Re: Changing functions without recompiling

From: Cole Gleason (
Date: Mon Oct 18 2010 - 21:24:01 CDT

On Mon, Oct 18, 2010 at 8:20 PM, Nicholas Musolino <> wrote:
> Alex K. has provided some super-helpful information, as always, about using tabulated potential functions.
> I just wanted to check in and ask, are you sure that you (and your professor) are on the same page about what it takes to recompile NAMD?  It's possible he's used to bigger (more complicated) software projects that spend a very long while for compile time.

I think this might be the case. I wasn't sure that I would even have
to recompile all of it. Hopefully asking him to go this route won't
break his heart, as he seems kind of attached to this function parser
for some reason.

> I have found that compiling NAMD take a couple of minutes after a "make clean," and only half a minute (or less) after modifying one or two source files.  This is with serial compiling, not with multiple CPUs.
> The GNU make utility, which NAMD uses, will recompile only the changed source code (to make one .o object file for each .C source file) and then link all of the relevant files.

So if I go this route, it would just be a 'make clean', 'make', and
'make install' sequence? If that is the case, then it isn't that bad.

> Anyways, Axel's response is probably better if you want to record a version of the potential you're using for each simulation, and there will be 1 "special" potential for each simulation.  But if you want to include new terms and then run many simulations, recompiling shouldn't present any special barriers.

This also seems like an interesting route, as I want other members of
the team to be able to edit functions, but I don't need them to be
recompiling code. Do you know if there are any good tutorials
regarding this?

> Hope this helps!
> Nicholas
> PS.  I think it's awesome you're able to manage small cluster as a high school student... we're a group of half a dozen computational scientists/engineers and we're still trying to figure that out.


Cole Gleason
Student, Marmion Academy

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