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resif_modules.yaml
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base:
ULHPC-gpu:
desc: Generic Module bundle for GPU accelerated User Software in use on the UL
HPC Facility
versions:
2019b:
swsets:
2019b:
archs:
- gpu
clusters:
- iris
www: http://hpc.uni.lu/
bio:
ABySS:
desc: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
versions:
2.2.5:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.bcgsc.ca/platform/bioinfo/software/abyss
BEDTools:
desc: 'BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities
allow one to address common genomics tasks such as finding feature overlaps
and computing coverage. The utilities are largely based on four widely-used
file formats: BED, GFF/GTF, VCF, and SAM/BAM.'
versions:
2.29.2:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2.30.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://bedtools.readthedocs.io/
BLAST+:
desc: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing
primary biological sequence information, such as the amino-acid sequences of
different proteins or the nucleotides of DNA sequences.
versions:
2.11.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
2.9.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://blast.ncbi.nlm.nih.gov/
BWA:
desc: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively
short nucleotide sequences against a long reference sequence such as the human
genome.
versions:
0.7.17:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: http://bio-bwa.sourceforge.net/
BamTools:
desc: BamTools provides both a programmer's API and an end-user's toolkit for
handling BAM files.
versions:
2.5.1:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://github.com/pezmaster31/bamtools
BioPerl:
desc: Bioperl is the product of a community effort to produce Perl code which
is useful in biology. Examples include Sequence objects, Alignment objects and
database searching objects.
versions:
1.7.2:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
1.7.8:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://bioperl.org/
Bowtie2:
desc: ' Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing
reads to long reference sequences. It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good at aligning
to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with
an FM Index to keep its memory footprint small: for the human genome, its memory
footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end
alignment modes.'
versions:
2.3.5.1:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2.4.2:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
FastQC:
desc: FastQC is a quality control application for high throughput sequence data.
It reads in sequence data in a variety of formats and can either provide an
interactive application to review the results of several different QC checks,
or create an HTML based report which can be integrated into a pipeline.
versions:
0.11.9:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
GROMACS:
desc: 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.
This is a CPU only build, containing both MPI and threadMPI builds for both
single and double precision. It also contains the gmxapi extension for the single
precision MPI build.
versions:
'2019.4':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
'2019.6':
swsets:
2019b:
archs:
- gpu
clusters:
- iris
'2020':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
'2021':
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
'2021.2':
swsets:
2020b:
archs:
- gpu
clusters:
- iris
www: https://www.gromacs.org
HTSlib:
desc: A C library for reading/writing high-throughput sequencing data. This package
includes the utilities bgzip and tabix
versions:
1.10.2:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
'1.12':
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.htslib.org/
Jellyfish:
desc: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
versions:
2.3.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: http://www.genome.umd.edu/jellyfish.html
SAMtools:
desc: SAM Tools provide various utilities for manipulating alignments in the SAM
format, including sorting, merging, indexing and generating alignments in a
per-position format.
versions:
'1.10':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
'1.12':
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.htslib.org/
Salmon:
desc: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
quantification estimates from RNA-seq data.
versions:
1.1.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://github.com/COMBINE-lab/salmon
TopHat:
desc: TopHat is a fast splice junction mapper for RNA-Seq reads.
versions:
2.1.2:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: http://ccb.jhu.edu/software/tophat/
Trinity:
desc: 'Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent
software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to
process large volumes of RNA-Seq reads.'
versions:
2.10.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://trinityrnaseq.github.io
kallisto:
desc: kallisto is a program for quantifying abundances of transcripts from RNA-Seq
data, or more generally of target sequences using high-throughput sequencing
reads.
versions:
0.46.1:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://pachterlab.github.io/kallisto/
cae:
ABAQUS:
desc: Finite Element Analysis software for modeling, visualization and best-in-class
implicit and explicit dynamics FEA.
