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  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:
    Code Block
    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:
    Code Block
    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.

Using the queue system

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

Code Block
qsub jobscript.sh

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

Code Block
#!/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