Hello Bob,
I have the whole backtraces for tst1, so it is not necessary to debug
program once again. I will send it with other information later.
Petr
Robert Duke wrote:
> Petr -
> Quick update. My earlier assertion about the seg violation for test
> case 1 being due to an unallocated velocity array in minimization is
> incorrect. This was probably true for earlier pmemd code, and then I
> changed it to prevent just this sort of thing from occurring. So there
> is still a seg violation, due to unknown causes, which I will track
> down. I suspect the 10-12 vdw code may have problems in pmemd, as it is
> pretty much untested (there are no standard amber test cases for this,
> as far as I know). Anyway, I will attempt to get to the bottom of all
> your test cases, and either find an alternate cause or definitively show
> a wrong result from dnint(). In the meantime, as I said earlier, it
> would be helpful if you gave me more info on how your prmtop was made.
> Thanks - Bob Duke
>
> ----- Original Message ----- From: "Petr Kulhanek" <kulhanek.chemi.muni.cz>
> To: <amber.scripps.edu>
> Sent: Monday, July 04, 2005 12:33 PM
> Subject: AMBER: pmemd - bug report
>
>
>> Dear AMBER developers,
>>
>> I would like to report a bug in PMEMD code (AMBER 8.0).
>>
>> The bug is responsible that some atoms are incorrectly addressed to
>> respective subcells. The bug occures only if some atoms are very close
>> to box walls (confirmed) or if they are on subcell interfaces (just
>> hypothesis). As the result, program can crash or the non-bonded energy
>> is not calculated correctly. The bug probably depends on architecture
>> and/or used compiler.
>>
>> Test cases (for IA32, ifort 8.1.024, and 1CPU) can be downloaded from:
>>
>> segmentation fault
>> http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/tst1.tar.gz
>>
>> infinity Eel
>> http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/tst2.tar.gz
>>
>> incorrect Eel
>> http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/tst3.tar.gz
>>
>> In each archive, six results are present:
>>
>> mdout_bug_reference - calculated by pmemd on coordinates that leads to
>> incorrect results
>> mdout_bug_imaged_reference - calculated by pmemd on coordinates, which
>> were processed by ptraj (solut is centered and system is imaged)
>> mdout_fix_reference - calculated by modified pmemd (see below) on
>> coordinates that leads to incorrect results with non-modified pmemd
>> mdout_fix_imaged_reference - calculated by modified pmemd (see below)
>> on coordinates, which were processed by ptraj (solut is centered and
>> system is imaged)
>> mdout_sander_reference - calculated by sander on coordinates that
>> leads to incorrect results with non-modified pmemd
>> mdout_sander_imaged_reference - calculated by sander on coordinates,
>> which were processed by ptraj (solut is centered and system is imaged)
>>
>>
>> The bug is located in following files:
>>
>> ew_direct_cit.f90 -> subroutine get_fract_crds (confirmed)
>> fraction could be equal to 1.0 due to round errors, however the code
>> suppose that it has to be less than 1.0
>>
>> ew_direct_cit.f90 -> subroutine setup_crd_idx_lst_tbl (confirmed)
>> indexes to crd_idx_lst_tbl array are not checked if they are in legal
>> ranges
>> if fractions calculated in get_fract_crds are equal to 1.0 then
>> indexes overflow crd_idx_lst_tbl boundaries
>>
>> ew_pairlist.f90 -> subroutine get_nb_list (confirmed) and probably
>> get_nb_list_nonorthog (not tested)
>> indexes to x_bkts, y_bkts, and especially z_bkts arrays are not
>> checked if they are in legal ranges
>> array overflows could occur even if fractions are in legal ranges
>> because the indexes are calculated directly from imaged coordinates
>> (different approach -> different round errors)
>>
>> ew_recip_cit.f90 -> subroutine claim_recip_imgs (hypothesis) and
>> probably claim_recip_imgs_nonorthog (not tested)
>> z_bkt_lo and z_bkt_hi, the same as above
>>
>>
>> I prepared two patches for testing purposes. (reference source is
>> amber8 distro + bugfixes 1-44)
>> http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/check.patch
>> http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/fix.patch
>>
>> The first one extends code with boundary check in above mentioned
>> subroutines. If some overflow occures then the program is immediatelly
>> stop with error message. The second one fixes the problem (boundary
>> check is still present).
>> fix.patch is only intended for testing purposes because it does not
>> solve possible problems in simulations using truncated octahedral box
>> and it was not tested under parallel execution.
>>
>> Some comments at the end:
>>
>> I found this bug when I did postprocessing analysis of trajectory
>> calculated by pmemd (MD was run without any problems as I remember).
>> In the analysis, the electrostatic energy is calculated for several
>> system subparts still under PBC. In the reported cases, only solut and
>> solvent are present (ions were stripped away), so the test cases
>> represent rare systems. However observed errors depend only on
>> coordinates and I do not see any reason why it could not occur during
>> normal MD !
>> I think that it is neccessary to carefully check the pmemd code and
>> remove possible problems with reported round errors when subcell
>> indexes are calculated. Secondly, it is also important to keep the
>> parts, in which subcell indexes are calculated, as same as possible to
>> avoid different round errors.
>>
>> For SANDER developers:
>>
>> Please look to tst1.tar.gz archive. mdout_sander_reference and
>> mdout_sander_imaged_reference differ. The difference is about 3
>> kcal/mol in Eel as well as in Evdw. I think that this could be a bug
>> in sander.
>>
>> Best regards,
>> Petr
>>
>> --
>> ##################################################
>> Petr Kulhanek
>> ------------------------------------------------
>> kulhanek.chemi.muni.cz
>> ------------------------------------------------
>> National Centre for Biomolecular Research
>> Masaryk University Brno
>> Kotlarska 2, CZ-611 37 Brno
>> Czech Republic
>> ##################################################
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
##################################################
Petr Kulhanek
------------------------------------------------
kulhanek.chemi.muni.cz
------------------------------------------------
National Centre for Biomolecular Research
Masaryk University Brno
Kotlarska 2, CZ-611 37 Brno
Czech Republic
##################################################
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jul 05 2005 - 11:53:00 PDT
