Biologics, Molecular Dynamics and Small Molecule Docking

AmberAMBER (Assisted Model Building with Energy Refinement) is a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs which includes source code and demos. Installed versions include Amber 12 and 14.

Amber is built to run on the CPUs (optionally via MPI) and GPUs (single and multiple). In addition a specially built version of Amber 14 has been implemented, in-house, that incorporates the accelerated RaMD-db originally developed by Donald Hamelberg at Emory.
Developer Website Amber on Gemini
Compound LibrariesSmall molecule chemical compound libraries are available for large scale in-silico docking. Currently there are over 5.9 million compounds in our database. The eMolecules database as well as all FDA approved drugs are available.
DesmondDesmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.
Developer Website
Schrodinger SuiteThe Schrodinger software suite consists of a number of applications comprised of small-molecule lead discovery and optimization, quantum mechanics, homology modeling, protein analysis, protein-protein docking, ligand docking and antibody modeling tools.
Developer Website Schrodinger on Gemini
TINKERThe TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field. Parameter sets for other widely-used force fields are under consideration for future releases.
Developer Site

Structural Biology

SBGrid SuiteThe full suite of over 270 structural biology programs maintained by the SBGrid consortium is available for use. The suite consists of applications for macromolecular X-ray crystallography, NMR, cryo-electron microscopy, computational chemistry and structural visualization and analysis.
SBGrid Website Software Listing

Numerics

ACMLAMD Core Math Library, or ACML, provides a free set of thoroughly optimized and threaded math routines for HPC, scientific, engineering and related compute-intensive applications.
AMD ACML Website
BLASThe BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. The Level 1 BLAS perform scalar, vector and vector-vector operations, the Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform matrix-matrix operations.
FFTW2/FFTW3FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST)
FFTW Website
Global ArraysGlobal Arrays, or GA, is the library developed by scientists at Pacific Northwest National Laboratory for parallel computing. GA provides a friendly API for shared-memory programming on distributed-memory computers for multidimensional arrays. The GA library is a predecessor to the GAS (global address space) languages currently being developed for high-performance computing.
HDF5Hierarchical Data Format (HDF) is a set of file formats designed to store and organize large amounts of numerical data.
LAPACKLAPACK (Linear Algebra Package) is a standard software library for numerical linear algebra. It provides routines for solving systems of linear equations and linear least squares, eigenvalue problems, and singular value decomposition.
NetCDF 4NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
ScaLAPACKScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines.

Development Tools

Allinea ForgeParallel software debugger (Allinea DDT) and profiling (Allinea MAP) tools can be used for debugging and profiling applications running on the cluster without needing to instrument the code.
Allinea Website
CUDA ToolkitNVIDIA CUDA toolkit and SDK for GPU software development and execution.
NVIDIA CUDA Website
gcc/gfortranGNU compiler collection for compiling C, C++ and Fortran applications.
Compilers on Gemini
Intel CompilersOptimized compilers for Intel CPUs. C, C++ and Fortran compilers are available, as is the math-kernel library (MKL) and threaded building blocks (TBB) library.
Compilers on Gemini
MVAPICH/MVAPICH2MPI implementation for applications using the Message Passing Interface. On Gemini, OpenMPI is the preferred MPI stack as it has been tuned for the cluster hardware.
OpenCLThe Open Compute Language runtime allows programming of any supported compute device (on Gemini they are CPUs and GPUs). OpenCL is platform and device agnostic.
OpenMPIOpen Message Passing Interface is the default MPI implementation used on Gemini. The current build supports process and memory affinity, openib, smcuda and tcp byte-transport layers. In addition, RDMA and GRDMA (GPU-RDMA over Infiniband) are also supported.
OpenMPI on Gemini

General Cluster Tools

Module FilesMost of the primary applications on Gemini use module files for configuring and setting up the user environment.
Modules on Gemini.
SLURMSLURM is the default job scheduler for submitting jobs to the cluster. SLURM has replaced Sun Grid Engine as the default scheduler and SGE is no longer available. Converting job submission scripts is relatively straightforward.
SLURM on Gemini.