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
h4. Notes on compiling NAMD 2.6
# Run {{./config Linux-amd64-MPI.postfix}} to create an installation.
# 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
# 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
# Try {{make}} in the installation directory.
/usr/mpi/gcc/openmpi-1.4.1/bin/mpirun /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI/namd2 apoa1.namd