/tag/mpi
Spark on Rivanna
Description Spark is Hadoop MapReduce done in memory Software Category: devel
For detailed information, visit the Spark website.
Available Versions To find the available versions and learn how to load them, run:
module spider spark The output of the command shows the available Spark module versions.
For detailed information about a particular Spark module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider spark/3.1.2 ModuleVersion Module Load Command spark3.1.2 module load spark/3.1.2 Using Spark interactively There are three ways to use Spark interactively:
AlphaFold on Rivanna
Description Open source code for AlphaFold
Software Category: bio For detailed information, visit the AlphaFold website.
Available Versions The current installation of AlphaFold incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider alphafold The output of the command shows the available AlphaFold module versions.
For detailed information about a particular AlphaFold module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider alphafold/2.3.0 ModuleVersion Module Load Command alphafold2.3.0 module load singularity/3.7.1 alphafold/2.3.0 AlphaFold Installation Details Dockerfile We prepared a Docker image based on the official Dockerfile with some modifications.
ANSYS on Rivanna
Description ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Software Category: cae
Local support is minimal; users should make an account at the student forum through the ANSYS website for technical support and for obtaining detailed information.
Available Versions The current installation of ANSYS incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider ansys The output of the command shows the available ANSYS module versions.
For detailed information about a particular ANSYS module, including how to load the module, run the module spider command with the module’s full version label.
Code Debugging on Rivanna
TotalView TotalView is a full-featured, source-level, graphical debugger for applications written in C, C++, Fortran (77 and 90/95/2003), assembler, and mixed source/assembler codes. It is a multiprocess, multithread debugger that supports multiple parallel programming paradigms including MP and OpenMP. The University has a near-site license (256 tokens) for Totalview on all versions of Linux. Visit the TotalView website for detailed documentation.
Available Versions To find the available versions and learn how to load them, run:
module spider totalview The output of the command shows the available TotalView module versions.
For detailed information about a particular TotalView module, including how to load the module, run the module spider command with the module’s full version label.
NAMD on Rivanna
Description NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Software Category: chem
For detailed information, visit the NAMD website.
Available Versions The current installation of NAMD incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider namd The output of the command shows the available NAMD module versions.
For detailed information about a particular NAMD module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider namd/2.14 ModuleVersion Module Load Command namd2.
ORCA on Rivanna
Description ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Software Category: chem
For detailed information, visit the ORCA website.
Available Versions The current installation of ORCA incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider orca The output of the command shows the available ORCA module versions.
A Short MPI Tutorial
Tutorials and books on MPI A helpful online tutorial is available from the Lawrence Livermore National Laboratory. The following books can be found in UVA libraries:
Parallel Programming with MPI by Peter Pacheco. Using MPI : Portable Parallel Programming With the Message-Passing Interface by William Gropp, Ewing Lusk, and Anthony Skjellum. Using MPI-2: Advanced Features of the Message- Passing Interface by William Gropp, Ewing Lusk, and Rajeev Thakur. MPI: The Complete Reference : The MPI Core by Marc Snir, Steve Otto, Steven Huss-Lederman, David Walker, and Jack Dongarra. MPI: The Complete Reference : The MPI-2 Extensions by William Gropp, Steven Huss-Lederman, Andrew Lumsdaine, Ewing Lusk, Bill Nitzberg, and Marc Snir.
Building and Running MPI Code
Building an MPI Code All implementations provide wrappers around the underlying compilers that simplify compilation. As it is very important to use the headers that correspond to a given library, users are urged to make use of the wrappers whenever possible. For OpenMPI and MVAPICH2 these are:
mpicc (C) mpicxx (C++) mpif90 (Fortran free or fixed format) For Intel MPI these use gcc/g++/gfortran by default, which is generally not recommended; to use the Intel compilers the corresponding wrappers are:
mpiicc mpiicpc mpiifort Note: At this time, we recommend MPI users build with Intel 18.0 and IntelMPI 18.
Abinit on Rivanna
Description ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Software Category: chem
For detailed information, visit the Abinit website.
Available Versions The current installation of Abinit incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider abinit The output of the command shows the available Abinit module versions.
For detailed information about a particular Abinit module, including how to load the module, run the module spider command with the module’s full version label.
Gaussian on Rivanna
Description Gaussian is a suite of electronic-structure codes. Software Category: chem
For detailed information, visit the Gaussian website.
Available Versions The current installation of Gaussian incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider gaussian The output of the command shows the available Gaussian module versions.
For detailed information about a particular Gaussian module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gaussian/g16 ModuleVersion Module Load Command gaussiang16 module load gaussian/g16 gaussiangrads16 module load gaussian/grads16 License and Permission We have a site license.
GROMACS on Rivanna
Description GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Software Category: URL: http://www.gromacs.org
For detailed information, visit the GROMACS website.
Available Versions To find the available versions and learn how to load them, run:
module spider gromacs The output of the command shows the available GROMACS module versions.
For detailed information about a particular GROMACS module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gromacs/2022.4 ModuleVersion Module Load Command gromacs2022.
Message Passing Interface (MPI) on Rivanna
Overview MPI stands for Message Passing Interface. The MPI standard is defined by the Message Passing Interface Forum. The standard defines the interface for a set of functions that can be used to pass messages between processes on the same computer or on different computers. MPI can be used to program shared memory or distributed memory computers. There is a large number of implementations of MPI from various computer vendors and academic groups. MPI is supported on the Rivanna cluster.
MPI On Rivanna MPI is a standard that describes the behavior of a library. It is intended to be used with compiled languages (C/C++/Fortran).
