This tutorial will provide an introduction to the Linux operating system, with particular attention paid to working from the command line. The tutorial will cover basics such as fundamental commands, editing files, understanding directories and permissions, and remote access.
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mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST . mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processor computers. The primary advantage to using mpiBLAST versus traditional NCBI BLAST is performance. mpiBLAST can increase performance by several orders of magnitude while still retaining identical results as output from NCBI BLAST.
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.
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.
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.
Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/22/17. If you need this software, please contact firstname.lastname@example.org . Clover is a program for identifying functional sites in DNA sequences. For a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.
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.
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...
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.