[BIOSAL] Causality and ACTION_STOP

Wed Nov 26 11:26:55 CST 2014

Ok, I think I am mostly understanding the general idea. I may need you to
walk me through this in person next week.

So I should have an ACTION_PUSH_DATA and then I can just refer to the same
variable (in my case, actors_to_greet) w/o doing an explicit unpack?

George K. Thiruvathukal, PhD
*Professor of Computer Science*, Loyola University Chicago
*Director*, Center for Textual Studies and Digital Humanities
*Guest Faculty*, Argonne National Laboratory, Math and Computer Science
Division
Editor in Chief, Computing in Science and Engineering
<http://www.computer.org/portal/web/computingnow/cise> (IEEE CS/AIP)
(w) thiruvathukal.com (v) 773.829.4872

On Wed, Nov 26, 2014 at 11:14 AM, Boisvert, Sebastien <boisvert at anl.gov>
wrote:

> > From: George K. Thiruvathukal [gkt at cs.luc.edu]
> > Sent: Wednesday, November 26, 2014 10:56 AM
> > To: Boisvert, Sebastien
> > Cc: biosal at lists.cels.anl.gov
> > Subject: Re: Causality and ACTION_STOP
> >
> >
> >
> >
> > Seb,
> >
> >
> > In your assembly code, I cannot find where the map that you packed is
> being unpacked. For completeness, I looked for all references to
> core_map_unpack in all of biosal:
> >
> >
> > mininuevo:biosal gkt$ grep core_map_unpack $(find . -name '*.[hc]')
> > ./core/structures/map.c:int core_map_unpack(struct core_map *self, void
> *buffer)
> > ./core/structures/map.h:int core_map_unpack(struct core_map *self, void
> *buffer);
> > ./genomics/data/coverage_distribution.c:        core_map_unpack(&map,
> buffer);
>
> You got it. coverage_distribution.c contains the script
> biosal_coverage_distribution.
>
>
> core_map_unpack is called when receiving ACTION_PUSH_DATA.
>
>
>
> On the sender side:
>
> Parallel code path: the message is sent here.
> assembly_graph_store.c 503
>     thorium_actor_send(self, customer, &new_message)  (with action
> specifier ACTION_PUSH_DATA,)
>
> customer is assigned here:
> assembly_graph_store.c 434
>     customer = concrete_self->customer;
>
> concrete_self->customer is set when receiving ACTION_SET_CONSUMER:
> assembly_graph_store.c 285
>         concrete_self->customer = customer;
>
>
>
>
>
> >
> > ./tests/test_map.c:        core_map_unpack(&map2, buffer);
> >
> > I can always use the example in test_map.c, but I'm trying to understand
> how your Spate code is unpacking the coverage_distribution map
>
> The sender is a "struct biosal_assembly_graph_store
> (with script "struct thorium_script biosal_assembly_graph_store_script")
> and it sends a "struct core_map" to an actor using its name.
> The sender does not know the script of the destination. It only knows its
> name.
>
> The receiver is a "struct biosal_coverage_distribution" object (with script
> "struct thorium_script biosal_coverage_distribution_script").
> It receives a "struct core_map" since the sender packed such a core_map
> anyway. Any other
> behavior for this action specifier and for this destination would cause a
> problem anyway or strange behavior.
> There is some sort of contract between the source and the destination for
> the action ACTION_PUSH_DATA.
>
> As usual, the source is free to do whatever it wants with the
> ACTION_PUSH_DATA message since it "controls
> its destiny". It could for example do nothing at all with the message and
> just reply with
> ACTION_PUSH_DATA_REPLY. This is how we get robustness.
>
> > (from assembly_graph_store.c, line 494). It would seemingly need to be
> unpacked somewhere.
>
> Yes. I agree.
>
> The answer is:
>
> coverage_distribution.c in the list you provided.
>
> >
> > George
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > George K. Thiruvathukal, PhD
> >
> > Professor of Computer Science, Loyola University Chicago
> >
> > Director, Center for Textual Studies and Digital Humanities
> > Guest Faculty, Argonne National Laboratory, Math and Computer Science
> Division
> > Editor in Chief, Computing in
> >  Science and Engineering (IEEE CS/AIP)
> >
> > (w)
> > thiruvathukal.com (v) 773.829.4872
> >
> >
> >
> >
> >
> >
> >
> >
> > On Wed, Nov 26, 2014 at 10:23 AM, Boisvert, Sebastien
> > <boisvert at anl.gov> wrote:
> >
> > > From: George K. Thiruvathukal [gkt at cs.luc.edu]
> > > Sent: Wednesday, November 26, 2014 10:11 AM
> > > To: Boisvert, Sebastien
> > > Subject: Re: Causality and ACTION_STOP
> > >
> > >
> > >
> > >
> > > Hi Seb,
> > >
> > >