versions:
'2018':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
'2021':
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.simulia.com/products/abaqus_fea.html
OpenFOAM:
desc: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive
range of features to solve anything from complex fluid flows involving chemical
reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
versions:
'8':
swsets:
2020b:
archs:
- epyc
clusters:
- aion
v1912:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://www.openfoam.org/
OpenFOAM-Extend:
desc: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive
range of features to solve anything from complex fluid flows involving chemical
reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
versions:
4.1-20200408:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: http://www.extend-project.de/
Salome:
desc: 'The SALOME platform is an open source software framework for pre- and post-processing
and integration of numerical solvers from various scientific fields. CEA and
EDF use SALOME to perform a large number of simulations, typically related to
power plant equipment and alternative energy. To address these challenges, SALOME
includes a CAD/CAE modelling tool, mesh generators, an advanced 3D visualization
tool, etc. '
versions:
8.5.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
9.8.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.salome-platform.org/
gmsh:
desc: Salome is an open-source software that provides a generic Pre- and Post-Processing
platform for numerical simulation. It is based on an open and flexible architecture
made of reusable components.
versions:
4.4.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: http://gmsh.info/
chem:
ABINIT:
desc: 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.
versions:
9.4.1:
swsets:
2020b:
archs:
- epyc
clusters:
- aion
www: https://www.abinit.org/
ASE:
desc: ASE is a python package providing an open source Atomic Simulation Environment
in the Python scripting language. From version 3.20.1 we also include the ase-ext
package, it contains optional reimplementations in C of functions in ASE. ASE
uses it automatically when installed.
versions:
3.19.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
3.20.1:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
3.21.1:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://wiki.fysik.dtu.dk/ase
CRYSTAL:
desc: The CRYSTAL package performs ab initio calculations of the ground state
energy, energy gradient, electronic wave function and properties of periodic
systems. Hartree-Fock or Kohn- Sham Hamiltonians (that adopt an Exchange-Correlation
potential following the postulates of Density-Functional Theory) can be used.
versions:
'17':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: http://www.crystal.unito.it
GPAW:
desc: GPAW is a density-functional theory (DFT) Python code based on the projector-augmented
wave (PAW) method and the atomic simulation environment (ASE). It uses real-space
uniform grids and multigrid methods or atom-centered basis-functions.
versions:
20.1.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://wiki.fysik.dtu.dk/gpaw/
GPAW-setups:
desc: PAW setup for the GPAW Density Functional Theory package. Users can install
setups manually using 'gpaw install-data' or use setups from this package. The
versions of GPAW and GPAW-setups can be intermixed.
versions:
0.9.20000:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://wiki.fysik.dtu.dk/gpaw/
NAMD:
desc: NAMD is a parallel molecular dynamics code designed for high-performance
simulation of large biomolecular systems.
versions:
'2.13':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://www.ks.uiuc.edu/Research/namd/
PLUMED:
desc: PLUMED is an open source library for free energy calculations in molecular
systems which works together with some of the most popular molecular dynamics
engines. Free energy calculations can be performed as a function of many order
parameters with a particular focus on biological problems, using state of the
art methods such as metadynamics, umbrella sampling and Jarzynski-equation based
steered MD. The software, written in C++, can be easily interfaced with both
fortran and C/C++ codes.
versions:
2.5.3:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2.7.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.plumed.org
QuantumESPRESSO:
desc: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure
calculations and materials modeling at the nanoscale. It is based on density-functional
theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
versions:
'6.7':
swsets:
2019b:
archs:
- broadwell
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.quantum-espresso.org
Wannier90:
desc: A tool for obtaining maximally-localised Wannier functions
versions:
3.1.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: http://www.wannier.org
kim-api:
desc: Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a
collection of interatomic models (potentials) for atomistic simulations. This
is a library that can be used by simulation programs to get access to the models
in the OpenKIM database. This EasyBuild only installs the API, the models can
be installed with the package openkim-models, or the user can install them manually
by running kim-api-collections-management install user MODELNAME or kim-api-collections-management
install user OpenKIM to install them all.
