[BIOSAL] Causality and ACTION_STOP

Wed Nov 26 11:14:08 CST 2014

> 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
> >
> >
> >
> 
> 
> 
> 