[AMBER-Developers] Having to run configure multiple times

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 28 Jun 2012 12:46:16 -0700

Hi All,

With regards to the patch_amber.py script and configure automatically
applying bugfixes. Right now one has to always run configure twice (for a
clean tree) in order to make sure all the bugfixes are applied. This is not
obvious to most users - even I forget to do it most of the time and so only
get the first 3 AmberTools bugfixes apply and a message from patch_amber.py
saying it will quit - which makes me thing configure will quit but of course
it doesn't.

It would nice if we could figure out a workaround for this so users don't
have to worry about it. The issue is, I assume that we can't fix configure
retroactively in the release to check the return status of patch_amber.py
and we similarly can't patch patch_amber.py in an automated fashion such
that it keeps applying the bugfixes.

On idea I had that might work is to move bugfix.3 to always be the LAST
bugfix applied. This would mean moving it to the AMBER bugfixes and
continually updating it when we add new bugfixes but at least that would
work around this problem. I guess we could call it bugfix.999 so it is
always the last one (although I haven't looked at patch_amber.py to see if
it can handle gaps in the bugfix numbering.)

If we can find a reasonable way around this though I think it would be
helpful. I suspect right now that a LOT of people (I know I do it all the
time) are building their serial CPU code with just the AMBER Tools bugfixes
1 to 3 applied and it is only when they run configure again for parallel or
cuda that they actually get all the bugfixes. The issue will be when we
release the very large kepler patch shortly since I am also betting there
are a lot of people who only build the GPU code and so their serial CUDA
build from a clean tree will not get the new bugfix unless they run
configure twice.

I know Jason's wiki says to run the patch_amber.py script before configure
but since configure supposedly runs this anyway I am betting a lot of people
skip / don't know they need that additional step.

Comments or suggestions?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |

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Received on Thu Jun 28 2012 - 13:00:04 PDT
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