Hi Rejwan,
This should not happen. What are you trying to simulate - this typically
only occurs if you are trying to do some monster gas phase calculation or
you have a VERY large cutoff defined. (or alternatively a very
inhomogenous - read 'bad' initial structure).
All the best
Ross
On 8/19/13 12:06 PM, "Rejwan" <rejwan_88.yahoo.com> wrote:
>Hi
>
>An AMBER minimization job was aborted due to overflow of non-bonded list.
> My system is of 52 K atoms size. How I can perform minimization in such
>situation ? Thank you.
>
>Rejwan
>
>_____________________
>
>
>#!/bin/csh
>#$ -N min1
>#$ -V
>#$ -cwd
>#$ -o $JOB_NAME.o$JOB_ID
>#$ -j y
>#$ -q normal
>#$ -pe 2way 180
>#$ -l h_rt=24:00:00
>module load amber/12.0
>ibrun sander.MPI -O \
> -i min_lipid.in \
> -p 438_POP.top \
>
>
>
>TACC: Done.
>TACC: Starting up job 1364911
>TACC: Setting up parallel environment for MVAPICH ssh-based mpirun.
>TACC: Setup complete. Running job script.
>TACC: starting parallel tasks...
>
>
>
>
>Exit code -5 signaled from c321-214
> * NB pairs 522 1219601 exceeds capacity ( 1219712) 23
> SIZE OF NONBOND LIST = 1219712
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> * NB pairs 1178 1218874 exceeds capacity ( 1219712) 22
> SIZE OF NONBOND LIST = 1219712
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 23
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
>MPI process (rank: 23) terminated unexpectedly on
>c321-214.ls4.tacc.utexas.edu
> * NB pairs 1000 1218841 exceeds capacity ( 1219712) 11
> SIZE OF NONBOND LIST = 1219712
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11
> * NB pairs 989 1219077 exceeds capacity ( 1219712) 9
> SIZE OF NONBOND LIST = 1219712
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
>MPI process (rank: 9) terminated unexpectedly on
>c309-213.ls4.tacc.utexas.edu
>forrtl: error (69): process interrupted (SIGINT)
>Image PC Routine Line
>Source
>libpthread.so.0 000000388BE0B725 Unknown Unknown
>Unknown
>libmlx4-rdmav2.so 00002B84CCE77ECC Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBBBDD0F Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB5727F Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB56D21 Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB59E31 Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB304B6 Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB2CDB8 Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B84CBB30B48 Unknown Unknown
>Unknown
>sander.MPI 000000000055AD7C Unknown Unknown
>Unknown
>sander.MPI 00000000007B70E4 Unknown Unknown
>Unknown
>sander.MPI 00000000004A69E6 Unknown Unknown
>Unknown
>sander.MPI 00000000004A0495 Unknown Unknown
>Unknown
>sander.MPI 000000000040E01C Unknown Unknown
>Unknown
>libc.so.6 000000388B61D994 Unknown Unknown
>Unknown
>sander.MPI 000000000040DF29 Unknown Unknown
>Unknown
> * NB pairs 746 1219615 exceeds capacity ( 1219712) 24
> SIZE OF NONBOND LIST = 1219712
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 24
>MPI process (rank: 24) terminated unexpectedly on
>c326-304.ls4.tacc.utexas.edu
>MPI process (rank: 11) terminated unexpectedly on
>c310-106.ls4.tacc.utexas.edu
>forrtl: error (69): process interrupted (SIGINT)
>Image PC Routine Line
>Source
>libmpich.so.1.2 00002B1C2B32CCA7 Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B1C2B2C627F Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B1C2B2C43DD Unknown Unknown
>Unknown
>libmpich.so.1.2 00002B1C2B32A52C Unknown
>
> Rejwan Ali
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Received on Mon Aug 19 2013 - 13:00:25 PDT
