Re: [cctbxbb] Boost Python 1.56

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 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, 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: [email protected] [cctbxbb-bounces@phenix-online .org] on behalf of Pavel Afonine [[email protected]] 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

...

Hi Pavel

These all seem sensible

If you have the original non pdf document it may be easier to

On 4/6/17 13:45, [email protected] wrote: 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

[email protected]>> 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-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.orghttps://phenix-online.org/

On Wed, Apr 5, 2017 at 8:12 AM, Charles Ballard < [email protected]mailto:[email protected]> 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) 486-5713tel:%28510%29%20486-5713

On Wed, Feb 10, 2016 at 2:41 PM, Luc Bourhis mailto:[email protected]> 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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