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 - 12:30:03 PDT
