Software Centrally Managed¶
On Thorny Flat there packages centrally managed from three different sources. Packages provided via Environment Modules, Software included in Conda Environments and Software built inside Singularity Containers. The Software below is a catalog of the software offered on Thorny Flat on June 6, 2020. New packages are added over time and some old packages are deprecated and eventually removed.
Software via Environment Modules¶
Software Name |
TIER 0 |
Description |
Modules |
|---|---|---|---|
HPL |
Benchmarks |
High Performance Linpack Benchmarks |
benchmarks/hpl/2.3_gcc48
benchmarks/hpl/2.3_gcc82
|
CMake |
Developers |
Build System |
dev/cmake/3.15.2
dev/cmake/3.15.4
|
Doxygen |
Developers |
Create documentation from Sources |
dev/doxygen/1.8.15
|
GNU
Compiler
Collection
|
Languages |
Compilers for C, C++,
Fortran and more
|
lang/gcc/7.5.0
lang/gcc/8.2.0
lang/gcc/8.4.0
lang/gcc/9.3.0
|
Go Language |
Languages |
Go Programming Language |
lang/go/1.12.7
|
Intel Compiler Suite |
Languages |
Intel Compilers Sute: C, C++ and Fortran
Includes the Math Kernel Library (MKL)
and other Intel optimized Libraries
|
lang/intel/2018
lang/intel/2018_u4
lang/intel/2019
lang/intel/2019_u5
|
Java Developers Kit |
Languages |
Software to compile and run Java programs |
lang/java/jdk1.8.0_201
|
Julia |
Languages |
Fast Interpreted Language for
Scientific Computing
|
lang/julia/1.1.1
lang/julia/1.2.0
|
PGI Compiler Suite |
Languages |
PGI Compilers for C, C++ and Fortran |
lang/pgi/19.4
|
Python |
Languages |
Python Programming Language
CPython is the reference C
implementation
Intel Python offer several optimizations
for Numerical operations via MKL
Pypy is an optimized implementation
of Python
|
lang/python/cpython_3.6.9_gcc82
lang/python/cpython_3.7.2_gcc82
lang/python/cpython_3.7.4_gcc82
lang/python/intelpython_2.7.14
lang/python/intelpython_2.7.16
lang/python/intelpython_3.6.3
lang/python/intelpython_3.6.9
lang/python/pypy2.7-7.1.1-portable
lang/python/pypy3.6-7.1.1-portable
lang/python/pypy3.6-v7.1.1-thorny
|
R Language |
Languages |
R is a Language used for Statistics |
lang/r/3.5.2
lang/r/3.6.2
|
AtomPAW |
Libraries |
Projected Augmented Wave code
Used by several DFT codes
|
libs/atompaw/4.1.0.5_gcc48
libs/atompaw/4.1.0.5_intel18
|
Boost |
Libraries |
Portable C++ source Libraries |
libs/boost/1.70_gcc48_ompi216
libs/boost/1.70_gcc82_ompi216
libs/boost/1.70_intel18
|
CFITSIO |
Libraries |
FITS subroutine Library |
libs/cfitsio/3.47_gcc82
|
FFTW |
Libraries |
Fast Fourier Transforms |
libs/fftw/3.3.8_gcc48
libs/fftw/3.3.8_gcc75
libs/fftw/3.3.8_gcc75_ompi3.1.6
libs/fftw/3.3.8_gcc82
libs/fftw/3.3.8_gcc82b
libs/fftw/3.3.8_gcc82_ompi4
libs/fftw/3.3.8_gcc84
libs/fftw/3.3.8_gcc84_ompi3.1.6
libs/fftw/3.3.8_gcc93
libs/fftw/3.3.8_gcc93_ompi3.1.6
libs/fftw/3.3.8_intel18
|
HDF5 |
Libraries |
Open Source File Format for large
and complex Data
