[BIOSAL] question about Thorium build options

[George K. Thiruvathukal]

​I've mostly figured out how to get things working with CDT but it still
doesn't work. I'll keep trying tomorrow (during whatever free cycles I
have). Because we depend on mpicc to build the code, however, it makes
things much more complicated. You can't rely completely on make, except for
the building part. Most of these IDEs still want to know the underlying
toolchain. Perhaps I can trick CDT by getting mpicc to show what command it
is actually running under the hood.

Perhaps we can spend a bit of time discussing this on Wednesday. I
personally feel like I (and probably others) would be more productive if we
can use modern tools to develop Thorium programs. I'm able to do quite a
bit with vim/emacs and friends (and often prefer this once I get more
fluent with a code base) but think it would be great if we can support CDT
"out of box" so to speak.

George


Anyway, I'm going to put this on our agenda for Wednesday. I've spent a
substn​

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) gkt.tv (v) 773.829.4872


On Sat, Nov 1, 2014 at 8:52 PM, 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: Saturday, November 01, 2014 5:40 PM
> > To: biosal at lists.cels.anl.gov
> > Subject: [BIOSAL] question about Thorium build options
> >
> >
> >
> >
> > This is probably for Seb.
> >
> >
> > I have a crazy question to ask that probably has an answer of "no", but
> I'll ask anyway. Is it possible to build Thorium without MPI.
>
> Right now, this is not possible.
>
> However, there is a ticket for adding a build option to disable the
> transport subsystem.
>
> https://github.com/GeneAssembly/biosal/issues/555 (August 13, 2014)
>
> > That is, is there a way to compile/run Thorium for use on a standalone
> system (ok, my Linux box) and have the workers run as
> >  processes and all communication be done using shared memory (or Unix
> sockets)?
>
> If you run with mpiexec -n 4 with local processes, Open-MPI uses the BTL
> vader or sm by default to send messages between processes.
>
> With MPICH 3.1.1, I think poll() is used, I don't know more about that.
>
> > As an experiment, I was trying to run make CC=gcc, but I quickly ran
> into the MPI dependency when trying to build the transport, which
> presumably is hard-wired into the build process
> >  at the moment.
>
> Only thorium_node (node.c) knows about the transport. Disabling transport
> would not be too  complex I think: a couple of idef, and some conditions in
> the Makefile.mk in
> engine/thorium/.
>
> >
> >
> > In case you are wondering, I am looking at a couple of C IDEs (notably
> CodeLite, Eclipse CDT, and NetBeans).
>
> I did use Eclipse CDT for reviewing some biosal code  and I liked it. You
> can "Go to definition" and other fancy options like that.
> That's easy.
>
> > None of these projects does terribly well unless the code can compile
> directly with gcc, clang, and friends.
>
>
> A few years ago, I heard good things about kdevelop.
>
> On my side, I mostly just use vim.
>
> > I will be happy to share more details of
> >  why I'm looking into this later, but it seems like a great productivity
> enabler for Thorium if we can make it possible to work with it within an
> IDE. (There is also the Eclipse Parallel Tools Project, but I don't want to
> go down that road until it is absolutely
> >  necessary. It's kind of a heavyweight solution!)
>
> Right, I think figuring out how to invoke "make" from CDT would solve that.
>
> >
> >
> > 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
> >
> >
> >
> >
> >
> >
> >
> >
>
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