[AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py

From: Maria <maryamirza.gmail.com>
Date: Wed, 22 Jun 2011 17:18:47 -0400

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

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 ...

< Vibrational: 58.9727 6.1650
> Vibrational: 58.7605 3.1948
< Total: 84.4176 6.1896
> Total: 84.2055 3.2895
< Vibrational: 20.2758 0.6142
> Vibrational: 20.4811 0.1087
< Total: 42.7343 0.6035
> Total: 42.9396 0.0779
< 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

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

If it is to be, it's upto me.

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Received on Wed Jun 22 2011 - 14:30:03 PDT
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