<div dir="ltr">Hi Allan,<div><br></div><div>Great!</div><div><br></div><div>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.</div><div>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),</div><div><br></div><div>a) source activate test</div><div>b) conda install ipython</div><div>c) source <cctbx installation directory>/build/setpaths_all.sh</div><div>d) libtbx.refresh</div><div><br></div><div>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).</div><div><br></div><div>Let us know if you have any other questions. Thanks!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 21, 2017 at 2:31 PM, Allan Lyckegaard <span dir="ltr"><<a href="mailto:alyckegaard@xnovotech.com" target="_blank">alyckegaard@xnovotech.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Billy,<div><br></div><div>Thanks, it works!</div><div><br></div><div>It now compiles and when adding it to the path, “source build/setpaths.sh”, it can be imported in python.</div><div><br></div><div>A few questions, though:</div><div>- 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.</div><div>- can I update any packages in my new environment without breaking cctbx? I would i.e. be wonderful to have access to ipython</div><div><br></div><div>Cheers,</div><div>Allan</div><div><br></div><div><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>******************************<wbr>**************************</div><div>Allan Lyckegaard, PhD, Scientist</div><div>Xnovo Technology ApS</div><div>Galoche Alle 15</div><div>4600 Køge</div><div>CVR: 3489 4221</div><div>Mail: <a href="mailto:alyckegaard@xnovotech.com" target="_blank">alyckegaard@xnovotech.<wbr>com</a></div><div>Mobile: <a href="tel:+45%2053%2073%2085%2081" value="+4553738581" target="_blank">+45 5373 8581</a></div><div>******************************<wbr>*************************</div><div><span style="color:rgb(128,128,128);font-family:Arial,sans-serif;font-size:x-small">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.</span></div><div><div style="word-wrap:break-word"><div><font face="Calibri, sans-serif"><font color="#808080" face="Arial, sans-serif" size="1"><br></font></font></div></div></div></div><br class="m_5477458027578247706Apple-interchange-newline"></div><br class="m_5477458027578247706Apple-interchange-newline"></div><br class="m_5477458027578247706Apple-interchange-newline"><br class="m_5477458027578247706Apple-interchange-newline">
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<br><div><blockquote type="cite"><div>On 21 Mar 2017, at 20.00, <a href="mailto:cctbxbb-request@phenix-online.org" target="_blank">cctbxbb-request@phenix-online.<wbr>org</a> wrote:</div><br class="m_5477458027578247706Apple-interchange-newline"><div><div>Send cctbxbb mailing list submissions to<br><span class="m_5477458027578247706Apple-tab-span" style="white-space:pre-wrap"> </span><a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="m_5477458027578247706Apple-tab-span" style="white-space:pre-wrap"> </span><a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/cctbxbb</a><br>or, via email, send a message with subject or body 'help' to<br><span class="m_5477458027578247706Apple-tab-span" style="white-space:pre-wrap"> </span><a href="mailto:cctbxbb-request@phenix-online.org" target="_blank">cctbxbb-request@phenix-online.<wbr>org</a><br><br>You can reach the person managing the list at<br><span class="m_5477458027578247706Apple-tab-span" style="white-space:pre-wrap"> </span><a href="mailto:cctbxbb-owner@phenix-online.org" target="_blank">cctbxbb-owner@phenix-online.<wbr>org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of cctbxbb digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Build error, bootstrap.py (Billy Poon)<br><br><br>------------------------------<wbr>------------------------------<wbr>----------<br><br>Message: 1<br>Date: Mon, 20 Mar 2017 12:38:31 -0700<br>From: Billy Poon <<a href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@lbl.gov</a>><br>To: cctbx mailing list <<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>><br>Subject: Re: [cctbxbb] Build error, bootstrap.py<br>Message-ID:<br><span class="m_5477458027578247706Apple-tab-span" style="white-space:pre-wrap"> </span><CAHmYUcY2oJp=D9w_de=<a href="mailto:S%2B%2Bfn4D9rzanB%2BzFtqU8ME9OgWmSu-Q@mail.gmail.com" target="_blank">S++<wbr>fn4D9rzanB+zFtqU8ME9OgWmSu-Q@<wbr>mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi Allan,<br><br>Your command should have installed the hdf5 dependency among the other<br>dependencies. The hdf5 dependency is required because there are functions<br>for reading image data. Was there an error in compiling HDF5? There should<br>be a log file in <cctbx installation directory>/base_tmp named<br>HDF5_install_log.