Hi Brian,
I VERY much doubt it is up to date since it used to be ME who kept things
up to date but I don't do that anymore so I doubt they've been keeping up
to date. My advice would ALWAYS be to compile and install the software
yourself. Trusting centralized models on those machines is never a good
idea in my experience.
It's pretty easy to do. Just untar Amber 12 and AmberTools 13 - run
./update_amber.py --update a couple of times until it is fully updated.
Make sure the cuda 5.0 module is loaded and then do:
cd amber12
export AMBERHOME=`pwd`
./configure -cuda gnu
make
And you should be good.
All the best
Ross
On 9/10/13 10:25 AM, "Brian Radak" <radak004.umn.edu> wrote:
>It might be worth noting that I am not sure the Amber12 compile available
>on Stampede via "module load" is up to date with bug fixes. This could
>especially cause problems with the GPU code if I'm not mistaken.
>
>I'm still awaiting a response from the TACC staff on the matter.
>
>Regards,
>Brian
>
>
>On Mon, Sep 9, 2013 at 5:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> > lines, respectively. The graduate student I work under informed me
>>there
>> > should be twice as many lines in the NVT.restrt file; however, it is
>> three
>>
>> This is not strictly true. The Amber ASCII restart format is:
>>
>> Title line
>> Natom [time] [temp0]
>> <Natom * 3 Coordinates>
>> [<Natom * 3 Velocities>]
>> [Box Info]
>>
>> In your initial restart (presumably from a minimization) there is no
>> velocity information, whereas in your MD restart you do have velocity
>> information. Therefore the number of lines in the MD restart (M)
>> compared to the number of lines in the Min restart (N) should be:
>>
>> M = ((N - 3) * 2) + 3
>> M = 2N - 3
>> (if you had no box info it would be M = 2N - 2)
>>
>> So the number of lines in your second restart appears fine (this of
>> course doesnt preclude their being some other kind of problem with the
>> restart). You could do some basic checking of the restart via the
>> 'check' command in cpptraj.
>>
>> Your best bet when troubleshooting an error like this is to simplify
>> the run as much as you can. So try running only a few steps (10-100)
>> using the serial version of the code, printing out information every
>> step. Sometimes error messages are harder to find when running
>> multiple threads.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>================================ Current Address =======================
> Brian Radak : BioMaPS
>Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
>University of New Jersey
> University of Minnesota - Twin Cities : Center for
>Integrative
>Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
>08854-8066
> radak004.umn.edu :
>radakb.biomaps.rutgers.edu
>====================================================================
>Sorry for the multiple e-mail addresses, just use the institute
>appropriate
>address.
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Received on Tue Sep 10 2013 - 11:00:02 PDT
