[Dock-fans] Check_serial.out

[Francesco Pietra]

Hi


--- On Thu, 5/8/08, Scott Brozell <sbrozell at scripps.edu> wrote:

> From: Scott Brozell <sbrozell at scripps.edu>
> Subject: Re: [Dock-fans] Check_serial.out
> To: "Francesco Pietra" <chiendarret at yahoo.com>
> Cc: "dock-fans" <dock-fans at docking.org>
> Date: Thursday, May 8, 2008, 7:10 PM
> Hi,
>
> Ok, your  system upgrade probably explains all the dock
> test diffs.
> As far as your linux issues, I have no specific
> suggestions.
>
> good luck,
> Scott

I have something new, bad or good as it might be.

I downloaded DOCK6.2 again, applied the already elaborated bugfix 1 and 2, and compiled serial on the same Supermicro/debian lenny system below (to rule out any trivial mistake from my previous doing).

Then I examined the dock6.2 compilation of 13 Mar 2008, currently renamed old_dock6 (check_serial.out attached). At that time the system was a couple of dual-opterons on a Tyan motherboard under Debian amd64 etch (stable) and there were no bugfixes. The two raid1 HDDs from this system were simply moved to the new system Supermicro motherboard with four dual-opteron cpus. RAM from Tyan (Kingston ECC 400MHz) was also moved to Supermicro.


Well, both the good agreement and the large diff you remarked below as unrelated to bugfixes:

> > >
> > > bugfix 1 can only affect tests with
> > > amber_score_movable_region=distance.
> > > There are two such tests
> > > amber_score_1lgu/move_by_distance
> > > amber_score_1lgu/verbose_move_by_distance
> > > The diffs for the latter and all your other amber
> tests are
> > > showing
> > > round off errors:
> > >
> ./amber_score_1lgu/verbose_move_by_distance.dockout.dif
> > > 176,177c176,177
> > > < ff:   1    -63.      8.      4.    -67.     
> 0.   
> > > -8.  2.E+1
> > > < md:           1      0.      12.     -63.   
>  -50.   
> > > 292.
> > > ---
> > > > ff:   1    -62.      8.      4.    -67.     
> 0.   
> > > -8.  2.E+1
> > > > md:           1      0.      12.     -62.   
>  -50.   
> > > 292.
> > > I saw no such diffs in before and after bugfix1
> testing.
> > >
> > > bugfix 2 should affect only test
> anchor_and_grow/flex5
> > > I saw no other diffs in before and after bugfix2
> testing.
> > > Id be less surprised to find issues with bugfix
> 2, but
> > > I am skeptical that this bugfix is the cause of
> your diffs.
> > >
> > > Note these diffs in a program unaffected by the
> bugfixes:
> > > ./sphere_generation/selected_spheres.sph.dif
> > > 12c12
> > > <   101  18.49   9.24  66.76   1.    3 0  0
> > > ---
> > > >   101  18.49   9.24  66.76   1.  209 0  0
> > >
> > > All this suggests to me that more has changed
> than just
> > > applying
> > > the bugfixes.  Are the OS, compilers, etc
> unchanged ?
> > > Your diffs look like the usual ones due to
> inadequacies in
> > > the
> > > test suite as far eliminating noise from binary
> files,
> > > floating point arithmetic, etc. across different
> platforms.


are exactly the same in both instances, the new compilation from scratch and the old one on a different motherboard. I apologize for having overlooked such diff in the 13 Mar 2008 compilation. Though, it is not the new hardware/OS that has introduced that problem. Assuming that other users were not faced by such issues, at the moment I can't imagine what best to do. As to the Debian list, so far I only posed a question about the two installations of gnu; all other issues could not be understood.

Thanks
francesco


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