<br><br>Are you using a recent version of bootstrap.py? I just tested this on macOS<br>10.12.3 with conda 4.3.11 and the command-line tools for Xcode 8.2.1. The<br>steps I followed (in a clean directory with just bootstrap.py) are,<br><br>1) conda create -n test python=2<br>2) source activate test<br>3) python bootstrap.py --with-python=`which python` --builder=cctbx<br>--nproc=8<br>4) cd build; make<br><br>The `which python` command in step 3 just returns the path for the python<br>in the "test" environment. Step 4 is just to make sure everything is<br>compiled.<br><br>Let us know if you it still does not work. Thanks!<br><br>--<br>Billy K. Poon<br>Research Scientist, Molecular Biophysics and Integrated Bioimaging<br>Lawrence Berkeley National Laboratory<br>1 Cyclotron Road, M/S 33R0345<br>Berkeley, CA 94720<br>Tel: <a href="tel:(510)%20486-5709" value="+15104865709" target="_blank">(510) 486-5709</a><br>Fax: <a href="tel:(510)%20486-5909" value="+15104865909" target="_blank">(510) 486-5909</a><br>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a><br><br>On Fri, Mar 17, 2017 at 7:27 AM, Allan Lyckegaard <<a href="mailto:alyckegaard@xnovotech.com" target="_blank">alyckegaard@xnovotech.com</a><br><blockquote type="cite">wrote:<br></blockquote><br><blockquote type="cite">Hi all,<br><br>I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my<br>Anaconda python.<br><br>When executing 'python bootstrap.py --with-python=/Users/myuser/<br>miniconda2/envs/python2/bin/<wbr>python --builder=cctbx? I get the following<br>error:<br><br>/usr/bin/c++ -o dxtbx/format/boost_python/<wbr>nexus_ext.o -c<br>-DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost<br>-Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs<br>-I/Users/myuser/Development/<wbr>cctbx/modules/boost -fPIC<br>-fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3<br>-ffast-math -I/Users/myuser/miniconda2/<wbr>envs/python2/include<br>-I/Users/myuser/Development/<wbr>cctbx/base/include<br>-I/Users/myuser/Development/<wbr>cctbx/build/include<br>-I/Users/myuser/Development/<wbr>cctbx/modules/cctbx_project<br>-I/Users/myuser/miniconda2/<wbr>envs/python2/include/python2.7<br>/Users/myuser/Development/<wbr>cctbx/modules/cctbx_project/<br>dxtbx/format/boost_python/<wbr>nexus_ext.cc<br>warning: unknown warning option '-Wno-unused-local-typedefs'<br>[-Wunknown-warning-option]<br>1 warning generated.<br>/usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined<br>dynamic_lookup dxtbx/format/boost_python/<wbr>nexus_ext.o<br>-L/Users/myuser/Development/<wbr>cctbx/base/lib -lm -lhdf5<br>ld: library not found for -lhdf5<br>clang: error: linker command failed with exit code 1 (use -v to see<br>invocation)<br>scons: *** [lib/dxtbx_format_nexus_ext.<wbr>so] Error 1<br>scons: building terminated because of errors.<br>usr+sys time: 8.69 seconds<br>wall clock time: 21.70 seconds<br>Process failed with return code 2<br><br>Any suggestions to how I solve this? I have not seen anywhere in the<br>documentation that an hdf5 installation is a prerequisite.<br><br>Cheers,<br>/Allan<br><br><br>______________________________<wbr>_________________<br>cctbxbb mailing list<br><a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/cctbxbb</a><br><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://phenix-online.org/pipermail/cctbxbb/attachments/20170320/31a93617/attachment.html" target="_blank">http://phenix-online.org/<wbr>pipermail/cctbxbb/attachments/<wbr>20170320/31a93617/attachment.<wbr>html</a>><br><br>------------------------------<br><br>______________________________<wbr>_________________<br>cctbxbb mailing list<br><a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/cctbxbb</a><br><br><br>End of cctbxbb Digest, Vol 96, Issue 3<br>******************************<wbr>********<br></div></div></blockquote></div><br></div></div><br>______________________________<wbr>_________________<br>
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