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Darius is a 32-node cluster with InfiniBand QDR interconnections. It runs CentOS 5.4 (Linux kernel version 2.6), which is closely related to Red Hat Enterprise Linux. Its hostname is darius.mit.edu.

Performance

Notes on performance are coming soon.

Using the queue system

All programs run on Darius must use the queue system. Users can check what jobs are running using qstat; XWindows users can try xpbs, although load times are long. 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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