Thanks a lot Jason!
I think we've just fixed the bug. All pbsa_frc tests can now pass with
the 64-bit linux/gfortran combination. MJ will check in the fix soon ...
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
Jason Swails wrote:
> Hello,
>
> I downloaded this tarball and made 4 different installations to test
> different environments (all Linux installations are done on ubuntu 9.04 with
> csh, flex, bison, gfortran, etc. installed from software repositories):
>
> 1. Linux, intel 11.0.083 compilers, intel MKL 11
> 2. Linux, intel 11.0.083 compilers, goto
> 3. Linux, gcc 4.3.3 gfortran 4.3.3, goto
> 4. Mac OS X 10.6.2, gcc 4.2.1 gfortran 4.5.0, goto
> (I do not have intel compilers for the Mac, so I did not run those tests).
> I tested ptraj.MPI on the first two using MPICH2-1.1.0
>
> 1 and 2 passed all tests with minor deviations in some of the charge
> derivations for antechamber, but well within tolerable limits IMO. The only
> difference not using MKL was the "global minimum," yet both values were
> within the tolerable limits.
>
> 3 showed the same variations as 1 and 2, but failed dbf_1.polyALA force and
> dbf_1.polyAT force. I removed the "rm" statements in the respective run
> scripts and 'diff -y' the resulting file with the save. The first chunk,
> Atomic qE Forces, were exactly the same, but Atomic DB Forces were all
> considerably different on many occasions (well more than 10% difference in
> some occasions).
>
> 4. showed the same variations in antechamber as the first two, but failed
> much worse in the pbsa_frc section.
>
> checking argasp force
> FAILED: argasp force
> dbf_1.dadt
> checking dadt force
> FAILED: dadt force
> dbf_1.dgdc
> checking dgdc force
> FAILED: dgdc force
> dbf_1.lysasp
> checking lysasp force
> FAILED: lysasp force
> dbf_1.polyALA
> checking polyALA force
> FAILED: polyALA force
> dbf_1.polyAT
> checking polyAT force
> FAILED: polyAT force
>
> In addition to these, it also printed to TEST_FAILURES.diff some potentially
> worrisome values for EPB. I've included the polyALA.diff, polyAT.diff (test
> case 3), and TEST_RESULTS.diff (test case 4) on this email.
>
>
> On a side note, there has been a decent amount of discussion on the Amber
> mailing list with users having trouble compiling and running Amber on
> Ubuntu, and since it's a fairly popular distro due to its ease of use it may
> be helpful to keep a list of common pitfalls users run into (like not having
> csh installed by default) and which packages to install (apt-get) to fix
> it. The same could probably be said for Macs, especially with the
> architecture problems snow leopard so generously introduced. Since a large
> fraction of Amber users likely fall into one of the categories above,
> perhaps it would be useful to have some place where developers (and users?)
> could list easy fixes to common problems associated with these two platforms
> so issues don't continue to periodically circulate on the reflector. What
> do others think?
>
> All the best,
> Jason
>
> On Mon, Dec 7, 2009 at 9:53 AM, case <case.biomaps.rutgers.edu> wrote:
>
>
>> I have placed the current release candidate here:
>>
>> http://ambermd.org/downloads/AmberTools.04dec09.tar.bz2
>>
>> I think we are getting close! As usual, it is like pulling teeth to get
>> anyone to look at and update the documentation. I may have to just lock
>> all developers in a room at the January meeting and require a certain
>> number
>> of updates before allowing them out. But please make changes now if you
>> can.
>> As I have mentioned before, this is an excellent opportunity for students
>> and post-docs to gain some recognition outside their own group by
>> contributing
>> to a common project.
>>
>> ...thx...dac
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>
>
>
>
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Received on Mon Dec 07 2009 - 19:30:04 PST