> > > See below!
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Nov 26, 2014 at 10:03 AM, Boisvert, Sebastien
> > > <boisvert at anl.gov> wrote:
> > >
> > >
> > > > I am looking at spate_metagenome_assembler/spate.c but don't see any
> usage of core_map. I did see a usage of core_map in argonnite.c, but the
> map is not actually being sent in a message, AFAICT. :)
> > >
> > > Spate uses the BioSAL actor library in genomics/
> > >
> > > Check out genomics/assembly/assembly_graph_store.c line 494
> > >
> > >
> > >
> > >
> > >
> > > This looks like the magic formula! I didn't look too closely at the
> inclusion list.
> > >
> > >
> >
> > This is basically the same pattern used in thorium_actor_send_vector.
> >
> > So you can just take that as a starting point for thorium_actor_send_map.
> >
> > >
> > >     new_count =
> core_map_pack_size(&concrete_self->coverage_distribution);
> > >     new_buffer = thorium_actor_allocate(self, new_count);
> > >     core_map_pack(&concrete_self->coverage_distribution, new_buffer);
> > >
> > >     printf("SENDING %s/%d sends map to %d, %d bytes / %d entries\n",
> > >
> > >                         thorium_actor_script_name(self),
> > >                     thorium_actor_name(self),
> > >                     customer, new_count,
> > >
>  (int)core_map_size(&concrete_self->coverage_distribution));
> > >
> > >     thorium_message_init(&new_message, ACTION_PUSH_DATA, new_count,
> new_buffer);
> > >     thorium_actor_send(self, customer, &new_message);
> > >
> > >
> > >     thorium_message_destroy(&new_message);
> > >
> > >
> > >
> > >
> > > :-) Thanks!
> > >
> > >
> > >
> > >
> > > If we do thorium_message_destroy(), does it also free the underlying
> buffer?
> > >
> > > 
> > >
> >
> > No.
> >
> > thorium_message_destroy() does not free any memory because
> > thorium_message_init() does not allocate any memory neither.
> >
> > I guess this is just because I use to do more C++.
> >
> > >
> > > >
> > > >
> > > > I'm planning to add these functions to make sending/receiving maps
> easy.
> > >
> > > That a good idea. I like it.
> > >
> > >
> > >
> > > Great! I will give myself this task. I'm going to end up figuring
> everything out as part of the new version of hello_acq.c.
> > >
> > > I want maps primarily because I am mapping an actor name to its
> (boolean) status of having been greeted or not.
> >
> > This makes sense.
> >
> > Also, for your information, core_map can never be full although it uses
> a hash table for the implementation.
> >
> > Here is the hierarchy:
> >
> > - core_set is implemented on top of core_map
> > - core_map is implemented on top of core_dynamic_hash_table (dynamic
> hash table uses incremental resizing, so it can never be full and
> >                 all calls are still O(1) because of amortization.)
> > - core_dynamic_hash_table is implemented on top of core_hash_table
> (hash_table uses double hashing / open addressing)
> > - core_hash_table is implemented on top of core_hash_table_group (right
> now, there is 1 group per table, but this could be use to
> >                 implement a sparse container like in Google Sparse Hash
> Table based on Donald Knuth's algorithm for that).
> >
> > >
> > > 
> > >
> > >
> > > > Similar to your view, I think lists and maps are among the most
> important collections.
> > >
> > > There is the free_list structure, but it is only used in memory
> management right now.
> > >
> > > > I once read a paper that most of the reuse in OOP comes from lists
> and associative structures.
> > >
> > > When you say lists, does that include vector. Usually, vector means
> array and list means
> > > linked list.
> > >
> > >
> > >
> > > Yes, it does in an evolutionary sense. I tend to think of vector and
> lists as being connected. In modern programming libraries, you often see
> the interfaces conflated (i.e. lists have array-like interfaces and vice
> versa). Java Vector is kind of an interesting
> > >  case study!
> >
> > But a Java ArrayList<Integer> has O(1) random access but can trigger a
> resize of capacity on insertion which is O(n).
> >
> > A Java LinkedList<Integer> has O(n) random access but has O(1) insertion.
> >
> > Sure, both implement the List<Integer> interface, but each has a better
> use case anyway.
> >
> >
> > >
> > >
> > > TTYL,
> > > George
> > >
> > >
> > >
> >
> >
> >
> >
>
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