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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 submit their jobs using the qsub command:

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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.

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