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Using the queue system

All programs run on Darius must use the queue system. Users can submit their jobs using the qsub command:

qsub jobscript.sh

Here is an example of a simple PBS script, which is like an ordinary BASH script, but with the addition of special #PBS directives:

#!/bin/bash                                                                                                                                                                        
#PBS -k o                                                                                                                                                                          
#PBS -N apoa                                                                                                                                                                       
#PBS -l nodes=1:ppn=4,walltime=12:00:00                                                                                                                                            
#PBS -j oe                                                                                                                                                                         
cd /home/musolino/namd/apoa1
/usr/mpi/gcc/openmpi-1.4.1/bin/mpirun /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI/namd2 apoa1.namd

Notes on compiling NAMD 2.6

  1. Run ./config Linux-amd64-MPI.postfix to create an installation.
  2. The new Charm++ and NAMD 2.7 use different platform names (e.g. Linux-x86_64-OpenMPI for NAMD 2.7, but Linux-amd64-MPI for NAMD 2.6. This causes problems when looking for the Charm++ installation, so edit Make.charm in NAMD directory: 
    CHARMBASE = /share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx
  3. Then edit Makearch in the Linux-amd64-MPI.postfix directory as follows, by changing the CHARM=... line: 
    include .rootdir/Make.charm
include .rootdir/arch/Linux-amd64-MPI.arch
CHARM = $(CHARMBASE)
NAMD_PLATFORM = $(NAMD_ARCH)-MPI
include .rootdir/arch/$(NAMD_ARCH)$(NAMD_SUBARCH).base
  4. Try make in the installation directory.
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