Re: [ESPResSo-devel] Bond-deleting strangeness

[Florian Weik]

Actually simply switching to memmove does the trick... Now its even standard conform, so it will never break again *cough*

On Wed, Jan 7, 2015 at 11:24 PM, Ulf Schiller <address@hidden> wrote:

Maybe a bit dirty, but could playing around with something like

__asm__(".symver memcpy,...

do the trick?

On 01/07/2015 10:20 PM, Axel Arnold wrote:
> Well, I was more polite about this change than Linus...
>
> https://bugzilla.redhat.com/show_bug.cgi?id=638477#c129
>
> But I do like his statement about standards :-). The other funny thing
> is that he thinks they just forgot to handle overlapping in early memcpy
> and therefore introduced memmove with guaranteed behavior. I just wrote
> try_delete_bond in the golden window when both were the same...
>
> Cheers,
> Axel
>
>> On 07.01.2015, at 23:10, Florian Weik <address@hidden
>> <mailto:address@hidden>> wrote:
>>
>> This is a joke, right?
>>
>> On Wed, Jan 7, 2015 at 10:56 PM, Axel Arnold
>> <address@hidden <mailto:address@hidden>>
>> wrote:
>>
>>     Hi!
>>
>>     No, that problem is more subtle, and will probably stick around
>>     for a while. glibc < 2.14 aliased memcpy to memmove, which allows
>>     for overlapping memory regions, while memcpy doesn't. The current
>>     glibc versions have a more efficient memcpy, that does not allow
>>     for overlap, which in this case however occurs.
>>
>>     I can’t test on my Mac, since Apple decided wisely that an
>>     unmeasurable speed gain (according to Linus) isn’t worth breaking
>>     hundreds of applications, but most Linux distros seem to have this
>>     problem. Shooting yourself (or others) in the foot seems to be
>>     great fun...
>>
>>     Best,
>>     Axel
>>
>>>     On 07.01.2015, at 15:52, Florian Weik <address@hidden
>>>     <mailto:address@hidden>> wrote:
>>>
>>>     Hi,
>>>     the function looks suspicious to me, might be an off by one
>>>     error. I'll get back to you if I've got it figured out.
>>>
>>>     Florian
>>>
>>>     On Wed, Jan 7, 2015 at 3:45 PM, Rudolf Weeber
>>>     <address@hidden

>>>     <mailto:address@hidden>> wrote:
>>>
>>>         Hi,
>>>         On Wed, Jan 07, 2015 at 02:42:27PM +0100, Rudolf Weeber wrote:
>>>         > I encountered very strange behaviour when deleting individual bonds from particles which have more than one bond.
>>>         > In some cases, the code works correctly, in some cases, the wrong bond seems to be deleted and in some cases, the bond list gets screwed up completely.
>>>         > The code, which is supposed to delete the bond is in particle_data.cpp:try_delete_bond()
>>>         And here is a case, where the bond list is screwed up entirely:
>>>
>>>
>>>         {0 FENE 47.396 2.5 1.0} {1 angle_harmonic 473.96000000000004
>>>         1.0471975512} {2 FENE 473960.0 2.0 1.0} {3 FENE 473960.0 0.1
>>>         0.0} {1 1 lennard-jones 1000.0 2.672696154421018 3.0 0.25 0.0
>>>         0.0 0.0 } {magnetic 1.0  dawaanr }
>>>         I.e., bond 0 and 2 have one partner, bond 1 has two partners
>>>
>>>
>>>
>>>         Initial bond configurations
>>>         { {0 21746} {0 21747} {0 22047} {1 22047 21746} {1 22049
>>>         21747} {1 22348 22047} {1 22349 22049} }
>>>           Del: 0 21746
>>>         { {0 21747} {0 22047} {1 22047 21746} {1 22049 21747} {22047
>>>         1} {22047 1} {22349 22049} }
>>>
>>>         ---------------------------------
>>>
>>>         The relevant code is
>>>         proc makeBondRigid { id bond} {
>>>         global bondMeshPairSoft 0
>>>         global bondMeshAngleSoft 1
>>>         global bondMeshPairStiff 2
>>>         global bondParticleMesh 3
>>>
>>>          puts "$id: Making bond rigid: $bond"
>>>          # First delete the old bond
>>>          puts "[part $id print bond]"
>>>          puts "  Del: $bond"
>>>          eval "part $id bond delete $bond"
>>>          puts "[part $id print bond]"
>>>
>>>          # Make new bond with changed type
>>>          lset bond 0 $bondMeshPairStiff
>>>          # Add
>>>          puts "  Add: $bond"
>>>          eval "part $id bond $bond"
>>>          puts "[part $id print bond]"
>>>         }
>>>
>>>
>>>         Regards, Rudolf
>>>
>>>
>>>
>>>
>>>
>>>     --
>>>     Florian Weik
>>>

>>>     address@hidden <mailto:address@hidden>
>>>     ++49 157 85939252 <tel:%2B%2B49%20157%2085939252>
>>>
>>
>>     ------------------------------------------------
>>     JP Dr. Axel Arnold
>>     ICP, Universität Stuttgart
>>     Allmandring 3
>>     70569 Stuttgart, Germany
>>     Email: address@hidden
>>     <mailto:address@hidden>
>>     Phone: +49 711 685 67609 <tel:%2B49%20711%20685%2067609>
>>
>>
>>
>>
>> --
>> Florian Weik
>>
>> address@hidden <mailto:address@hidden>
>> ++49 157 85939252
>>
>
> ------------------------------------------------
> JP Dr. Axel Arnold
> ICP, Universität Stuttgart
> Allmandring 3
> 70569 Stuttgart, Germany
> Email: address@hidden <mailto:address@hidden>
> Phone: +49 711 685 67609
>


--
Ulf D. Schiller
Centre for Computational Science
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom

Phone: +44 (0)20 7679 5300

--

Florian Weik

address@hidden
++49 157 85939252