[Dock-fans] Check_serial.out

[Scott Brozell]

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

On Thu, 8 May 2008, Francesco Pietra wrote:

> I should have better explained what "lenny" (Debian Linux) means in present context.
> 
> I recently upgraded Debian Linux amd64 from "etch" (the stable distribution) to "lenny" (the intermediate distribution) as I used in the past the intermediate distribution (at that time it was "etch"). Then, I applied the bug fixes (I should say carefully so that there should be no misprint) and re-compiled on the former install directory, i.e., overwriting the executables (after running "./configure gnu" for serial and "./configure gnu parallel" for parallel). I saved a copy of former compilation, renamed dock6_old.
> 
> Change from "etch" to "lenny" involves a major change in libraries (I know vaguely not only release but also the system. Though, Amber9 works and NWchem works without recompilation (tests not tried). Dock6.2 also worked without recompilation (not tried tests for that after upgrading to lenny).
> 
> Must add that, at the moment, any attempt at package upgrading reports errors for
> 
> exim4-daemon-ligth
> at
> exim4
> bsd-mailx
> acpid
> mailx
> 
> because of a bug that, so far, has only been fixed in the "unstable" distribution, and is waiting to be fixed in "lenny" until the new release of perl also migrates. There should be no relationship between this issue and the compilation above, I guess. However, I am going to pose the question to Debian, also for a clarification about the two installations of gnu compilers.
> 
> Should someone have a suggestion about remedies to apply, please help.
> 
> Thanks
> francesco
> 
> 
> --- 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, 1:09 PM
> > Hi,
> > 
> > On Wed, 7 May 2008, Francesco Pietra wrote:
> > 
> > > Following bug1 and bug2 fixes and re-compilation of
> > Dock6.2, it seems to me that some diff from the test are
> > rather large. I wonder whether that is correct. As such
> > alleged large diff are many, the check_serial.out is
> > attached here. That from parallel compilation of dock6.mpi
> > would also be available on request.
> > > 
> > 
> > It does not look like the only change was applying those
> > 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.
> > 
> > 
> > > UMA type machine dual-opterons, Debian Linux amd64
> > lenny;
> > > gcc -v
> > > reports
> > > gcc 4.2.3 (Debian 4.2.3-3)
> > > 
> > > 
> > > g77 -v (or f77 -)
> > > report:
> > > reading from /usr/lib/gcc/x86_64-linux-gnu/3.4.6/specs
> > > Configured with: ../src/configure -v
> > --enable-languages=c,c++,f77,pascal --prefix=/usr
> > --libexecdir=/usr/lib
> > --with-gxx-include-dir=/usr/include/c++/3.4 --enable-shared
> > --with-system-zlib --enable-nls --without-included-gettext
> > --program-suffix=-3.4 --enable-__cxa_atexit
> > --enable-clocale-clocale=gnu --enable-libstdcxx-debug
> > x88_64-linux-gnu
> > > Thread model: posix
> > > gcc version 3.4.6 (Debian 3.3.6-6)
> > > 
> > > I do not understand why different versions of gcc are
> > reported from the two different commands above.
> > 
> > You have two separate gnu compiler installations.
> > Probably new compilers were installed.
> > Recent versions of gnu compilers do not have g77.
> > Probably we shall retire g77 or at least prefer gfortran
> > soon.
> > 
> > Scott