[AMBER] TI calculation Fatal error in PMPI_Bcast

From: Changqing Yan <ycqchemical.gmail.com>
Date: Fri, 28 Feb 2014 15:40:33 +0800

Dear,

I want to run a thermodynamical integration calculation. input file and
script are like this:

Initial minimisation of protein side chains and ions
 &cntrl
  imin=0, irest=1, ntx=5,
  cut=10, ntb=2, ntr=0,
  pres0=1.0, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=5000000, dt=0.001,
  ntpr=5000, ntwx=5000, ntwr=50000,
  icfe=1, clambda=0.0
 /

#! /bin/sh

#PBS -q dq2
#PBS -N Amber12
#PBS -l nodes=1:ppn=12
##PBS -l mem=1024MB
#PBS -e mpi_amber.err2b
#PBS -o mpi_amber.log2b
#PBS -m bea
#PBS -M ycqchemical.gmail.com

export PATH=/opt/share/Python-2.7.3/bin/:$PATH
export LD_LIBRARY=/opt/share/Python-2.7.3/lib:$LD_LIBRARY
export AMBERHOME=/opt/share/amber12
source /opt/share/etc/mpich-3.0.4.intel.sh

cd /scratch/s1007018600/comp1/input/TI/0.0
pwd
date

pbs_mpirun $AMBERHOME/bin/sander.MPI -O -i ligand-md2.in -o
ligand-md2-1.out -p complex-sol.prmtop -c ligand-md1.rst -r
ligand-md2-1.rst -x ligand-md2-1.mdcrd -ref ligand-md1.rst

date

however, when I submitted my job (qsub xxx), a mistake comes out, saying:

Fatal error in PMPI_Bcast: Invalid communicator, error stack:
PMPI_Bcast(1525): MPI_Bcast(buf=0x4b2f608, count=1, MPI_INTEGER, root=0,
comm=0x0) failed
PMPI_Bcast(1466): Invalid communicator

and the outfile is like this:

| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.

| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

how can I fix this?

Thx.
C.Q.
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Received on Fri Feb 28 2014 - 00:00:03 PST
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