Hi Allan, Great! 1) You should not have to create a new environment. Maybe you had a conflict somewhere and HDF5 failed to compile. I generally build in clean environments and then add things as needed. 2) You can add (or update) more packages to the cctbx environment, but I'm not sure of any incompatibilities. iPython should work fine and has been tested. Here are the steps (assuming the "test" environment has cctbx installed), a) source activate test b) conda install ipython c) source <cctbx installation directory>/build/setpaths_all.sh d) libtbx.refresh You should have a new command called "libtbx.ipython" that starts the iPython interpreter with the cctbx bits. The ipython command, by itself, will not have the correct paths set for importing cctbx modules (libtbx.ipython just sets a bunch of environment variables before starting ipython). Let us know if you have any other questions. 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 Tue, Mar 21, 2017 at 2:31 PM, Allan Lyckegaard

wrote:

Hi Billy,

Thanks, it works!

It now compiles and when adding it to the path, “source build/setpaths.sh”, it can be imported in python.

A few questions, though: - is it necessary to create a new conda environment to make it work? My first try where I got the error was in an existing environment. - can I update any packages in my new environment without breaking cctbx? I would i.e. be wonderful to have access to ipython

Cheers, Allan

******************************************************** Allan Lyckegaard, PhD, Scientist Xnovo Technology ApS Galoche Alle 15 4600 Køge CVR: 3489 4221 Mail: [email protected] Mobile: +45 5373 8581 <+45%2053%2073%2085%2081> ******************************************************* The information in this email, including any attachments, is confidential and intended only for the recipient(s) listed. Any use of this email for any other purpose is prohibited. If you have received this email in error, please notify me immediately by reply email, delete this email, and do not disclose its contents to anyone.

On 21 Mar 2017, at 20.00, [email protected] wrote:

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Today's Topics:

1. Re: Build error, bootstrap.py (Billy Poon)

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Message: 1 Date: Mon, 20 Mar 2017 12:38:31 -0700 From: Billy Poon To: cctbx mailing list Subject: Re: [cctbxbb] Build error, bootstrap.py Message-ID: Content-Type: text/plain; charset="utf-8"

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 < [email protected]

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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