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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.

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
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