Hi Jason, David
thanks for your replies. I had explicitly checked for TESTSander and
it was unset but somehow the test still failed with the MPI error. But
maybe something was messed up in the environment ... I would ignore
those for now.
I am actually concerned about mmpbsa_py tests for AmberTools which
show large deviations (I see that for NAB especially, the test does
set a relatively large relative error expecting deviations but the
diffs re quite large.)
For both 06_NAB_NMode and 08_Stability from AmberTools, here is the
output (Hoping this is also a fluke and I can ignore it)
possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
/home/msafi/amber11/AmberTools/test/mmpbsa_py/06_NAB_Nmode
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
---------------------------------------
possible FAILURE: check FINAL_RESULTS_MMPBSA2.dat.dif
/home/msafi/amber11/AmberTools/test/mmpbsa_py/08_Stability
14c14
< EPB -3256.9 15.5 10.9
> EPB -3259.1 17.6 12.5
17c17
< G solv -3189.4 15.7 11.1
> G solv -3191.6 17.9 12.6
18c18
< TOTAL -5345.3 13.1 9.2
> TOTAL -5347.4 10.9 7.7
### Maximum absolute error in matching lines = 2.20e+00 at line 14 field 2
### Maximum relative error in matching lines = 6.90e-04 at line 17 field 3
---------------------------------------
possible FAILURE: check FINAL_DECOMP_MMPBSA2.dat.dif
/home/msafi/amber11/AmberTools/test/mmpbsa_py/08_Stability
13c13
< ASP 7 | 109. +/- 3. | -6. +/- 0. | -67. +/- 1. | -96. +/-
1. | 0. +/- 0. | -60. +/- 4.
> ASP 7 | 109. +/- 3. | -6. +/- 0. | -67. +/- 1. | -96. +/- 0. | 0. +/- 0. | -61. +/- 4.
17c17
< ASP 15 | 99. +/- 2. | -4. +/- 0. | -35. +/- 1. | -124. +/-
2. | 0. +/- 0. | -65. +/- 3.
> ASP 15 | 99. +/- 2. | -4. +/- 0. | -35. +/- 1. | -125. +/- 2. | 0. +/- 0. | -66. +/- 3.
25c25
< LEU 4 | -20. +/- 0. | -4. +/- 0. | 8. +/- 0. | 2. +/-
0. | 0. +/- 0. | -14. +/- 1.
> LEU 4 | -20. +/- 0. | -4. +/- 0. | 8. +/- 0. | 2. +/- 0. | 0. +/- 0. | -13. +/- 1.
46c46
< VAL 10 | 73. +/- 3. | -4. +/- 0. | -65. +/- 1. | -7. +/-
0. | 0. +/- 0. | -3. +/- 3.
> VAL 10 | 73. +/- 3. | -4. +/- 0. | -65. +/- 1. | -7. +/- 0. | 0. +/- 0. | -4. +/- 3.
### Maximum absolute error in matching lines = 1.00e+00 at line 13 field 18
### Maximum relative error in matching lines = 1.00e+00 at line 13 field 18
---------------------------------------
Thanks again
Maria
On Thu, Jun 23, 2011 at 8:07 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jun 22, 2011, Maria wrote:
>>
>> 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?
>
> It sounds like somehow you have set the environment variable TESTsander: it
> that variable is set (say to sander.MPI) then that is what the script will
> use. See if unsetting that variable helps.
>
>> 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
>
> This looks OK. I'll be pushing for a better test in the next release, but for
> the current test, even seemingly large deviations are expected; (reasons are
> complicated here.)
>
> ....dac
>
>
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>
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Received on Thu Jun 23 2011 - 07:00:03 PDT
