Re: [AMBER] Installation of AmberTools 1.5 (and Amber 11)

From: Ben Ahmady <>
Date: Tue, 18 Oct 2011 18:41:34 +0100

Dear Amber users/developers,

Thank you very much, Dr. Luchko: that fixed the problem I was having

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:

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

Ben Ahmady
EngD candidate
M3S Doctoral Training Centre
University College London
Please try to avoid sending me Word or PowerPoint attachments.
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Received on Tue Oct 18 2011 - 11:00:03 PDT
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