Hi,
On Thu, Sep 27, 2012 at 9:08 PM, Kira Armacost
<kza0004.tigermail.auburn.edu> wrote:
> Size (60000) of SymmetricMatrix is too big. Please limit the size to be less than 32768.
> The first pass through the trajectory is complete.
Mea culpa - I was totally unaware of this size limit.
I have 3 suggestions:
1) Use the 'sieve' keyword, something like 'sieve 5' or 'sieve 10' -
this will cut down on the initial matrix size.
2) Try clustering with cpptraj; there is no sieve keyword but also no
size limit (other than available memory). This may take a while though
and cpptraj only uses a hierarchical agglomerative algorithm.
3) Remove the size limitation from ptraj - just comment out lines
5428-5431 of clusterLib.c and recompile. However I can't vouch for the
behavior after this; it's not my code and I'm not sure if the size
limitations are there for a specific reason.
Good luck,
-Dan
>
> I used a .binpos file.
>
> Kira
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Thursday, September 27, 2012 3:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Large trajectory for cluster analysis in ptraj
>
> Hi,
>
> On Thu, Sep 27, 2012 at 2:33 PM, Kira Armacost
> <kza0004.tigermail.auburn.edu> wrote:
>> I was reading somewhere about it. It originally failed me with 60,000
>> frames, so I reduced the size of it after reading it only accepted 32,000
>> frames. I could be wrong, but I couldn't get it to work with 60,000
>> frames.
>
> What version of AmberTools are you using? How exactly did the
> calculation fail (segmentation fault etc)? Did it fail immediately or
> was it after some calculation had occurred? Also, do you happen to
> have the exact output given to you by ptraj available? If so, please
> send it to me off-list. I have run clustering for similar-length
> trajectories and have not run into any issues, so it may be you have
> run into a bug in the version of ptraj you are using.
>
> -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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--
-------------------------
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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Received on Thu Sep 27 2012 - 20:30:03 PDT
