[cctbxbb] Boost Python 1.56

Wed Apr 5 20:55:56 PDT 2017

To Pavel’s comment. Now that we have a new location for cctbx maybe we can add this document somewhere prominent on the web site. 

> On Apr 5, 2017, at 8:00 PM, Pavel Afonine <pafonine 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> 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
>>> 
>>> On Wed, Apr 5, 2017 at 8:12 AM, Charles Ballard <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> 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
>>>>> 
>>>>> On Wed, Feb 10, 2016 at 2:41 PM, Luc Bourhis <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
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> cctbxbb mailing list
>>>>> cctbxbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>> 
>>>>> _______________________________________________
>>>>> cctbxbb mailing list
>>>>> cctbxbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>> 
>>>> _______________________________________________
>>>> cctbxbb mailing list
>>>> cctbxbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>> 
>>> 
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>> 
>>> 
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>> 
>> 
>> _______________________________________________
>> cctbxbb mailing list
>> 
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
> 
> <cctbx-developer-guidance-08-2015.pdf>_______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]
--