|
libs/hdf5/1.10.5_gcc48
libs/hdf5/1.10.5_gcc48_ompi31
libs/hdf5/1.10.5_gcc82
libs/hdf5/1.10.5_gcc82_ompi31
libs/hdf5/1.10.5_intel18
libs/hdf5/1.10.5_intel18_impi18
libs/hdf5/1.10.5_intel19
libs/hdf5/1.10.5_intel19_impi19
libs/hdf5/1.10.6_gcc82_ompi31
libs/hdf5/1.12.0_gcc75
libs/hdf5/1.12.0_gcc75_ompi31
libs/hdf5/1.12.0_gcc84
libs/hdf5/1.12.0_gcc84_ompi31
libs/hdf5/1.12.0_gcc93
libs/hdf5/1.12.0_gcc93_ompi31
|
LibPSML |
Libraries |
Pseudopotential Markup Language
Used by DFT codes
|
libs/libpsml/1.1.7_gcc82
|
LibXC |
Libraries |
Library for Exchange Correlation
Functionals
Used by DFT codes
|
libs/libxc/3.0.1_gcc48
libs/libxc/3.0.1_gcc82
libs/libxc/3.0.1_intel18
libs/libxc/4.2.3_intel18
libs/libxc/4.3.4_gcc82
libs/libxc/4.3.4_intel18
|
Magma |
Libraries |
Dense Linear Algebra for
hybrid Multicore+GPUs
|
libs/magma/2.5.1_gcc48
|
NetCDF |
Libraries |
Open Source File Format for
Scientific Data
|
libs/netcdf/4.1.1_gcc48
libs/netcdf/4.7.1_gcc82
libs/netcdf/4.7.1_intel18
libs/netcdf/4.7.1_intel19
libs/netcdf/4.x_gcc48
libs/netcdf/4.x_gcc48_ompi2
libs/netcdf/4.x_gcc82
libs/netcdf/4.x_gcc82_ompi4
libs/netcdf/4.x_intel18
libs/netcdf/4.x_intel18_impi18
libs/netcdf/fortran-4.5.2_intel18
|
BLAS/LAPACK
(Netlib)
|
Libraries |
Standard Linear Algebra Routines |
libs/netlib/3.8.0_gcc82
libs/netlib/3.8.0_intel18
|
OpenBLAS |
Libraries |
Optimized BLAS/LAPACK with
multithreading and CPU extensions
like AVX
|
libs/openblas/0.3.5_gcc48
libs/openblas/0.3.5_gcc82
libs/openblas/0.3.7_gcc82
libs/openblas/0.3.9_gcc75
libs/openblas/0.3.9_gcc84
libs/openblas/0.3.9_gcc93
|
BLAS/LAPACK
(Reference)
|
Libraries |
Reference Libraries BLAS/LAPACK |
libs/refblas/3.8_gcc82
|
Suitesparse |
Libraries |
Routines for Sparse Linear Algebra
operations
|
libs/suitesparse/5.4.0_gcc82
|
Swig |
Libraries |
Building Scripting Language interfaces
to C and C++
|
libs/swig/4.0.1_gcc82
|
XMLF90 |
Libraries |
Support for XML in Fortran 90 |
libs/xmlf90/1.5.4_gcc48
libs/xmlf90/1.5.4_gcc82
|
YaML |
Libraries |
Yet Another Markup Language |
libs/yaml/0.2.2_gcc82
|
ZeroMQ |
Libraries |
libs/zeromq/4.3.1_gcc82
|
|
Cuda |
Parallel |
CUDA compiler and runtime |
parallel/cuda/10.0.130
|
HWLOC |
Parallel |
Hardware Location library |
parallel/hwloc/1.10.1_gcc48
parallel/hwloc/1.10.1_gcc82
parallel/hwloc/1.10.1_intel18
parallel/hwloc/1.11.13_gcc82
parallel/hwloc/2.0.3_gcc82
parallel/hwloc/2.0.3_intel18
|
Intel MPI |
Parallel |
Intel MPI library 2017 |
parallel/impi/2017
|
MPICH |
Parallel |
MPICH Implementation of MPI |
parallel/mpich/3.3_gcc82
|
MVAPICH |
Parallel |
MVAPICH Implementation of MPI |
parallel/mvapich2/2.3.1_gcc82
|
OpenMPI |
Parallel |
OpenMPI Implementation of MPI |
parallel/openmpi/2.1.2_gcc48
parallel/openmpi/2.1.6_gcc48
parallel/openmpi/2.1.6_gcc82
parallel/openmpi/2.1.6_intel18
parallel/openmpi/3.1.4_gcc48
parallel/openmpi/3.1.4_gcc82
parallel/openmpi/3.1.4_intel18
parallel/openmpi/3.1.6_gcc75
