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Researchers who use LoBoS require a wide array of software to conduct
molecular modeling and simulations, as well as support software to keep
everything running.
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The primary modeling tool used on the cluster is the
CHARMM (Chemistry at HARvard Molecular Mechanics) software package. Dr. Bernard
Brooks, the head of the LCB, is one of the primary developers of CHARMM.
The CHARMM Development Project involves a network of developers in the
United States and elsewhere working with Professor Karplus and his group
at Harvard to develop and maintain the package.
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Another molecular dynamics package we use is
AMBER (Assisted Model Building with Energy Refinement). It is designed with
particular emphasis on studying the dynamics ofbiomolecules. AMBER consists of a
variety of tools such as SANDER, which performs basic molecular dynamics and PTRAJ,
which analyzes the coordinate files produced by the simulation.
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For ab initio quantum mechanical calculations we have available
GAMESS-US and
GAMESS-UK.
Both software packages provide means of performing QM/MM calculations via
a CHARMM QM/MM interface.
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A commercial tool, Gaussian,
also performs ab initio analyses of complex molecular systems. It contains
many advanced features such as the ONIOM method of analyzing the electribuc
structure of large molecules and the Polarizable Continuum Model for studying
molecules in solution.
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Another piece of commercial software that performs quantum calculations is
Q-Chem. Q-Chem uses efficient techniques
to parallelize methods such as Hartree-Fock and DFT single-point energies, geometry
optimizations, and frequency calculations. Q-Chem combines these advanced techniques
into a single package for use in ab initio computations. Q-Chem is also
capable of performing QM/MM calculations via a CHARMM QM/MM interface.
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NAMD is a parallel
molecular dynamics program. Its main feature is its extreme scalability. It
can be run on hundreds of processors to efficiently characterize the dynamics
of very large systems. It is compatible with input files of other software such
as CHARMM, AMBER, and X-PLOR.
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VMD is a multiplatform
molecular visualization program. It supports many different coordinate and
structure file formats, including those used by CHARMM, PQR, and AMBER. It
also is able to read GAMESS log files. We use it to create beautifully rendered
images of the molecular systems which we study (some of which can be found
on this Web site).
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- Most of our compiling is done with the open-source
GNU Compiler Collection. The version of MPICH that we currently use
is compiled with version 3.3.3 of gcc. Other software is compiled with the
non-free Portland Group compiler suite.
- MPICH is a portable
implementation of the MPI parallel computing standard. The software was
developed at Argonne National Laboratory. We currently use the 1.2.5 series,
but MPICH-2, which supports both the MPI-1 and MPI-2 standards, is now
available. The parallel CHARMM jobs we run on LoBoS use MPICH to handle their
MPI functionality.
- LA-MPI is another
implementation of the MPI standard, developed at Los Alamos National
Laboratory. It is no longer in active development, but existing versions
continue to be maintained. Development efforts are focusing on releasing
Open MPI.
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- The LoBoS job scheduler is the
TORQUE Resource Manager distributed by
Cluster Resources, Inc. We currently use version 1.1.0p6 with a couple of
small patches by Tim Miller and others. TORQUE is an improvement over
OpenPBS and in tests it has been able
to scale to managing over one thousand jobs simulataneously.
- We've found Nagios useful for general
cluster monitoring and supervising important systems such as our RAID arrays. Nagios
can automatically notify an administrator by e-mail when it detects a problem.
- For performance monitoring, we also have
Ganglia configured. Ganglia is useful because it requires little configuration
and scales well.
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We use GNUPlot for many
of our graphing needs. This software makes it easy to create good looking
graphs of data on the Unix command line.
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 Department of Health and Human Services
 National Institutes of Health
 National Heart, Lung, and Blood Institute
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