The EVB patch seems to work well, but I am still having problems with a few
of the tests:
cd evb/poh_dbonds_umb_dg_UFF_9DG && ./Run.evb
cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_ld_full && ./Run.evb
cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_nhc_full && ./Run.evb
cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full && ./Run.evb
cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full_TST-freqf && ./Run.evb
Previously however I was having issues with these tests that Mark was not
seeing. Does anybody else have these tests fail with an MPI_abort? I've had
it happen to me with both gnu and intel compilers (2 versions, 10 and 11) as
well as 2 different MPICH2 versions.
-Dan
On Thu, Apr 1, 2010 at 10:04 PM, Kim F. Wong <kimberlyyellow.gmail.com>wrote:
> 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
>>
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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>
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Apr 02 2010 - 05:30:02 PDT
