[cctbxbb] Boost Python 1.56

[Billy Poon]

I can do the switch to Boost 1.56 next Wednesday now that Dials 1.5 has
been released. I'm just double-checking some other Phenix tests.

Once the update is live, bootstrap.py should delete the existing
modules/boost directory and replace it with the new one. And then scons
should recompile anything that depends on boost. If in doubt, you can
manually delete the module/boost and build directories.

--
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, Apr 6, 2017 at 9:32 AM, Billy Poon <bkpoon at lbl.gov> wrote:

> Hi James,
>
> I agree with Graeme's tests and I would add
>
> cctbx_regression.test_nightly
>
> That command is a shortcut for running the test modules for libtbx,
> boost_adaptbx, scitbx, cctbx, iotbx, dxtbx, and smtbx. The mmtbx module is
> also tested if chem_data is available. Should we add rstbx to the shortcut
> (cctbx_project/cctbx/command_line/cctbx_test_nightly.py)?
>
> --
> 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, Apr 6, 2017 at 1:37 AM, <richard.gildea at diamond.ac.uk> wrote:
>
>> I've made a start on transcribing this document here:
>>
>> https://github.com/cctbx/cctbx_project/wiki/cctbx-Developer-Guidance
>>
>> It probably still needs cleaning up a bit (e.g. I couldn't figure out
>> quickly how to do 3-level list nesting, 1.a.i etc.) and updating to reflect
>> current practice (e.g. git not svn).
>>
>> Cheers,
>>
>> Richard
>>
>> Dr Richard Gildea
>> Data Analysis Scientist
>> Tel: +441235 77 8078
>>
>> Diamond Light Source Ltd.
>> Diamond House
>> Harwell Science & Innovation Campus
>> Didcot
>> Oxfordshire
>> OX11 0DE
>>
>> ________________________________________
>> From: cctbxbb-bounces at phenix-online.org [cctbxbb-bounces at phenix-online
>> .org] on behalf of Pavel Afonine [pafonine at lbl.gov]
>> Sent: 06 April 2017 09:07
>> To: cctbx mailing list
>> Subject: Re: [cctbxbb] Boost Python 1.56
>>
>> Hi Graeme,
>>
>> hm.. this is a good question. We've been through back-and-forth
>> iterations of editing this file and I think the latest I have is from
>> Paul. But I can't find a non-PDF version of it. Paul: do you have an
>> editable version of this file?
>>
>> Thanks,
>> Pavel
>>
>> On 4/6/17 13:45, Graeme.Winter at diamond.ac.uk wrote:
>> > Hi Pavel
>> >
>> > These all seem sensible
>> >
>> > If you have the original non pdf document it may be easier to
>> transcribe this over..
>> >
>> > I also note that it lacks the actual detail on how to run tests!
>> However would be happy to add this once on wiki
>> >
>> > Best wishes Graeme
>> >
>> > On 6 Apr 2017, at 04:00, Pavel Afonine <pafonine at lbl.gov<mailto:pafon
>> ine at lbl.gov>> wrote:
>> >
>> > Not sure if that answers your questions but once upon a time we here at
>> Berkeley tried to write a some sort of document that was supposed to answer
>> questions like this. Attached. By no means it is complete, up-to-date, etc,
>> but it might be worth reading for anyone who contributes to cctbx. (Even
>> not sure if I'm sending the latest version).
>> > Unfortunately, nobody bothered to put it in some central place.
>> >
>> > Pavel
>> >
>> > On 4/6/17 10:51, James Holton wrote:
>> > Hey Billy,
>> >
>> > On a related note. How do I run these regression tests before
>> committing something into Git? Is there a document on dials regression
>> testing I can't find?
>> >
>> > -James
>> >
>> > On Apr 5, 2017, at 3:38 PM, Billy Poon <bkpoon at lbl.gov<mailto:bkpoon@
>> lbl.gov>> wrote:
>> >
>> > Hi all,
>> >
>> > I tested Boost 1.56 on our buildbot servers and got some new test
>> failures with
>> >
>> > cctbx_project/scitbx/array_family/boost_python/tst_flex.py
>> > cctbx_project/scitbx/random/tests/tst_random.py
>> >
>> > The full log for CentOS 6 can be found at
>> >
>> > http://cci-vm-6.lbl.gov:8010/builders/phenix-nightly-intel-l
>> inux-2.6-x86_64-centos6/builds/601/steps/test%20cctbx_regres
>> sion.test_nightly/logs/stdio
>> >
>> > It looks like the errors are related to random number generation. For a
>> given seed, would the sequence of numbers change when Boost is changed? I
>> did a diff between Boost 1.56 and the current Boost and could not see any
>> changes that immediately stood out as being related to random numbers.
>> >
>> > Are these tests failing for others as well?
>> >
>> > --
>> > 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<https://phenix-online.org/>
>> >
>> > On Wed, Apr 5, 2017 at 8:12 AM, Charles Ballard <
>> charles.ballard at stfc.ac.uk<mailto:charles.ballard at stfc.ac.uk>> wrote:
>> > FYI,  we (CCP4) have been using 1.56 for building cctbx/phaser/dials
>> for the last while with no issues.  Don't know about 1.60, but 1.59 causes
>> issues with the boost python make_getter and make_setter (initialisation of
>> none const reference if the passed type is a temporary).
>> >
>> > Charles
>> >
>> > On 3 Apr 2017, at 14:31, Luc Bourhis wrote:
>> >
>> > Hi all,
>> >
>> > everybody seemed to agree but then it was proposed to move straight to
>> Boost 1.60, and this caused troubles. Could we consider again to move to at
>> least 1.56? As far as I can tell, this does not cause any issue and as
>> stated one year ago, it would help me and Olex 2.
>> >
>> > Thanks,
>> >
>> > Luc
>> >
>> > On 10 Feb 2016, at 15:17, Nicholas Sauter <nksauter at lbl.gov<mailto:
>> nksauter at lbl.gov>> wrote:
>> >
>> > Nigel, Billy & Aaron,
>> >
>> > I completely endorse this move to Boost 1.56.  Can we update our build?
>> >
>> > 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<tel:%28510%29%20486-5713>
>> >
>> > On Wed, Feb 10, 2016 at 2:41 PM, Luc Bourhis <luc_j_bourhis at mac.com
>> <mailto:luc_j_bourhis at mac.com>> wrote:
>> > Hi,
>> >
>> > I have improvements to the smtbx on their way to be committed which
>> require Boost version 1.56. This is related to Boost.Threads, whose support
>> I re-activated a few months ago on Nick’s request. I need the function
>> boost::thread::physical_concurrency which returns the number of physical
>> cores on the machine, as opposed to virtual cores when hyperthreading is
>> enabled (which it is by default on any Intel machine). That function is not
>> available in Boost 1.55 which is the version currently used in the nightly
>> tests: it appeared in 1.56.
>> >
>> > So, would it be possible to move to Boost 1.56? Otherwise, I will need
>> to backport that function. Not too difficult but not thrilling.
>> >
>> > Best wishes,
>> >
>> > Luc
>> >
>> >
>> > _______________________________________________
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>> >
>> > <cctbx-developer-guidance-08-2015.pdf>______________________
>> _________________________
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>> >
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