Re: [cctbxbb] Boost Python 1.56

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 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 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-...

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 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 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 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 [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list

[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] 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 [ [email protected] ][ 1-510-495-2506 ] --