Hi,
To follow up, I've tested AmberTools1.5-on-top-of-Amber11 and I've run the
MTK++ examples and tests on Mac. Everything appears to be in order.
Cheers,
Martin.
On 13 Apr 2011, at 03:24, Jason Swails wrote:
> Sorry -- [tab-space] accidentally sent the unfinished email. I'll finish
> now...
>
>
>> 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, since that file significantly changed (and is no longer
> compatible). It also changes sander's and pmemd's Makefiles to adjust for
> changes to where netcdf.mod is located. If these lines are changed by
> future patches, it won't match the pattern and will just skip it (so patches
> can be made against the standard amber11-with-patches and at15-with-patches
> branches). It also gets rid of mmpbsa_py source/tests from the Amber
> directory (since it's now in AmberTools).
>
> Thus ends my endless treatise,
> Jason
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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Received on Wed Apr 13 2011 - 03:30:03 PDT
