[cctbxbb] bootstrap.py build on Ubuntu

David Waterman dgwaterman at gmail.com
Tue Jun 14 14:54:10 PDT 2016


Hi Billy

Thanks for the advice. I have come across this before on Ubuntu, where
older libraries don't work with the debian multi-arch conventions. I think
generally this is not a problem with newer packages, so for example I doubt
there would be an issue with a reasonably recent Pillow in place of PIL.

Cheers
David

On Tue, 14 Jun 2016, 21:44 Billy Poon, <bkpoon at lbl.gov> wrote:

> Hi David,
>
> Scratch the lib64z1 and lib64z1-dev packages. Apparently, those are for
> i386.
>
> For 12.04, 14.04, and 16.04, libz.so is placed in
> /usr/lib/x86_64-linux-gnu by the zlib1g-dev package. It looks like Ubuntu
> libraries are now placed in a directory named by architecture to better
> support multiple architectures on the same machine.
>
> I updated install_base_packages to supply that directory for building PIL.
> This is specific to x86_64, so this won't work on 32-bit Ubuntu. But if you
> want a 32-bit Ubuntu build, installing lib64z1-dev should work.
>
> Let me know if you have any more issues. 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, Jun 14, 2016 at 11:29 AM, David Waterman <dgwaterman at gmail.com>
> wrote:
>
>> Hey Billy,
>>
>> Thanks. I'm travelling at the moment, but once I'm back I'll give that a
>> go.
>>
>> Cheers
>> David
>>
>> On Tue, 14 Jun 2016, 17:34 Billy Poon, <bkpoon at lbl.gov> wrote:
>>
>>> Hi David,
>>>
>>> Actually, it looks like the lib64z1-dev package provides libz.so in
>>> /usr/lib64, so installing that package should fix your issue. It's a bit
>>> odd that the lib64z1 package does not provide that file.
>>>
>>> --
>>> 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 Mon, Jun 13, 2016 at 1:53 PM, Billy Poon <bkpoon at lbl.gov> wrote:
>>>
>>>> Hi David,
>>>>
>>>> I don't have a fix yet, but here is a workaround. It seems like
>>>> setup.py is looking for libz.so instead of libz.so.1, so you can fix the
>>>> issue by making a symbolic link for libz.so in /usr/lib64.
>>>>
>>>> sudo ln -s /usr/lib64/libz.so.1 /usr/lib64/libz.so
>>>>
>>>> This requires root access, so that's why it's just a workaround.
>>>>
>>>> --
>>>> 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 Sat, Jun 11, 2016 at 5:05 PM, Billy Poon <bkpoon at lbl.gov> wrote:
>>>>
>>>>> Hi David,
>>>>>
>>>>> Sorry it look so long! Setting up all the virtual machines was a time
>>>>> sink and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a
>>>>> little tricky.
>>>>>
>>>>> It looks like Ubuntu 16.04 moved its libraries around. I used apt-get
>>>>> to install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1
>>>>> file in /lib/x86_64-linux-gnu and in /usr/lib64.
>>>>>
>>>>> I have not gotten it to work yet, but I'm pretty sure this is the
>>>>> issue. I'll have to double-check 12.04 and 14.04.
>>>>>
>>>>> As for Pillow, I did test it a few months ago, but I remember there
>>>>> being API changes that will need to fixed.
>>>>>
>>>>> --
>>>>> 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 Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Billy,
>>>>>>
>>>>>> I'm replying on this old thread because I have finally got round to
>>>>>> trying a bootstrap build for DIALS out again on Ubuntu, having waited for
>>>>>> updates to the dependencies and updating the OS to 16.04.
>>>>>>
>>>>>> The good news is, the build ran through fine. This is the first time
>>>>>> I've had a bootstrap build complete without error on Ubuntu, so thanks to
>>>>>> you and the others who have worked on improving the build in the last few
>>>>>> months!
>>>>>>
>>>>>> The bad news is I'm getting two failures in the DIALS tests:
>>>>>>
>>>>>> dials/test/command_line/tst_export_bitmaps.py
>>>>>> dials_regression/test.py
>>>>>>
>>>>>> Both are from PIL
>>>>>>
>>>>>>       File
>>>>>> "/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py",
>>>>>> line 401, in _getencoder
>>>>>>         raise IOError("encoder %s not available" % encoder_name)
>>>>>>     IOError: encoder zip not available
>>>>>>
>>>>>> Indeed, from base_tmp/imaging_install_log it looks like PIL is not
>>>>>> configured properly
>>>>>>
>>>>>> --------------------------------------------------------------------
>>>>>> PIL 1.1.7 SETUP SUMMARY
>>>>>> --------------------------------------------------------------------
>>>>>> version       1.1.7
>>>>>> platform      linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32)
>>>>>>               [GCC 5.3.1 20160413]
>>>>>> --------------------------------------------------------------------
>>>>>> *** TKINTER support not available
>>>>>> *** JPEG support not available
>>>>>> *** ZLIB (PNG/ZIP) support not available
>>>>>> *** FREETYPE2 support not available
>>>>>> *** LITTLECMS support not available
>>>>>> --------------------------------------------------------------------
>>>>>>
>>>>>> Any ideas? I have zlib headers but perhaps PIL can't find them.
>>>>>>
