On Tue, Apr 12, 2011 at 6:12 PM, case <case.biomaps.rutgers.edu> wrote:
> > On Tue, Apr 12, 2011, Martin Peters wrote:
> > >
> > > Is the following recipe ok for final testing?
>
> Sorry: looks like my earlier reply was wrong, since I think I misunderstood
> what you were proposing (or I was just too tired.)
>
> > > % git clone gitosis.git.ambermd.org:amber.git amber11
> > > % git checkout amber11-with-patches
> > > % csh mkrelease [ "./mkrelease" would be better]
> > > % cd .. ; mkdir RC ; cd RC
> > > % mv ../Amber11.12apr11.tar.bz2 .
> > > % bunzip Amber11.12apr11.tar.bz2 ; tar -xvf Amber11.12apr11.tar
> > > % wget http://ambermd.org/downloads/AmberTools.10apr11.tar.bz2
> > > % bunzip AmberTools.10apr11.tar ; tar -xvf AmberTools.10apr11.tar
> > > ... configure/build/test...
>
> The above *should* work (assuming the the current "mkrelease" script
> still reflects what was done a year ago. (A quick look at the git log
> suggests that this is the case.)
>
> This tests the AmberTools1.5-on-top-of-Amber11 scenario, which is probably
> not
> tested enough. So, yes, please try the above. Apologies for the earlier
> mis-post.
>
I don't know if I've reported this at all, but I've tried this combination
with every release candidate that you've made to make sure that it works.
I've tested it with
Mac OS X 10.6 + GNU 4.4 [ ./configure -macAccelerate {-mpi} gnu ]
Ubuntu Linux + Intel 11.1.069 (+CUDA) [ ./configure {-mpi &| -cuda} intel ]
Athena Cray XT 4 + PGI 10.6 [ ./configure -crayxt5 {-mpi} pgi ]
and it compiles successfully. I've always unpacked a fresh amber11 copy and
applied the bug fixes to AT 1.5 + Amber 11. Some of the patches fail, but
that's because some of the CUDA patches had to modify configure, which is
part of AmberTools. These patches just miss completely, though, and create
a configure.rej and configure.orig, leaving configure alone. This may panic
some users, but I don't see how that's avoidable.
Also, many of the sander+pbsa tests will fail with numerical differences due
to changes in PBSA, but I don't see how that's avoidable either (and that's
beyond the ability of AT15_Amber11.py to deal with unless you want to just
turn those tests off completely).
The most serious issues come from several PBSA tests that result from (I
think) a removed namelist variable (I'm not sure which namelist; &cntrl or
&pb):
cd sander_pbsa_frc && ./test
dbf_0.argasp
forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
5, file
/home/swails/newamber/fusion/amber11/test/sander_pbsa_frc/dbf_0/argasp/
min.in, line 10, position 29
Image PC Routine Line
Source
libintlc.so.5 00002AD3E34A6B1D Unknown Unknown Unknown
libintlc.so.5 00002AD3E34A5625 Unknown Unknown Unknown
libifcore.so.5 00002AD3E2CF4D4C Unknown Unknown Unknown
...
(All of the tests in this directory failed; these I can turn off in
AT15_Amber11.py if that's desired.)
Conspicuously absent from my list of tests: sander.PUPIL and sander.APBS.
However, sander.APBS works just fine with Amber11 and the git tree as of a
couple months ago, so I don't expect any issues on that front. Also, I've
never tested trying to extract AmberTools 1.5 on top of a dirty AmberTools
1.4 + Amber 11 directory. I *think* for the most part that AmberTools 1.5
will just overwrite all of the files that are actually used in AmberTools
1.4, so it'll work just fine, but I can't say that with 100% certainty.
A final note on AT15_Amber11.py. The *most* work it does is on the config.h
>
> ...dac
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 12 2011 - 19:00:03 PDT
