Re: [AMBER] amber14 parallel build problems

From: David Case <>
Date: Sun, 15 Jan 2017 13:42:00 -0500

On Sat, Jan 14, 2017, Ada Sedova wrote:
> My colleagues at the NCCS Scientific Computing group also were wondering
> why you would HAVE to build in serial first (it is not a common procedure).

The reasoning is this: Amber users potentially need all the programs
in the suite, but only a few are configured for parallel operation.
Furthermore, the parallel programs need to be compiled with mpicc/mpif90,
whereas the other codes don't need this. So it makes sense to ask
parallel users to compile both serial and parallel versions (the latter
only creates a few executables.)

But since there are some users who need only parallel programs for a
particular computer (cluster), we will try to allow for parallel-only builds
in the next release of AmberTools.

> Also, it is strange that after advising me to do this, they are also
> telling me that there is a common problem with residual files from the
> serial build interfering with the parallel build, and I should use <make
> distclean>; furthermore there is no rule for distclean, only for clean, in
> the top Makefile. Very confusing.

This is more or less inevitable in a mailing list. The Amber16 distribution's
Makefile has a "distclean" target, whereas that from Amber14 apparently does

And no, these problems are not "common". Since it is often hard to debug
problems that do arise remotely, a reasonable suggestion is to try to make
sure that we understand the environment at the remote site, hence the
suggestion to try to start from a clean environment.

> While I have your attention, I was wonder what it would take to get an
> upgrade of our site license to amber16/AmberTools16.

Please visit (Note: be sure to check your mpicc
command as I suggested earlier, or you may find the same problem with Amber16:
I'm not sure that the root cause of your problem has really been identified.
Also note that you can see if things work just with AmberTools16, since the
problem you report was with the AmberTools parallel build.)


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Received on Sun Jan 15 2017 - 11:00:02 PST
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