Re: [AMBER] addles segmentation fault

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 9 Mar 2009 07:45:24 -0400

it's possible that you are creating an array that is too large
somewhere, such as the exclusion list which will be huge in this case.
it may not be very efficient- for example, each of your 8596*30 atoms
will have 8596*29 atoms in the exclusion list using LES NEB,
8596*30*8596*29=64 million excluded atoms. you might try making things
smaller (fewer neb beads) and see if it helps. I'm not sure if anyone
has tried a system this large using LES NEB.

> Dear Amber users
>     I am trying to do some nudged elastic banding simulation on a big protein (548 residues).
> I just went through this by reading the NEB tutorial, which is quite informative and helpful.
> (Many thanks to Dr. Ross Walker)
>     However, when I used addles to create 30 copies of my protein. The output file said
>  Checking topology sizes against compiled limits
>  exceeded MAXANG in SIZE.BLOCK.
>  MAXANG =         8000
>  ntheth =         9788
>  exceeded MAXDIH in SIZE.BLOCK.
>  MAXDIH =        15000
>  nphih =        18572
>  Change SIZE.BLOCK and recompile.
>
> I searched the mailing list and found the SIZE.h file and increased these values to 10000 and 20000 respectively to  fit my protein.
>
> after make clean,
> and make in the $AMBERHOME/src/addles/ folder
> I created a new addles program in this folder.
>
>
> But when I used this command in this folder to create the prmtop  and inpcrd file.
> There came a segmentation fault
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC        Routine            Line        Source
> addles             08051E1A  Unknown               Unknown  Unknown
> addles             0804CD72  Unknown               Unknown  Unknown
> addles             08049B95  Unknown               Unknown  Unknown
> libc.so.6          0076EE33  Unknown               Unknown  Unknown
> addles             08049AD1  Unknown               Unknown  Unknown
>
> The input and output files are attached.
>
> I really don't know the reason for this.
>
>
> Please give some suggestions.
>
>
> Best Regards!
>
> Xiaonan Zhang
>
> Shanghai Public Health Clinical Center
>
>
>
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>

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Received on Wed Mar 11 2009 - 01:09:04 PDT
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