[BIOSAL] question about Thorium build options

Sat Nov 1 22:40:59 CDT 2014

Great news! I'm able to work with Thorium in CDT. Now I will see whether
intelligent code sensing, etc. works properly. But there is hope!

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 9:22 PM, George K. Thiruvathukal <gkt at cs.luc.edu>
wrote:

> 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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