Thank you for the swift response. No, I don't expect to need to use
anything NOE-related, so I should be fine.
Many thanks again!
On 18/10/11 19:02, Jason Swails wrote:
> 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
>>
>>
>
>
>
--
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
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Received on Tue Oct 18 2011 - 11:30:06 PDT
