[BIOSAL] question about Thorium build options

[Boisvert, Sebastien]

> 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
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> This is probably for Seb.
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> 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/.

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> 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.

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> George
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> 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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