Re: [AMBER-Developers] EVB test errors

From: Kim F. Wong <kimberlyyellow.gmail.com>
Date: Thu, 01 Apr 2010 22:04:46 -0400

Dan,

Thanks for your help. I made a patch (see attached) earlier today & was
running the tests. Although I've verified that the patch works, I would
appreciate it if you can test it at your end before committing to the RC.

-Kim

On 4/1/2010 6:18 PM, Daniel Roe wrote:
> Hi All,
>
> This is regarding the previously discussed EVB test cases that segfault:
>
> cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF&& ./Run.evb
> cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF&& ./Run.evb
>
> I have made some modifications to the code that constitute a partial fix,
> but I can't proceed further without input from EVB people.
>
> These tests can both be protected from segfaults by making the loop at line
> 148 in pimd_force.f that references dmdlm dependent on the value of itimass
> (which is what triggers the init of dmdlm), e.g.
>
> pimd_force.f
> 148c148
> < if( i_qi> 0 ) then
> ---
>
>> if( i_qi> 0 .and. itimass> 0) then
>>
> At this point the tests will run but the output energies don't match at all.
> I was able to find a version of amber10 (from June 2008) that passed both of
> these test cases.
>
> I was able to recover the test results for the 2D-PMF test by modifying
> evb_umb.f, setting the array fharm(:) to zero outside of loops it is
> involved in (the way it was done previously) instead of inside (the way it
> is currently done).
>
> evb_umb.f
> 102c102
> < ! fharm(:) = 0.0d0
> ---
>
>> fharm(:) = 0.0d0
>>
> 106c106
> < fharm(:) = 0.0d0
> ---
>
>> ! fharm(:) = 0.0d0
>>
> 191c191
> < ! fharm(:) = 0.0d0
> ---
>
>> fharm(:) = 0.0d0
>>
> 195c195
> < fharm(:) = 0.0d0
> ---
>
>> ! fharm(:) = 0.0d0
>>
> You can even see that the fharm(:) statements were only commented out and
> not removed - does anyone familiar with the code know why it was changed?
> According to comments in the code it seems to have been changed around Dec.
> 2008. Anyway, when I reverse these changes the 2D-PMF test results match
> (aside from a few diffs that are output format-related). Of course, the test
> case itself could be wrong, but I have no easy way of knowing that.
>
> However, the corrF test still fails by a mile - as far as I can tell the
> likely culprit is with the qi_corrf_les() subroutine in pimd_force.f - much
> of it was changed around March 2009. These changes are far more extensive (>
> 100 lines at least) so I don't feel comfortable rolling them back.
>
> Anyway, I am attaching a patch that makes the changes that I discussed. If
> nothing else it prevents the ugly segfaults.
>
> Someone more familiar with what EVB *should* be doing should definitely have
> a close look at all of these changes.
>
> -Dan
>
>
>
>
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>



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Received on Thu Apr 01 2010 - 19:30:04 PDT
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