On Wed, Mar 19, 2014 at 11:55 AM, BERGY <nucleic81.gmail.com> wrote:
> Dear all,
>
> I get the following msg on submitting my job. all amber 12 and
> ambertools 13 update are done.
> ---------------------
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> rank 0 in job 4 mambo_42345 caused collective abort of all ranks
> exit status of rank 0: killed by signal 9
> -------------------
> The OUT file has the following error msg.
>
>
> | Largest sphere to fit in unit cell has radius = 33.861
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 03/19/14 Time = 03:20:35
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> CUDA (GPU): Prmtop appears to contain modified off-diagonal elements
> for VDW A coef.
> GPU code does NOT support such force field modifications.
> Found Aij = 787979.7920942737 expected
> 479622.7030000000
> i = 20 j = 1 Matrix element = 191
>
> Thanking you
>
How did you make your topology file?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 19 2014 - 09:30:04 PDT
