Hi Allan,
Your command should have installed the hdf5 dependency among the other
dependencies. The hdf5 dependency is required because there are functions
for reading image data. Was there an error in compiling HDF5? There should
be a log file in <cctbx installation directory>/base_tmp named
HDF5_install_log.
Are you using a recent version of bootstrap.py? I just tested this on macOS
10.12.3 with conda 4.3.11 and the command-line tools for Xcode 8.2.1. The
steps I followed (in a clean directory with just bootstrap.py) are,
1) conda create -n test python=2
2) source activate test
3) python bootstrap.py --with-python=`which python` --builder=cctbx
--nproc=8
4) cd build; make
The `which python` command in step 3 just returns the path for the python
in the "test" environment. Step 4 is just to make sure everything is
compiled.
Let us know if you it still does not work. Thanks!
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Fri, Mar 17, 2017 at 7:27 AM, Allan Lyckegaard wrote: Hi all, I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my
Anaconda python. When executing 'python bootstrap.py --with-python=/Users/myuser/
miniconda2/envs/python2/bin/python --builder=cctbx’ I get the following
error: /usr/bin/c++ -o dxtbx/format/boost_python/nexus_ext.o -c
-DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost
-Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs
-I/Users/myuser/Development/cctbx/modules/boost -fPIC
-fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3
-ffast-math -I/Users/myuser/miniconda2/envs/python2/include
-I/Users/myuser/Development/cctbx/base/include
-I/Users/myuser/Development/cctbx/build/include
-I/Users/myuser/Development/cctbx/modules/cctbx_project
-I/Users/myuser/miniconda2/envs/python2/include/python2.7
/Users/myuser/Development/cctbx/modules/cctbx_project/
dxtbx/format/boost_python/nexus_ext.cc
warning: unknown warning option '-Wno-unused-local-typedefs'
[-Wunknown-warning-option]
1 warning generated.
/usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined
dynamic_lookup dxtbx/format/boost_python/nexus_ext.o
-L/Users/myuser/Development/cctbx/base/lib -lm -lhdf5
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
scons: *** [lib/dxtbx_format_nexus_ext.so] Error 1
scons: building terminated because of errors.
usr+sys time: 8.69 seconds
wall clock time: 21.70 seconds
Process failed with return code 2 Any suggestions to how I solve this? I have not seen anywhere in the
documentation that an hdf5 installation is a prerequisite. Cheers,
/Allan _______________________________________________
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