[gmx-developers] Adding computing kernels in shared linked library

[Sebastian Jodłowski]

On 25 August 2011 12:09, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 25/08/2011 7:11 PM, Sebastian Jodłowski wrote:
>>
>> But how could it be a non-reproducible calculation if every run of
>> non-library version gives literally the same results and every run of
>> library version gives also the same results (but different from from
>> non-library version) - it is a deterministic algorithm and all
>> calculations are done in the same order.
>
> Each calculation on its own can be reproducible, but they do not necessarily
> reproduce each other. For example different compilation and/or linking
> optimization might lead to different orders of operations and thus results.
> See http://www.gromacs.org/Documentation/Terminology/Reproducibility
>
>>  Adding -reprod doesn't change
>> anything.
>
> OK. Can you compile both versions without optimizations, and link
> statically, and see if they can reproduce each other? If not, then you will
> have to get out a debugger and find the point they diverge.
>
> Mark
>

I run configure script with --disable-cpu-optimization
--disable-x86-64-sse, compiled and linked statically. Nothing changed
- results differ.
I run valgrind on mdrun and for 100 step of minimization set in
mini.mdp file do_cg() is called 148 times in non-library version
wherease in library version it is called only 132 times.

>> Sebastian
>>
>> On 25 August 2011 01:43, Mark Abraham<Mark.Abraham at anu.edu.au>  wrote:
>>>
>>> On 25/08/2011 12:52 AM, Sebastian Jodłowski wrote:
>>>>
>>>> I'm trying to add some features (e.g. interactions with membrane) into
>>>> nb_generic_kernel. I've written all my stuff, tested it hardly and
>>>> everything seems to work perfectly - all results are correct. Next
>>>> step, which I would like to performe, is to extract my kernels and
>>>> move them to the external library. So I added my lib(for now empty
>>>> lib) to gromacs makefiles(all of them), and inlcuded my lib header in
>>>> the nb_generic.c. In that place gromacs compiled and linked properly.
>>>> I cut my kernel code from the nb_generic_kernel() body and above it I
>>>> created function my_kernel() which consist body of my kernel. All
>>>> parametres are passed via pointers and kernel is called in its earlier
>>>> body's place in nb_generic_kernel(). Then I tested it again -
>>>> everything works great. So I finally moved my_kernel into the library.
>>>> Gromacs compiled and linked properly so I started testing. The results
>>>> are already wrong at the stage of minimization. I performed 100 steps
>>>> of minimization and version without external library calls 78144 times
>>>> my_kernel wherease with external library my_kernel is called 69696.
>>>> (What the hell?)The results start to differ at about 60% (45000th
>>>> calls of my_kernel).
>>>
>>> Sounds like you're managing to do a non-reproducible calculation
>>> non-reproducibly. Perhaps mdrun -reprod will help.
>>>
>>> Mark
>>>
>>>>  I have no idead what's going on and I spent
>>>> several days looking for the bug and couldn't find it. I would like to
>>>> notice that i don't know how gromacs minimization works and have no to
>>>> time for studing these code(but I pretty good analised how computing
>>>> of forces works).
>>>> Has anybody ever met something similar? Or has any experience with
>>>> writing libraries for gromacs?
>>>> Greetings
>>>> Sebastian Jodlowski
>>>
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