Ok thanks !
it seems like there are two independent repositories:
#1
here
http://ambermd.org/bugfixes12.html
#2
that which is used by configure script to download
given patch.
So even if in #1 the patch is not uploaded yet important is
that was already uploaded to #2 :))
So let's try to update and to see if something changed regarding
to our tests.
M.
Dne Sat, 01 Jun 2013 22:27:18 +0200 ET <sketchfoot.gmail.com> napsal/-a:
> Hi Marek,
>
> I managed to get this installed. Not sure why you got that error. Perhaps
> give it another try. :)
>
> └──21:25──$ ./update_amber -v
> Version is reported as <version>.<patches applied>
>
> AmberTools version 13.06
> Amber version 12.18
>
>
> #######
>
> └──21:25──$ ./update_amber --show-applied-patches
> AmberTools 13 Applied Patches:
> ------------------------------
> update.1 (modifies cpptraj)
> update.2 (modifies MMPBSA.py, and, ParmEd)
> update.3 (modifies cpptraj, ParmEd, calcpka)
> update.4 (modifies pbsa)
> update.5 (modifies cpptraj, MMPBSA.py, ParmEd)
> update.6 (modifies configure2)
>
>
> Amber 12 Applied Patches:
> -------------------------
> bugfix.1, bugfix.2, bugfix.3, bugfix.4, bugfix.5, bugfix.6, bugfix.7,
> bugfix.8, bugfix.9, bugfix.10,
> bugfix.11, bugfix.12, bugfix.13, bugfix.14, bugfix.15, bugfix.16,
> bugfix.17, bugfix.18
>
>
> br,
> g
>
>
>
>
> On 1 June 2013 19:22, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Dear all,
>> I just found that in Updates section (
>> http://ambermd.org/bugfixes12.html
>> ) is already record of the
>> expected bugfix-18 announced recently by Ross.
>>
>> i.e.
>> --------
>> bugfix.18: Fixes a number of issues with pmemd and pmemd.cuda:
>> Updates GPU code to v12.3
>> Adds check to prevent running ntb=2 with gamma_ln=0 and ntt=3 or 4.
>> Fixes Hamiltonian Replica Exchange on GPUs and CPUs in explicit solvent.
>> Fixes issue with nmropt DUMPAVE printing in pmemd for H-REMD.
>> Fixes extra-points support for the GLYCAM force field which was leading
>> to
>> a segfault in pmemd and pmemd.cuda.
>> Improves stability for NPT simulations on GPUs.
>> Adds check to make sure code quits if skinnb would go negative in GPU
>> calculations due to large reductions in box size.
>> Fixes issues with restart of NPT simulations on GPUs in cases where the
>> box size had shrunk considerably.
>> Fixes minimizations on GPUs with the SPFP precision model by truncating
>> large forces that occur during the beginning of a minimization.
>> Changes pmemd.cuda and pmemd.cuda.MPI links to be relative instead of
>> absolute in AMBERHOME/bin directory.
>> Updates configure script to optimize for sm35 GPU hardware (Kepler II)
>> in
>> cases where cuda v5.0 is detected.
>> Makes GTX680 output the gold standard for test cases.
>> Fixes incorrect timings that were reported at the end of a run with REMD
>> runs in pmemd.
>> --------
>>
>> but it seems that this bugfix was not uploaded to the given server as
>> after the attempt
>> to click on the given link I have obtained this err.
>>
>> ------
>> Not Found
>>
>> The requested URL /bugfixes/12.0/bugfix.18 was not found on this server.
>>
>> Apache/2.2.3 (CentOS) Server at ambermd.org Port 80
>> ------
>>
>> So I assume that this bugfix was still not uploaded and will be soon,
>> am I
>> right ?
>>
>> Best wishes,
>>
>> Marek
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Jun 01 2013 - 14:00:02 PDT
