lineno' may be used
uninitialized in this function
tables/utilsExtension.c: In function
'__pyx_f_6tables_14utilsExtension_AtomToHDF5Type':
tables/utilsExtension.c:2454: warning: '__pyx_v_tid' may be used
uninitialized in this function
gcc -pthread -shared build/temp.linux-x86_64-2.6/tables/utilsExtension.o
build/temp.linux-x86_64-2.6/src/utils.o
build/temp.linux-x86_64-2.6/src/H5ARRAY.o
build/temp.linux-x86_64-2.6/src/H5ATTR.o
-L/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib
-L/home/01225/bbelson/local/Python-2.6.5/lib -lhdf5 -lpython2.6 -o
/home/01225/bbelson/local/tables-2.1.2/tables/utilsExtension.so
/usr/bin/ld:
/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib/libhdf5.a(H5.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a shared
object; recompile with -fPIC
/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib/libhdf5.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld:
/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib/libhdf5.a(H5.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a shared
object; recompile with -fPIC
/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib/libhdf5.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared
build/temp.linux-x86_64-2.6/tables/utilsExtension.o
build/temp.linux-x86_64-2.6/src/utils.o
build/temp.linux-x86_64-2.6/src/H5ARRAY.o
build/temp.linux-x86_64-2.6/src/H5ATTR.o
-L/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/lib
-L/home/01225/bbelson/local/Python-2.6.5/lib -lhdf5 -lpython2.6 -o
/home/01225/bbelson/local/tables-2.1.2/tables/utilsExtension.so" failed with
exit status 1
Thanks
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