Those failures and errors are documented and known for Amber11 when paired
with AmberTools 1.5 (except maybe the NOE test -- do you plan on using that
functionality?)
All the best,
Jason
On Tue, Oct 18, 2011 at 1:41 PM, Ben Ahmady <uccabha.ucl.ac.uk> wrote:
> Dear Amber users/developers,
>
> Thank you very much, Dr. Luchko: that fixed the problem I was having
> before.
>
> I have now successfully compiled/installed both AmberTools 1.5 and Amber
> 11 now; but at the moment running 'make test' gives the following:
>
> 363 file comparisons passed
> 15 file comparisons failed
> 4 tests experienced errors
> Test log file saved as logs/test_amber_serial/2011-10-18_15-13-17.log
> Test diffs file saved as logs/test_amber_serial/2011-10-18_15-13-17.diff
>
> I have uploaded the full .log and .diff files to my personal webspace at
> my university:
>
> http://www.homepages.ucl.ac.uk/~uccabha/2011-10-18_15-13-17.diff
> http://www.homepages.ucl.ac.uk/~uccabha/2011-10-18_15-13-17.log
>
> I have read that since 'PBSA' has been recently changed, some errors may
> in fact be false alarms - and should this be the case of course I
> realise that I wouldn't have anything to be concerned about - but as a
> new user I don't know whether this is the case or not; many of the
> errors do appear to be pbsa-related but I did also find what look like
> non pbsa-related blocks.
>
>
> Any help would be greatly appreciated (further details about my system
> etc. are in my previous e-mail).
>
> Thank you very much in advance,
>
> Ben Ahmady
>
> On 17/10/11 17:19, Tyler Luchko wrote:
> >
> > On 10/17/2011 12:11 PM, Ben Ahmady wrote:
> >
> >> Dear Amber users/developers
> >>
> >> I am a new user currently trying to install Amber 11 alongside
> >> AmberTools 1.5 on a system with the following broad specifications:
> >>
> >> processor : 1
> >> vendor_id : GenuineIntel
> >> cpu family : 6
> >> model : 15
> >> core id : 1
> >> cpu cores : 2
> >> model name : Intel(R) Core(TM)2 Duo CPU E6550 . 2.33GHz
> >> cache size : 4096 KB
> >> clflush size : 64
> >> cache_alignment : 64
> >>
> >> I use 64-bit 'CrunchBang Linux', a Debian (Squeeze) derivative. Sincere
> >> apologies if somebody has already asked for help with the problem I'm
> >> about to describe, but I did Google the salient points as search terms
> >> along with 'Amber' and nothing quite right came up.
> >>
> >> I have checked all of the following packages to ensure they are
> >> up-to-date with stable releases (e.g. gcc is version 4.4.5):
> >>
> >> gcc g++ libxt-dev libxext-dev flex gfortran tcsh
> >> libnetcdf-dev patch csh bison xorg-dev
> >>
> >>
> >> The problem I am having at this stage is only in installing AmberTools.
> >>
> >> I have followed the instructions provided in the AmberTools manual and
> >> have ensured AMBERHOME is properly defined (as /home/ben/amber11) in
> >> Bash, in the .bashrc file; I have applied the bugfix.all patch (which
> >> was successful); and I have gone into the AmberTools/src directory to
> >> run the following command:
> >>
> >> ./configure gnu
> >>
> >> ... At this stage, I am told to enter 'make serial', which I do
> >> accordingly, only to be met (after the compilation) with the following:
> >>
> >> Error: Object 'totalmem' at (1) must have the SAVE attribute for default
> >> initialization of a component
> >> make[1]: *** [safemem.o] Error 1
> >> make[1]: Leaving directory `/home/ben/amber11/AmberTools/src/rism'
> >> make: *** [serial] Error 2
> >>
> >>
> > This came up recently. In both cases the GNU 4.4 compiler is involved.
> > From what I have seen all other compilers think that this is legal
> > Fortran 95 but it is possible that it is not.
> >
> > Anyway, the solution is to change the offending line in safemem.f (not
> > _safemem.f) to read
> >
> > type(memTracker),private,save :: totalMem
> >
> >
> >> After this, I attemped to run 'make test' in the AmberTools/tests
> >> directory anyway, and it came up with:
> >>
> >> make[1]: Target `test.serial' not remade because of errors.
> >> make[1]: Leaving directory `/home/ben/amber11/AmberTools/test'
> >> 352 file comparisons passed
> >> 9 file comparisons failed
> >> 120 tests experienced errors
> >> Test log file saved as logs/test_at_serial/2011-10-17_16-49-45.log
> >> Test diffs file saved as logs/test_at_serial/2011-10-17_16-49-45.diff
> >>
> >>
> > If you do not successfully compile the software and then try to run the
> > tests, the tests will fail.
> >
> > Hope this helps,
> >
> > Tyler
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Ben Ahmady
> EngD candidate
> M3S Doctoral Training Centre
> University College London
>
> Please try to avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 18 2011 - 11:30:05 PDT
