[BIOSAL] Thorium - logging?

Tue Nov 25 17:03:28 CST 2014

This is great.

So just to be clear, do I need to set up lttng to use this new function, or
is it a completely separate idea? I may actually try using it. It's a very
cool framework.

I have since figured out what my bug actually was (in my code). So the
urgency of logging has suddenly gone down in importance.

Now I am trying to understand how to do non-local spawning. It seems like
thorium_actor_spawn() does all of its work locally, right?  Can you help me
to understand the correct way to do non-local spawning of actors without
having to pass a message to one of the initial remote actors and having it
do a local spawn?  (Sorry for asking this dumb question!)

Thanks,
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
<http://www.computer.org/portal/web/computingnow/cise> (IEEE CS/AIP)
(w) thiruvathukal.com (v) 773.829.4872

On Tue, Nov 25, 2014 at 11:48 AM, Boisvert, Sebastien <boisvert at anl.gov>
wrote:

> > From: George K. Thiruvathukal [gkt at cs.luc.edu]
> > Sent: Tuesday, November 25, 2014 10:56 AM
> > To: Boisvert, Sebastien
> > Cc: biosal at lists.cels.anl.gov
> > Subject: Re: [BIOSAL] Thorium - logging?
> >
> >
> >
> >
> > Hi Seb,
> >
> >
> > I like your idea of thorium_actor_log(). We can start with something
> simple.
>
> I added:
>
> void thorium_actor_log(struct thorium_actor *self, const char *format,
> ...);
>
>
> Usage:
>
>         thorium_actor_log(self, "processed_vertices %" PRIu64
>                         " vertices_with_unitig_flag %" PRIu64 "",
>                         concrete_self->processed_vertices,
>                         concrete_self->vertices_with_unitig_flag);
>
>
> Output (in stdout):
>
> [11:38:10.973412705] [ACTOR_LOG] biosal_unitig_manager 1000212 ...
> processed_vertices 2846919 vertices_with_unitig_flag 2842866
>
> Known bug:
>
> localtime_r does not set daylight saving time, so the time reported by
> thorium_actor_log does not have daylight saving time.
>
> > The two things I often want to log (and filter) are actor and the
> message tag (ideally, putting these toward the beginning of the log output.
>
> If you want to log and filter received messages (on the action specifier,
> destination, or source), you should really
> try LTTng. You don't need to add instrumentation, it is already there. You
> just need CONFIG_LTTNG (see build script) to enable
> instrumentation.
>
> It is actually easier than it sounds. LTTng actually has some formal proof
> in academic papers that show that
> it is correct and that the ordering of events (in nanoseconds) is
> best-in-class.
>
> Also, LTTng has a very low impact on running time because it uses the
> splice() syscall instead of the write() syscall (for printf).
>
>
>
> ./scripts/lttng/build.sh
> lttng create
> lttng enable-event -u \
>     thorium_actor:receive_enter,thorium_actor:receive_exit \
>     --filter "name == 1001563"
> lttng start
> mpiexec -n 4 ./applications/spate_metagenome_assembler/spate -k 51
> -threads-per-node 7 ~/dropbox/S.aureus.fasta.gz
> lttng stop
> lttng view > trace.txt
> llttng destroy
>
> less trace.txt
>
>
> Example of things found in trace.txt:
>
>
> [12:44:22.974332982] (+0.002822212) bigmem.biosal
> thorium_actor:receive_enter: { cpu_id = 58 }, { name = 1001563, script =
> 0xFFFFFFFFEB3B39FD, action = 0x7724, count = 41 }
> [12:44:22.974338367] (+0.000005385) bigmem.biosal
> thorium_actor:receive_exit: { cpu_id = 58 }, { name = 1001563, script =
> 0xFFFFFFFFEB3B39FD, action = 0x7724, count = 41 }
>
> The FFF in front of the script (32 bits) is a known bug in LTTng. I was
> the reporter for this bug a month ago.
>
>
> The tracepoint definition is located in the following file if you wish to
> change it (for instance, if you want to add the source and use %d instead
> of %x for the action:
>
> performance/tracepoints/lttng/actor.tp
>
> >
> >
> > 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) gkt.tv (v)
> >  773.829.4872
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Nov 25, 2014 at 9:41 AM, Boisvert, Sebastien
> > <boisvert at anl.gov> wrote:
> >
> > Just to be sure, do you want thorium_actor_log() or you are fine with
> LTTng ?
> >
> >
> > In both cases, I can take action so that you get what you need to move
> forward.
> >
> >
> > > From: George K. Thiruvathukal [gkt at cs.luc.edu]
> > > Sent: Tuesday, November 25, 2014 9:38 AM
> > > To: Boisvert, Sebastien
> > > Cc:
> > biosal at lists.cels.anl.gov
> > > Subject: Re: [BIOSAL] Thorium - logging?
> >
> > >
> > >
> > >
> > >
> > > Thanks for reminding me about this! Yes, that's exactly what I was
> hoping to find.
> > >
> > >
> > > I just don't want to be using explicit printf() statements.
> > >
> > >
> > > See you tomorrow. I am hoping to push out a new version of my
> hello_acquaintances today. :) We'll work on the paper tomorrow morning
> (among other things).
> > >
> > >
> > > 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 Tue, Nov 25, 2014 at 9:35 AM, Boisvert, Sebastien
> > > <boisvert at anl.gov> wrote:
> > >
> > > > From:
> > >
> > biosal-bounces at lists.cels.anl.gov [biosal-bounces at lists.cels.anl.gov]
> on behalf of George
> > >  K. Thiruvathukal [gkt at cs.luc.edu]
> > > > Sent: Tuesday, November 25, 2014 9:12 AM
> > > > To:
> > >
> > biosal at lists.cels.anl.gov
> > > > Subject: [BIOSAL] Thorium - logging?
> > > >
> > > >
> > > >
> > > >
> > > > Quick Thorium question...
> > > >
> > > >
> > > > Is there any sort of logging framework for Thorium?
> > >
> > > There are the LTTng tracepoints, and some "custom" tracepoints. LTTng
> is very useful to trace race conditions.
> > >
> > > There are already instrumentation for events such as
> thorium_actor:receive_enter.
> > >
> > >
> > > > Owing to a bit of a bug, I am suddenly seeing the need for a way to
> log distributed events (in example/application-oriented codes).
> > >
> > > If the ordering of these distributed events is important, than LTTng
> is the tool to use in my opinion.
> > >
> > > For any message that is received, there is a tracepoint event already
> instrumented.
> > >
> > > >
> > > >
> > > > In the simplest form, something like a log(format, args) would do
> the trick. What I would like is some way to prefix the output with the
> actor name (number) so I could filter out various logging events.
> > >
> > > In your case, I suppose that this could work for you:
> > >
> > > thorium_actor_log(self, format, args);
> > >
> > > example:
> > >
> > > thorium_actor_log(self, "foo = %d bar= %d", 42, 99);
> > >
> > > which would print
> > >
> > > [LOG] 2014-11-24T21:14:29+00:00 my_cool_actor_script/1234 says: foo=
> 42 bar= 99
> > >
> > > The first iteration of that would write to stdout, if that's all right
> with you.
> > >
> > >
> > >
> > > >
> > > >
> > > > Best,
> > > > 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
> > > >
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