[cctbxbb] cctbxbb Digest, Vol 96, Issue 3

Billy Poon bkpoon at lbl.gov
Tue Mar 21 16:28:41 PDT 2017


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 <alyckegaard at xnovotech.com
> 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: alyckegaard at xnovotech.com
> 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, cctbxbb-request at phenix-online.org wrote:
>
> Send cctbxbb mailing list submissions to
> cctbxbb at phenix-online.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://phenix-online.org/mailman/listinfo/cctbxbb
> or, via email, send a message with subject or body 'help' to
> cctbxbb-request at phenix-online.org
>
> You can reach the person managing the list at
> cctbxbb-owner at phenix-online.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of cctbxbb digest..."
>
>
> Today's Topics:
>
>   1. Re: Build error, bootstrap.py (Billy Poon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 20 Mar 2017 12:38:31 -0700
> From: Billy Poon <bkpoon at lbl.gov>
> To: cctbx mailing list <cctbxbb at phenix-online.org>
> Subject: Re: [cctbxbb] Build error, bootstrap.py
> Message-ID:
> <CAHmYUcY2oJp=D9w_de=S++fn4D9rzanB+zFtqU8ME9OgWmSu-Q at mail.gmail.com>
> 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 <
> alyckegaard at xnovotech.com
>
> 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
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/
> 20170320/31a93617/attachment.html>
>
> ------------------------------
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
> End of cctbxbb Digest, Vol 96, Issue 3
> **************************************
>
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20170321/6fbc9c96/attachment-0001.htm>


More information about the cctbxbb mailing list