parallel/openmpi/3.1.6_gcc84
parallel/openmpi/3.1.6_gcc93
|
UCX |
Parallel |
UCX library communication framework |
parallel/ucx/1.5.0_gcc82
|
TMUX |
Utils |
Terminal Multiplexer |
utils/tmux/3.0a
|
Software Name |
TIER 1 |
Description |
Modules |
|---|---|---|---|
Conda |
Package and Environmnet Management |
conda |
|
Matlab |
Interactive Scientific Computing |
matlab/2018b |
|
Singularity |
Containerization for HPC Clusters |
singularity/2.5.2 |
Software Name |
TIER 2 |
Description |
Modules |
|---|---|---|---|
ANSYS Fluids |
ANSYS |
Computational Fluid Dynamics |
ansys/fluids_19.2
|
CASA |
Astronomy |
Common Astronomy Software
Applications
|
astronomy/casa/5.3.0
astronomy/casa/5.4.1
astronomy/casa/5.6.0
|
ABINIT |
Atomistic |
Plane-wave based DFT code |
atomistic/abinit/8.10.2_intel18
atomistic/abinit/8.10.3_gcc82
atomistic/abinit/8.10.3_gcc82_mpiio
atomistic/abinit/8.10.3_intel18
atomistic/abinit/9.0.4_gcc82
|
AMBER |
Atomistic |
Molecular Dynamics |
atomistic/amber/18_cuda
atomistic/amber/18_mpi
atomistic/amber/18_openmp
|
ELK |
Atomistic |
All electron DFT |
atomistic/elk/5.2.14_intel18
|
Espresso |
Atomistic |
Plane-wave based DFT code |
atomistic/espresso/6.4_intel18_seq
atomistic/espresso/6.4_intel18_thd
|
Gaussian |
Atomistic |
Localized basis DFT code |
atomistic/gaussian/g16
atomistic/gaussian/g16_rev1
atomistic/gromacs/2016.6
atomistic/gromacs/2016.6_cuda
atomistic/gromacs/2016.6_gcc48_cuda
atomistic/gromacs/2016.6_gcc82
atomistic/gromacs/2016.6_plumed_gcc82
atomistic/gromacs/2018.8_gcc82
atomistic/gromacs/2018.8_plumed_gcc82
atomistic/gromacs/2019.3
atomistic/gromacs/2019.3_gcc48_cuda
atomistic/gromacs/2019.4
atomistic/gromacs/2019.4_double
atomistic/gromacs/2019.4_gcc82
atomistic/gromacs/2019.4_plumed_gcc82
atomistic/gromacs/5.1.5_cuda
|
LAMMPS |
Atomistic |
Force Field Molecular Dynamics |
atomistic/lammps/2018-12-12_gcc82
atomistic/lammps/2018-12-12_gcc82_ompi
atomistic/lammps/2019.06.05
atomistic/lammps/2019.08.07_gcc82_ompi
atomistic/lammps/2019.08.07_intel19_im
|
NAMD |
Atomistic |
Molecular Dynamics |
atomistic/namd/2.13_CPU
atomistic/namd/2.13_CUDA
atomistic/namd/NAMD_Git-2020-01-02-mpi
atomistic/namd/NAMD_Git-2020-01-02-mpi
atomistic/namd/NAMD_Git-2020-01-02-ofi
atomistic/namd/NAMD_Git-2020-01-02-ofi
|
Octopus |
Atomistic |
Real Space TD-DFT code |
atomistic/octopus/9.1_gcc82
atomistic/octopus/9.1_gcc82_ompi31
|
Orca |
Atomistic |
Molecular Dynamics |
atomistic/orca/4.2.1_ompi216
atomistic/orca/4.2.1_ompi314
|
Plumed |
Atomistic |
Molecular Dynamics |
atomistic/plumed/2.5.3_gcc82
|
Siesta |
Atomistic |
Localized Molecular Dynamics |
atomistic/siesta/4.0.2_intel18
atomistic/siesta/4.0.2_intel19
|
VASP |
Atomistic |
Plane-wave based DFT code |
atomistic/vasp/5.4.4_intel18_seq
atomistic/vasp/5.4.4_intel18_thd
atomistic/vasp/5.4.4_intel19_seq
atomistic/vasp/5.4.4_intel19_thd
|
Emboss |
Bioinformatics |
