Dear Jason and all,
After my tests, I have run AT15_Amber11.py, and the results are following.
Based on the results got, will you please kindly tell me which functions of my AMBER and AMBERTOOLS cannot be used fot the test failures? Does running AT15_Amber11.py gives the failures for AMBER tests and AMBERTOOLS tests? Why in the log files of the tests the failures are more than what got by AT15_Amber11.py?
If for my purpose I need to use PBSA, which should I do?
I am looking forward to getting a reply from you.
NOTE: Because PBSA has changed since Amber 11 was released, some
tests are known to fail and others are known to quit in error. These
can be safely ignored.
Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Tests that produce possible FAILUREs:
cd sander_pbsa_ipb2 && ./Run.110D.min
cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here)
cd sander_pbsa_tsr && ./Run.tsrb.min
cd sander_pbsa_decres && ./Run.pbsa_decres
mm_pbsa.pl tests 02, 03, and 05
Cheers,
Acoot
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: amber.ambermd.org
Sent: Monday, 2 April 2012 1:54 AM
Subject: Re: [AMBER] Can anyone point out whether my ambertools and amber test failures are significant
A couple notes here:
First, several PBSA tests are expected to fail in the Amber test suite.
This is due to a change between variable names in AmberTools 1.4 (which
was released with Amber 11) and AmberTools 1.5 (which was released a
year later). A full list of the failing tests can be found by running
the script AT15_Amber11.py in $AMBERHOME (alternatively, you can just
look at the script itself at the bottom).
As for the tests themselves, you can post them here, but I suggest
analyzing them yourself first. Round-off errors usually manifest
themselves in the last 1 or 2 decimal places reported. If the diffs are
greater than this, there is likely an error with that particular
functionality. Errors are more likely on Cygwin than Linux or Mac OS X
because it's tested less frequently and is really just a Unix emulator
for Windows with several limitations (e.g. a severely limited stack size
for one).
You should check the test failures and errors to make sure that the
functionality you're trying to use is properly working.
HTH,
Jason
On Sun, 2012-04-01 at 04:17 -0700, Acoot Brett wrote:
> Dear All,
>
> I just completed the amber 11 and ambertools 1.5 installation (in cygwin) and I finished the test.
>
> The summary of the ambertools test:
> 384 file comparisons passed
> 19 file comparisons failed
> 7 tests experienced errors
> Test log file saved as logs/test_at_serial/2012-04-01_19-57-50.log
> Test diffs file saved as logs/test_at_serial/2012-04-01_19-57-50.diff
>
> The summary of the amber test:
> 359 file comparisons passed
> 16 file comparisons failed
> 7 tests experienced errors
> Test log file saved as logs/test_amber_serial/2012-04-01_20-37-37.log
> Test diffs file saved as logs/test_amber_serial/2012-04-01_20-37-37.diff
>
> Currently I do not have the ability to make the conclusions on that whether the failaures are due to round errors or some other reasons, and whether the failures are significant which can influence my normal function of ambertools and amber.
>
> Thus I want to e-mail my log files and diffs files to experts or users of AMBER to make the judgment.
>
> Will you please send me an e-mail to et me know you can make this Judgment? And then I will forward the files to you for your feedback.
>
> I am looking forward to getting a reply from you.
>
> Cheers,
>
> Acoot
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 02 2012 - 21:00:05 PDT
