Hi, I'm trying to install pytables on a linux cluster and I do not have root access. I installed my own versions of python, numpy, and easy_install locally. Now when I try to use easy_install tables and from source (using python setup.py build_ext --inplace), I get an error. I set the env var HDF5_DIR to the right location (/opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3) beforehand. I also tried setting CFLAGS to /opt/apps/intel11_1/mvapich2/1.4/include, the location of mpi.h. The error is:
% easy_install tables Searching for tables Reading http://pypi.python.org/simple/tables/ Reading http://www.pytables.org/ Best match: tables 2.1.2 Downloading http://www.pytables.org/download/stable/tables-2.1.2.tar.gz Processing tables-2.1.2.tar.gz Running tables-2.1.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-W64JlB/tables-2.1.2/egg-dist-tmp-gXuCL9 * 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``. warning: no previously-included files matching '*' found under directory 'doc/xml' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5public.h:57:20: error: mpi.h: No such file or directory /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5public.h:59:21: error: mpio.h: No such file or directory In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:66: error: expected specifier-qualifier-list before 'MPI_Comm' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:71, from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:50: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:50: error: expected declaration specifiers or '...' before 'MPI_Info' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:51: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:52: error: expected declaration specifiers or '...' before 'MPI_Info' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:72, from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpiposix.h:46: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpiposix.h:47: error: expected declaration specifiers or '...' before 'MPI_Comm' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:99: error: expected ')' before 'mpi_off' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:100: error: expected declaration specifiers or '...' before 'MPI_Offset' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:101: error: expected ')' before 'comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:103: error: expected ')' before '*' token /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:108: error: expected declaration specifiers or '...' before 'MPI_Datatype' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:109: error: expected declaration specifiers or '...' before 'MPI_Datatype' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:115: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'H5FD_mpi_get_comm' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5public.h:57:20: error: mpi.h: No such file or directory /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5public.h:59:21: error: mpio.h: No such file or directory In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:66: error: expected specifier-qualifier-list before 'MPI_Comm' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:71, from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:50: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:50: error: expected declaration specifiers or '...' before 'MPI_Info' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:51: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpio.h:52: error: expected declaration specifiers or '...' before 'MPI_Info' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:72, from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpiposix.h:46: error: expected declaration specifiers or '...' before 'MPI_Comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpiposix.h:47: error: expected declaration specifiers or '...' before 'MPI_Comm' In file included from /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/hdf5.h:46, from src/H5ATTR.h:19, from src/H5ATTR.c:20: /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:99: error: expected ')' before 'mpi_off' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:100: error: expected declaration specifiers or '...' before 'MPI_Offset' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:101: error: expected ')' before 'comm' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:103: error: expected ')' before '*' token /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:108: error: expected declaration specifiers or '...' before 'MPI_Datatype' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:109: error: expected declaration specifiers or '...' before 'MPI_Datatype' /opt/apps/intel11_1/mvapich2_1_4/hdf5/1.8.3/include/H5FDmpi.h:115: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'H5FD_mpi_get_comm' error: Setup script exited with error: Command "gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes /opt/apps/intel11_1/mvapich2/1.4/include -fPIC -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/home/01225/bbelson/local/Python-2.6.5/include/python2.6 -c src/H5ATTR.c -o build/temp.linux-x86_64-2.6/src/H5ATTR.o /opt/apps/intel11_1/mvapich2/1.4/include -Isrc -DH5_USE_16_API" failed with exit status 1 /home/01225/bbelson/local/Python-2.6.5/lib/python2.6/site-packages/numpy/distutils/misc_util.py:248: RuntimeWarning: Parent module 'numpy.distutils' not found while handling absolute import from numpy.distutils import log I should mention that I've had similar problems on this cluster with not recognizing the location of mpi.h and other include and library folders. I get the same error message when I built from source. Is there a way to force pytables to look in particular folders for libraries and headers? Thank you
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