Tools for Sequence Analysis |
bioinformatics/emboss/6.6.0
|
GATK4 |
Bioinformatics |
Genome Analysis Toolkit |
bioinformatics/gatk/4.1.0
|
HDFVIEW |
Data |
Visualize HDF5 files |
data/hdfview/3.1.0
|
Dakota |
Math Modeling |
Mathematical Optimization
and Uncertainty Quantification
|
math/dakota/6.10
math/dakota/6.10-UI
math/dakota/6.8
math/dakota/6.8-UI
|
GAMS |
Math Modeling |
Mathematical Optimization Problems |
math/gams/26.1
|
Graphviz |
Visualization |
Visualize Graphs |
visual/graphviz/2.40.1_gcc82
|
Paraview |
Visualization |
Scientific Data Visualization Tool |
visual/paraview/5.6.0
|
Software Name |
TIER 3 |
Description |
Modules |
|---|---|---|---|
Metamodules |
GCC + Python + Julia …
Intel Compilers + Python
Jupyter Notebooks
R Version 3.5.2
R Version 3.6.2
|
general_gcc82
general_intel18
jupyter_kernels
r/3.5.2
r/3.6.2
|
Software via Conda Environment¶
Conda Environment Name |
Description |
|---|---|
base |
Base conda environment, the first environment when you activate conda |
genomics-core-2020b |
Set of packages for Bioinformatics |
neural_gpu |
Neural Networks and Deep Learning with GPUs |
python27 |
Environment with Python Scientific Packages using Python 2.7 |
python35 |
Environment with Python Scientific Packages using Python 3.5 |
python36 |
Environment with Python Scientific Packages using Python 3.6 |
python37 |
Environment with Python Scientific Packages using Python 3.7 |
qiime2-2020.2 |
QIIME2 Next-Generation Microbiome Bioinformatics |
Software via Singularity Images¶
Image Name |
Description |
Based on |
GUI |
GPU |
|
|---|---|---|---|---|---|
casa-5.6.2_centos6.simg |
CASA build on CentOS 6 |
centos:centos6 |
No |
No |
|
centos-final.simg |
Example of image using libgraph 1.0.2, run examples “circle”, “julia” and “sample” |
centos:latest |
Yes |
No |
|
dakota-6.10-release-public-rhel7.simg |
Dakota 6.10: Sandia software for optimization and Uncertainty Quantification |
centos:latest |
No |
No |
|
docs_hpc_wvu.simg |
Contains Sphinx, pandoc and scripts to create documentation for https://docs.hpc.wvu.edu |
ubuntu:bionic |
No |
No |
|
dolmades.simg |
Windows Apps under Linux using Singularity (using wine) |
c1t4r/dolmades |
Yes? |
No |
|
Grass-7.4.0.simg |
GRASS (Geographic Resources Analysis Support System), open source GIS |
ubuntu:trusty |
Yes |
No |
|
Grass-7.4.simg |
GRASS (Geographic Resources Analysis Support System), open source GIS |
ubuntu:trusty |
Yes |
No |
|
Grass-7.6.1.simg |
GRASS (Geographic Resources Analysis Support System), open source GIS |
ubuntu:bionic |
Yes |
No |
|
Jupyter-5.2.2_Python-3.6.8.simg |
Python 3.6.8 with a number of Scientific Packages and Jupyter Notebooks |
ubuntu:bionic |
Yes |
No |
|
jupyter_conda.simg |
Python 3.6.8 with a number of Scientific Packages and Jupyter Notebooks |
continuumio/miniconda3 |
Yes |
No |
|
jupyter.simg |
Python 3.6.8 with a number of Scientific Packages and Jupyter Notebooks |
