[BIOSAL] question about Thorium build options

Sun Nov 2 13:40:01 CST 2014

Yup, I got it working last night before following up! The ability to get
the exact C compiler command is precisely what the doctor ordered. I found
it by reading the man page, but thanks for following up to help me just in
case.

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
<http://www.computer.org/portal/web/computingnow/cise> (IEEE CS/AIP)
(w) gkt.tv (v) 773.829.4872

On Sun, Nov 2, 2014 at 11:42 AM, Boisvert, Sebastien <boisvert at anl.gov>
wrote:

> > From: George K. Thiruvathukal [gkt at cs.luc.edu]
> > Sent: Saturday, November 01, 2014 9:22 PM
> > To: Boisvert, Sebastien
> > Cc: biosal at lists.cels.anl.gov
> > Subject: Re: [BIOSAL] question about Thorium build options
> >
> >
> >
> >
> > 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.
>
> Actually, mpicc is just a wrapper.
>
> With MPICH:
>
> [seb at localhost biosal]$ mpicc -show
> cc -m64 -O2 -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64
> -L/usr/lib64/mpich/lib -Wl,-rpath -Wl,/usr/lib64/mpich/lib -lmpich -lopa
> -lmpl -lrt -lpthread
>
>
> With Open-MPI:
>
> [seb at localhost ~]$ mpicc -showme
> gcc -I/usr/include/openmpi-x86_64 -pthread -m64 -L/usr/lib64/openmpi/lib
> -lmpi
>
>
> You can probably set CC as gcc in CDT and add these CFLAGS to find MPICH
> or Open-MPI.
>
> >
> >
> > 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.
>
> Sure.
>
> But I don't know CDT at all.
> I use vim for software programming and gvim for email.
>
> >
> >
> > 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 (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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