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
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Received on Mon Oct 17 2011 - 09:30:06 PDT
