Re: [AMBER-Developers] Sander parallel build broken by PBSA updates

From: Ray Luo <>
Date: Thu, 18 Feb 2016 20:07:07 -0800

Speaking of makedepend. Looks like the sander depend file is not
updated ... I got a very different file when I makedepend inside
sander. In the end, I didn't use new file since the old one still

All the best,
Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Thu, Feb 18, 2016 at 7:12 PM, Jason Swails <> wrote:
> On Thu, Feb 18, 2016 at 2:23 PM, Ray Luo <> wrote:
>> Thanks, I'm downloading your fix ...
>> Also, the python-related installation seems to mess up the dependence
>> issue whether I use single or multi-thread make ... I don't know why
>> my changes in pbsa and sander have caused this to break.
> All of the Python build commands are single rules incapable of threading
> -- they cannot bring down a parallel build due to botched dependencies
> (since there are none).  Quite often the last thing you see when parallel
> make dies is *not* the thread that died.  Once a thread dies, it waits
> until all other threads are done doing whatever they're doing, then they
> all exit with an error code.  So it may look like the last thing "make" did
> was try to build a Python package before dying, but it was almost certainly
> a different thread that died doing something else.
> You can see which make thread died by looking through the output of make --
> the thread number responsible for informational messages are typically
> labeled with something like "make [#]", where # is the thread number
> responsible for that line.
> But it sounds like everything is fixed now -- thanks Gerald!  FTR, the fix
> that Gerald did here was to label several of the new Fortran modules as
> having separate LIBPBSA objects.  Any object file that has an #ifdef
> LIBPBSA or something inside of it needs to be added to the LIBPBSA hash map
> in the makedepend script (and that makedepend script needs to be rerun to
> regenerate an updated depend file).  That will keep the dependencies for
> PBSA in order.
> Thanks,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Feb 18 2016 - 20:30:03 PST
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