ubuntu:bionic |
Yes |
No |
|
jupyter-xenial.simg |
Python 3.5.2 with a number of Scientific Packages and Jupyter Notebooks |
ubuntu:xenial |
Yes |
No |
|
Keras-2.1.4_TensorFlow-1.5.0.simg |
Neural Networks and Deep Learning with Keras 2.1.4 and TensorFlow 1.5.0 |
gw000/keras-full:2.1.4 |
Yes |
Yes |
|
loos.simg |
Lightweight Object-Oriented Structure library (LOOS) |
ubuntu:trusty |
No |
No |
|
maxwell-b.simg |
Maxwell is a Multi-GPU FDFD solver |
nvidia/cuda:10.0-devel |
No |
Yes |
|
miniconda3_firefox.simg |
Jupyter from miniconda with Firefox |
continuumio/miniconda3 |
Yes |
No |
|
miniconda3.simg |
Jupyter from miniconda without firefox |
continuumio/miniconda3 |
Yes |
No |
|
orp-2.2.6.simg |
Oyster River Protocol |
macmaneslab/orp:2.2.6 |
No |
No |
|
pycbc-el7.simg |
PyCBC Software for Study Gravitational Waves |
pycbc/pycbc-el7:latest |
No |
No |
|
ParaView-5.6.0.simg |
ParaView 5.6: open-source, multi-platform data analysis and visualization |
ubuntu:bionic |
Yes |
No |
|
ParaView-5.7.0.simg |
ParaView 5.7: open-source, multi-platform data analysis and visualization |
ubuntu:bionic |
Yes |
No |
|
QGIS.simg |
QGIS Software for Geographic Information Systems |
ubuntu:bionic |
Yes |
No |
|
RStudio-desktop-1.2.5033_R-3.4.4.simg |
RStudio Desktop 1.2 with R 3.4.4 |
jekriske/r-base |
Yes |
No |
|
RStudio-server-1.2.5033_R-3.6.2.simg |
RStudio Server 1.2 with R 3.6.2 |
nickjer/singularity-r |
Yes |
No |
|
Stacks-2.5.simg |
Stacks: Pipeline for building loci from short-read sequences like illumina |
ubuntu:trusty |
No |
No |
|
Tensorflow-1.13.1-gpu-py3-jupyter.simg |
TensorFlow with support for GPUs |
tensorflow/tensorflow:1.13.1-gpu-py3-jupyter |
Yes |
No |
|
Tensorflow-1.13.1-py3-jupyter.simg |
TensorFlow without support for GPUs |
tensorflow/tensorflow:1.13.1-py3-jupyter |
Yes |
No |
|
TensorFlow_gpu_py3.simg |
TensorFlow with support for GPUs |
tensorflow/tensorflow:latest-gpu-py3 |
No |
Yes |
|
Ubuntu.simg |
Ubuntu Xenial |
ubuntu:xenial |
No |
No |
|
Visit-2.13.2.simg |
Visit: Interactive, scalable, visualization, animation and analysis tool |
ubuntu:trusty |
No |
No |
|
Visit-2.13.3.simg |
Visit: Interactive, scalable, visualization, animation and analysis tool |
ubuntu:bionic |
No |
No |
|
Visit-3.1.xenial.simg |
Visit: Interactive, scalable, visualization, animation and analysis tool |
ubuntu:xenial |
No |
No |
|
wkhtmltox-0.12.simg |
wkhtmltopdf command line tools to render HTML into PDF and other image formats |
ubuntu:trusty |
No |
No |
|
wkhtmltox.simg |
wkhtmltopdf command line tools to render HTML into PDF and other image formats |
ubuntu:trusty |
No |
No |
|
xfemm_v1_9_linux64.simg |
Cross platform electromagnetics finite element analysis based on FEMM |
debian:latest |
No |
No |
|
xfemm_v1_9_linux64.stretch.simg |
Cross platform electromagnetics finite element analysis based on FEMM |
debian:strecth |
No |
No |
|