AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
TotalView is a multiprocess debugger for applications written in C, C++, FORTRAN 77, Fortran 90, and PGI HPF. It supports multiple parallel programming paradigms including MPI, PVM and OpenMP.
The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. The code may be used to perform consistent studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces and crystalline solids.
CUDA, (the Compute Unified Device Architecture), is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives program developers direct access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. At MSI, CUDA is installed on Mesabi , our main cluster. There are 40 nodes with 2 K40 GPUs each. In order to request the GPU nodes, you need to use the k40 queue . In the PBS options, you should include the number of GPUs that are needed for the job. Below is an...
The Integrated Genome Browser (IGB, pronounced ig-bee) is an application intended for visualization and exploration of genomes and corresponding annotations from multiple data sources. It is an extension of the Affymetrix software suite.
MSI tracks the utilization of the software modules installed on our systems. When a module has not been utilized in more than a year, it becomes a candidate for decommissioning and removal from our systems. Once a candidate for decommissioning has been identified, access to that software will be...
posted on September 4, 2013 Dr. Matthew G. Knepley , University of Chicago , will present a hands-on tutorial for PETSc at MSI on September 30. Dr. Knepley is one of the authors of the widely used PETSc library for scientific computing from Argonne National Laboratory , and is a principal designer...
Comsol Multiphysics (formerly known as FEMLAB) is a Multiphysics modeling tool that solves all types of problems based on Finite Element Analysis and Partial Differential Equations (PDEs). Predefined applications modes include stress/strain, heat transfer, CFD, and electromagnetics. Additonal features of Comsol Multiphysics include specialized add-on modules for chemical Engineering, Structural Mechanics and Electromagnetics. MSI currently has both education and research licenses. The educational license is COMSOL version 4.1.
librra is a library to support synchronization with Windows Mobile devices.
Partek Genomics Suite (Partek GS) is a software suite of statistics and interactive data visualization designed to extract biological signals from noisy data. Partek GS is able to support microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA.