/tag/mpi
AlphaFold and UVA HPC
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 apptainer/1.2.2 alphafold/2.3.0 AlphaFold Installation Details Dockerfile We prepared a Docker image based on the official Dockerfile with some modifications.
Gaussian and UVA HPC
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 and UVA HPC
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: chem
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/2023.2 ModuleVersion Module Load Command gromacs2023.2 module load gcc/11.
Spark and UVA HPC
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/3.4.1 ModuleVersion Module Load Command spark3.4.1 module load spark/3.4.1 Using Spark interactively There are three ways to use Spark interactively:
Shell prompt Open OnDemand PySpark Open OnDemand Desktop If you need the Web UI you must use the third method (OOD Desktop).
ANSYS and UVA HPC
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
Code Debugging and UVA HPC
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 and UVA HPC
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 namd2.14 module load gcc/11.
ORCA and UVA HPC
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
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 18.0
module load intel/18.0 module load intelmpi/18.
Abinit and UVA HPC
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.
Message Passing Interface (MPI) and UVA HPC
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 HPC clusters.
MPI On the HPC System MPI is a standard that describes the behavior of a library. It is intended to be used with compiled languages (C/C++/Fortran).
