On Wed, Jun 22, 2011 at 3:18 PM, Maria <maryamirza.gmail.com> wrote:
> Hi All,
>
> I have been trying to install AmberTools 1.5 and Amber11. And it looks
> like 21 tests on Amber11 fail and one on Ambertools. Since I am
> running the AT15_Amber11.py file, I see that some of these failures
> can be safely ignored. However, I am still looking at other failures
> which are baffling me. I am not sure if they are all benign or if i
> need to be concerned. I have tried on two different machines with el5
> xen and centOS. and gcc 4.1.2. Surprisingly, even the numerical
> differences in test outputs are exactly the same on both machines
> (e.g. for sander_pbsa_decpw)
>
> On AMBER 11, I get the following failures:
>
> "cd ncsu && ./run-serial.sh
> >>>>>>> doing 'abmd_ANALYSIS'
> >>>>>>> doing 'abmd_FLOODING'
> >>>>>>> doing 'abmd_UMBRELLA'
> >>>>>>> doing 'smd'
> diffing save/mdout with mdout
> possible FAILURE: check mdout.dif
> ==============================================================
> cat: smd.txt: No such file or directory
> diffing save/smd.txt with smd.txt
> possible FAILURE: check smd.txt.dif
> ==============================================================
> >>>>>>> doing 'pmd'
> diffing save/mdout with mdout
> possible FAILURE: check mdout.dif
> ==============================================================
> cat: pmd.txt: No such file or directory
> diffing save/pmd.txt with pmd.txt
> possible FAILURE: check pmd.txt.dif
> ==============================================================
> >>>>>>> doing 'smd2'
> diffing save/mdout with mdout
> possible FAILURE: check mdout.dif
> ==============================================================
> cat: work.txt: No such file or directory
> diffing save/work.txt with work.txt
> possible FAILURE: check work.txt.dif"
>
> On running the tests, I find that the programs are looking for
> Sander.MPI in the exe directory and fail when it is not found.
> However, I am trying to compile a serial version, why is
> nscu/run-serial.sh looking for an MPI version?
>
>
> Then, for the following tests, I am getting numerical differences
> while testing sander_pbsa_radi: (diffs are attached)
>
> diffing ./out.save/da.out.save with da.out
> possible FAILURE: check da.out.dif
> ==============================================================
> diffing ./out.save/dc.out.save with dc.out
> possible FAILURE: check dc.out.dif
> ==============================================================
> diffing ./out.save/dg.out.save with dg.out
> possible FAILURE: check dg.out.dif
> ==============================================================
> diffing ./out.save/dt.out.save with dt.out
> possible FAILURE: check dt.out.dif
> ==============================================================
> diffing ./out.save/ru.out.save with ru.out
> possible FAILURE: check ru.out.dif
> diffing ./out.save/lys.out.save with lys.out
> possible FAILURE: check lys.out.dif
> ==============================================================
> diffing ./out.save/dap.out.save with dap.out
> possible FAILURE: check dap.out.dif
>
>
> cd sander_pbsa_decpw && ./Run.pbsa_decpw
> diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw
> possible FAILURE: check mdout.pbsa_decpw.dif
>
These are known. One of the latest bugfixes for AmberTools 1.5 prints out a
message about which tests you can expect to fail (sander PBSA tests)
>
>
>
> The AmberTools test also fails due to numeric mismatch for
> 06_NAB_Nmode (and then 08 stability if amber11 is installed) test
> under mmpbsa_py ...
>
> 9c9
> < Vibrational: 58.9727 6.1650
> > Vibrational: 58.7605 3.1948
> 10c10
> < Total: 84.4176 6.1896
> > Total: 84.2055 3.2895
> 16c16
> < Vibrational: 20.2758 0.6142
> > Vibrational: 20.4811 0.1087
> 17c17
> < Total: 42.7343 0.6035
> > Total: 42.9396 0.0779
> 25c25
> < DELTA S total= 11.7271 +/- 6.3139
> > DELTA S total= 11.3173 +/- 2.8760
> ### Maximum absolute error in matching lines = 3.44e+00 at line 25 field 6
> ### Maximum relative error in matching lines = 6.75e+00 at line 17 field 3
>
These are also benign. Not sure why you're getting the issues above.
Perhaps try making sure that TESTsander is either net set at all or set to
sander.
HTH,
Jason
>
>
> I reran the Ambertools test after installing Amber 11, and now 3 tests
> fails including the 06_NAB_Nmode and 08_Stability for mmpbsa_py
> (Attached files test_Ambertools_postAmber.log/diff)
>
> The errors are numerical and seem large enough for these tests to be
> ignored. Any ideas what I might be doing incorrectly or why this is
> happening?
>
>
>
> --
> If it is to be, it's upto me.
>
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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 Wed Jun 22 2011 - 20:30:04 PDT
