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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">HI Luc<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Re:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal">But you seem to want to write a Python interface to Boost::Thread. First, I would advise against that. I don’t see any need for it but please feel free to convince me otherwise!! <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nope thought had not occurred to me!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Our use case is to split into threads in C++ land and rejoin still in C++ land, to make the C++ code exercise more cores sharing one address space / one set
of input read-only data objects.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We may gather inputs in Python land, but that is a different problem<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Still, I can see no reason not to start using boost threading here…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers Graeme<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Luc Bourhis<br>
<b>Sent:</b> 28 September 2017 08:46<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] Should we enable boost threads in bootstrap?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 27 Sep 2017, at 09:21, <a href="mailto:Graeme.Winter@Diamond.ac.uk">
Graeme.Winter@Diamond.ac.uk</a> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In principle boost threads is all we need – if we *<b>are</b>* calling back from Python then I imagine it would be something like:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">at start of block: read data in Python (as hack)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">split of threads, do many calculations</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">join threads</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">move to next block</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I would hope that anyone who has decided to use threads and uses Python has heard of the GIL, so the fact that this can be a problem should not block us from
enabling boost threads</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Well, the standard cctbx pattern goes as follow.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">From the Python side, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">from scitbx.array_family import flex<o:p></o:p></p>
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<p class="MsoNormal">py_arr = flex.double((1,2,3,4))<o:p></o:p></p>
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<p class="MsoNormal">some_function(a)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">and then on the C++ side,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">void some_function(af::const_ref<double, grid_type> const &scitbx_arr) {<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>// work on scitbx_arr<o:p></o:p></p>
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<p class="MsoNormal">} <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The C++ code does not call back into the Python interpreter here. There are two separate reference counting: one for the Python object py_arr and one for the C++ handle scitbx_arr. For example, even if py_arr disappears after the call `some_function(a)`,
scitbx_arr will not go away because the reference counter of the data underneath is unaffected and it is not zero by construction of the automatic conversions performed through the Boost::Python bridge.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The only way something can go wrong is if from the C++ `some_function`, one does explicitly call into the C API of the Python interpreter, or it’s Boost::Python interface. There are hardly any place like that. I can think of the bridge
between Python and C++ I/O I wrote in boost_adaptbx but of nothing else actually. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Note of course that if we use Boost::Thread only in `some_function`, breaking the work into blocks in there and distributing it to thread, this is the end of the discussion.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">But you seem to want to write a Python interface to Boost::Thread. First, I would advise against that. I don’t see any need for it but please feel free to convince me otherwise!! <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">But for the sake of discussion, let’s see whether this can be done. I guess you (when I say you, I don’t mean you Graeme in particular) want to be able to use it like so, on the Python side,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">for block_index in xrange(…):<o:p></o:p></p>
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<p class="MsoNormal"> thread_me(some_function, py_arr, block_index, block_index + block_size)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">and on the C++ side,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">void some_function(af::const_ref<double, grid_type> const &scitbx_arr, unsigned int block_start, unsigned int block_end) {<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>// work on the block<o:p></o:p></p>
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<p class="MsoNormal">}<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">where `some_function` would be auto-magically run in its own thread. The issue here is how to pass the function from Python to C++. Is it possible to write a `thread_me` with the following signature and then have wrap it with Boost::Python?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">typedef void (*worker_type)(af::const_ref<double, grid_type> const &scitbx_arr, unsigned int block_start, unsigned int block_end);<o:p></o:p></p>
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<p class="MsoNormal">void thread_me(worker_type const f) {<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>// fire a Boost::Thread and execute f in it<o:p></o:p></p>
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<p class="MsoNormal">}<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I would not think so. So dead end I would say.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Luc<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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