>>>>>> On a related note, the free version of PIL has not been updated for
>>>>>> years. The replacement Pillow has started to diverge. I first noticed this
>>>>>> when Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system
>>>>>> python produced failures because it no longer supports certain deprecated
>>>>>> methods from PIL. I worked around that in r24587, but these things are a
>>>>>> losing battle. Is it time to switch cctbx over to Pillow instead of PIL?
>>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> -- David
>>>>>>
>>>>>> On 7 January 2016 at 18:12, Billy Poon <bkpoon at lbl.gov> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> Since wxPython was updated to 3.0.2, I have been thinking about
>>>>>>> updating the other GUI-related packages to more recent versions. I would
>>>>>>> probably update to the latest, stable version that does not involve major
>>>>>>> changes to the API so that backwards compatibility is preserved. Let me
>>>>>>> know if that would be helpful and I can prioritize the migration and
>>>>>>> testing.
>>>>>>>
>>>>>>> --
>>>>>>> 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 Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter at lbl.gov>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> David,
>>>>>>>>
>>>>>>>> I notice that the Pango version, 1.16.1, was released in 2007, so
>>>>>>>> perhaps it is no surprise that the latest Ubuntu does not support it.
>>>>>>>> Maybe this calls for stepping forward the Pango version until you find one
>>>>>>>> that works. I see that the latest stable release is 1.39.
>>>>>>>>
>>>>>>>> This would be valuable information for us..Billy Poon in the Phenix
>>>>>>>> group is supporting the Phenix GUI, so it might be advisable for him to
>>>>>>>> update the Pango version in the base installer.
>>>>>>>>
>>>>>>>> Nick
>>>>>>>>
>>>>>>>> Nicholas K. Sauter, Ph. D.
>>>>>>>> Computer Staff Scientist, Molecular Biophysics and Integrated
>>>>>>>> Bioimaging Division
>>>>>>>> Lawrence Berkeley National Laboratory
>>>>>>>> 1 Cyclotron Rd., Bldg. 33R0345
>>>>>>>> Berkeley, CA 94720
>>>>>>>> (510) 486-5713
>>>>>>>>
>>>>>>>> On Thu, Jan 7, 2016 at 8:54 AM, David Waterman <
>>>>>>>> dgwaterman at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi again
>>>>>>>>>
>>>>>>>>> Another data point: I just tried this on a different Ubuntu
>>>>>>>>> machine, this time running 14.04. In this case pango installed just fine.
>>>>>>>>> In fact all other packages installed too and the machine is now compiling
>>>>>>>>> cctbx.
>>>>>>>>>
>>>>>>>>> I might have enough for comparison between the potentially working
>>>>>>>>> 14.04 and failed 15.04 builds to figure out what is wrong in the second
>>>>>>>>> case.
>>>>>>>>>
>>>>>>>>> Cheers
>>>>>>>>>
>>>>>>>>> -- David
>>>>>>>>>
>>>>>>>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi folks
>>>>>>>>>>
>>>>>>>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following
>>>>>>>>>> the instructions here:
>>>>>>>>>> http://dials.github.io/documentation/installation_developer.html
>>>>>>>>>>
>>>>>>>>>> This failed during installation of pango-1.16.1. Looking
>>>>>>>>>> at pango_install_log, I see the command that failed was as follows:
>>>>>>>>>>
>>>>>>>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../..
>>>>>>>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\"
>>>>>>>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\"
>>>>>>>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED
>>>>>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include
>>>>>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2
>>>>>>>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c  -fPIC
>>>>>>>>>> -DPIC -o .libs/fribidi.o
>>>>>>>>>> In file included from fribidi.h:31:0,
>>>>>>>>>>                  from fribidi.c:28:
>>>>>>>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or
>>>>>>>>>> directory
>>>>>>>>>>
>>>>>>>>>> The file glib.h appears to be in base/include/glib-2.0/, however
>>>>>>>>>> this directory was not explicitly included in the command above, only its
>>>>>>>>>> parent. This suggests a configuration failure in pango to me. Taking a look
>>>>>>>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant
>>>>>>>>>> lines:
>>>>>>>>>>
>>>>>>>>>> configure:22227: checking for GLIB
>>>>>>>>>> configure:22235: $PKG_CONFIG --exists --print-errors
>>>>>>>>>> "$GLIB_MODULES"
>>>>>>>>>> configure:22238: $? = 0
>>>>>>>>>> configure:22253: $PKG_CONFIG --exists --print-errors
>>>>>>>>>> "$GLIB_MODULES"
>>>>>>>>>> configure:22256: $? = 0
>>>>>>>>>> configure:22304: result: yes
>>>>>>>>>>
>>>>>>>>>> but this doesn't tell me very much. Does anyone have any
>>>>>>>>>> suggestions as to how I might proceed?
>>>>>>>>>>
>>>>>>>>>> Many thanks
>>>>>>>>>>
>>>>>>>>>> -- David
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> cctbxbb mailing list
>>>>>>>>> cctbxbb at phenix-online.org
>>>>>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>
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