[cctbxbb] Boost Python 1.56

Thu Apr 6 09:32:59 PDT 2017

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-
> linux-2.6-x86_64-centos6/builds/601/steps/test%20cctbx_
> regression.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:nksau
> ter 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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