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
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
I'm not sure if they're useful but I have uploaded the test outputs to
my personal webspace:
http://www.homepages.ucl.ac.uk/~uccabha/
Any help would be really appreciated; of course I can provide any
further information as required.
Many thanks
--
Ben Ahmady
EngD candidate
M3S Doctoral Training Centre
University College London
Please try to avoid sending me Word or PowerPoint attachments.
Seehttp://www.gnu.org/philosophy/no-word-attachments.html
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Received on Mon Oct 17 2011 - 09:30:03 PDT
