[cctbxbb] Boost Python 1.56

Billy Poon bkpoon at lbl.gov
Wed Apr 12 13:47:22 PDT 2017


Hi everyone,

Boost 1.56 is now available and the tests have been updated. To update an
existing installtion, you have to delete the "build" directory first. If
you don't, I guess some files are not recompiled with the new Boost
headers, which will cause  cctbx_project/scitbx/random/tests/tst_random.py
to expect the old values. Then run bootstrap.py with hot, update, and build
to rebuild.

cd <installation directory>
rm -fr build
python bootstrap.py hot update build --builder=cctbx

Let me know if there are any issues. Thanks!


--
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 Fri, Apr 7, 2017 at 1:08 PM, Billy Poon <bkpoon at lbl.gov> wrote:

> 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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>>> >
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>>> >
>>> > <cctbx-developer-guidance-08-2015.pdf>______________________
>>> _________________________
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>>
>>
>
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