versions:
2.1.3:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://openkim.org/
libctl:
desc: libctl is a free Guile-based library implementing flexible control files
for scientific simulations.
versions:
4.0.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://github.com/stevengj/libctl
libxc:
desc: Libxc is a library of exchange-correlation functionals for density-functional
theory. The aim is to provide a portable, well tested and reliable set of exchange
and correlation functionals.
versions:
4.3.4:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
5.1.2:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.tddft.org/programs/libxc
spglib-python:
desc: Spglib for Python. Spglib is a library for finding and handling crystal
symmetries written in C.
versions:
1.16.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
www: https://pypi.python.org/pypi/spglib
yaff:
desc: Yaff stands for 'Yet another force field'. It is a pythonic force-field
code.
versions:
1.6.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://molmod.github.io/yaff/
compiler:
AOCC:
desc: AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0
versions:
3.1.0:
swsets:
2020b:
archs:
- epyc
clusters:
- aion
www: https://developer.amd.com/amd-aocc/
Clang:
desc: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard
library -- use libstdc++ from GCC.
versions:
11.0.1:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
9.0.1:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
www: https://clang.llvm.org/
GCC:
desc: The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Java, and Ada, as well as libraries for these languages (libstdc++,
libgcj,...).
versions:
10.2.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
8.3.0:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
www: https://gcc.gnu.org/
GCCcore:
desc: The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Java, and Ada, as well as libraries for these languages (libstdc++,
libgcj,...).
versions:
10.2.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
8.3.0:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
www: https://gcc.gnu.org/
Go:
desc: Go is an open source programming language that makes it easy to build simple,
reliable, and efficient software.
versions:
1.14.1:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
1.16.6:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://www.golang.org
LLVM:
desc: The LLVM Core libraries provide a modern source- and target-independent
optimizer, along with code generation support for many popular CPUs (as well
as some less common ones!) These libraries are built around a well specified
code representation known as the LLVM intermediate representation ("LLVM IR").
The LLVM Core libraries are well documented, and it is particularly easy to
invent your own language (or port an existing compiler) to use LLVM as an optimizer
and code generator.
versions:
10.0.1:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
11.0.0:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
9.0.0:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
9.0.1:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://llvm.org/
PGI:
desc: C, C++ and Fortran compilers from The Portland Group - PGI
versions:
'19.10':
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://www.pgroup.com/
iccifort:
desc: Intel C, C++ & Fortran compilers
versions:
2019.5.281:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
2020.4.304:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
www: https://software.intel.com/en-us/intel-compilers/
data:
Arrow:
desc: Apache Arrow (incl. PyArrow Python bindings)), a cross-language development
platform for in-memory data.
versions:
0.16.0:
swsets:
2019b:
archs:
- broadwell
- skylake
clusters:
- iris
www: https://arrow.apache.org
DB_File:
desc: Perl5 access to Berkeley DB version 1.x.
versions:
'1.855':
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
clusters:
- aion
- iris
www: https://perldoc.perl.org/DB_File.html
GDAL:
desc: GDAL is a translator library for raster geospatial data formats that is
released under an X/MIT style Open Source license by the Open Source Geospatial
Foundation. As a library, it presents a single abstract data model to the calling
application for all supported formats. It also comes with a variety of useful
commandline utilities for data translation and processing.
versions:
3.0.2:
swsets:
2019b:
archs:
- broadwell
- skylake
- gpu
clusters:
- iris
3.2.1:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters:
- aion
- iris
www: https://www.gdal.org
HDF:
desc: HDF (also known as HDF4) is a library and multi-object file format for storing
and managing data between machines.
versions:
4.2.15:
swsets:
2020b:
archs:
- broadwell
- epyc
- skylake
- gpu
clusters: