Clúster Hydra

En el programa ÓMICAS contamos con un clúster Hydra, sistema de cómputo de alto rendimiento (High Performance Computer – HPC) compuesto por varios nodos que en total ponen a disposición de los usuarios 324 núcleos (cores) y 960GB de memoria RAM compartida para ejecutar procesos o calculos con altos requerimientos de recursos, tales como calculos de mecánica cuántica, calculos de dinamica molecular (clasica y no clasica) y procesos de machine learninng. Todo el sistema funciona sobre el sistema operativo Linux y la gestión de los procesos y recursos se realiza mediante el administrador de tareas Slurm, teniendo instalados además paquetes de software middleware (e.g. lebrerías de paso de mensajes MPI, compiladores C/C++/Fortran, LAPACK, FFTW, etc.) y aplicaciónes especializadas como LAMMPS, VNL-ATK, Schrödinger, SCM-AMS y NAMD.

En el clúster Hydra contamos con las siguientes accesos de aplicaciones: 

Librería en clúster

Librería

Versión

Licencia

Arpack-ng
A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
https://github.com/opencollab/arpack-ng

3.6.2 Open source BSD

ATLAS
Automatically Tuned Linear Algebra Software is a software library for linear algebra
http://math-atlas.sourceforge.net/

3.10.3 Open source BSD

BLASTDB
The BLAST databases
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

2017.01.04  

Boost
Free peer-reviewed portable C++ source libraries
www.boost.org/

1.57.0 Open source BSL 1.0

CLAPACK
A C implementation of the LAPACK standard software library for numerical linear algebra
www.netlib.org/clapack/

3.2.1 Propietario Freeware

Essentia
Open-source library and tools for audio and music analysis, description and synthesis
https://essentia.upf.edu/

2.0.1 Open source AGPL

Ffmpeg
A vast software suite of libraries and programs for handling video, audio, and other multimedia files and streams
https://ffmpeg.org/

2.5.3 Open Source
LGPLv2.1+ , GPLv2+

FFTW
A software library for computing discrete Fourier transforms
www.fftw.org/

3.3.4, 3.3.6-pl2 Open Source GPL

HDF5
Hierarchical Data Format is a set of file formats designed to store and organize large amounts of data
www.hdfgroup.org/solutions/hdf5/

1.10.1 Propietario Freeware

LAPACK
A standard software library for numerical linear algebra
www.netlib.org/lapack/

3.6.1, 3.7.1 Open source BSD

Libgraph
An implementation of the TurboC graphics API (graphics.h) on GNU/Linux using SDL
https://savannah.nongnu.org/projects/libgraph/

1.0.2 Open Source GPLv2+

Libjpeg
A free library with functions for handling the JPEG image data format
http://libjpeg.sourceforge.net/

1.3.0 Open source BSD-style

Libjpeg-turbo
A JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression
https://github.com/libjpeg-turbo/libjpeg-turbo

1.5.2 Open source BSD-style

Libpng
Official Portable Network Graphics reference library
www.libpng.org/pub/png/libpng.html

1.6.32

Open Source PRLLv2

Libtricubic
Local interpolation scheme in three dimensions
https://github.com/nbigaouette/libtricubic

1.0 Open Source GPLv2

Libxc
A library of exchange-correlation functionals for density-functional theory
www.tddft.org/programs/libxc/

4.3.4 Open Source MPL 2.0

Libxdr
Library that allows to read GROMACS trr and xtc files and also to convert from one format to another
https://vessokolev.blogspot.com/2017/03/compiling-xdrfile-library-by-using-pgi.html

1.1.4 Open source BSD

Matheval
A small library of procedures for evaluating mathematical functions
www.gnu.org/software/libmatheval/

1.1.11 Open source GPL

METIS
A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices
http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

5.1.0 Open Source AL 2.0
MUMPS
A library that solves a sparse system of linear equations A x = b using Gaussian elimination
http://mumps.enseeiht.fr/
5.1.2 Propietario CeCILL-C

NetCDF
A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
www.unidata.ucar.edu/software/netcdf/

4.4.1.1 Propietario Freeware

OpenBLAS
An implementation of the BLAS API with many hand-crafted optimizations for specific processor types
www.openblas.net/

0.2.14, 0.2.20 Open Source BSD

PAPI
Performance Application Programming Interface. 
https://icl.utk.edu/papi/

5.4.0 Propietario Freeware

PETSc
The Portable, Extensible Toolkit for Scientific Computation, is a suite of data structures and routines developed by Argonne National Laboratory for the scalable solution of scientific applications modeled by partial differential equations
www.mcs.anl.gov/petsc/

3.5.3, 3.6.1 Open Source BSD

Samplerate
A library for performing sample rate conversion of audio data
https://github.com/erikd/libsamplerate

0.1.8 Open Source GPLv2

ScaLAPACK
A library of high-performance linear algebra routines for parallel distributed memory machines
www.netlib.org/scalapack/

2.0.2 Open Source BSD

SDL
A cross-platform software development library designed to provide a hardware abstraction layer for computer multimedia hardware components
www.libsdl.org/

1.2.15 Open Source LGPL

Spglib
A library for finding and handling crystal symmetries written in C
https://spglib.github.io/spglib/

1.10.3 Open Source BSD

Szip
Science Data Lossless Compression library
https://support.hdfgroup.org/doc_resource/SZIP/

2.1.1 Propietario

Taglib
A library for reading and editing audio meta data
https://taglib.org/api/

1.9.1 Open Source MPL. LGPL

Trillinos
A collection of open-source software libraries, called packages, intended to be used as building blocks for the development of scientific applications
https://trilinos.github.io/

11.14.2, 12.0.1  Open Source LGPL

Xmlf90
A fast XML parser and generator in Fortran
https://gitlab.com/siesta-project/libraries/xmlf90

1.5.4 Propietario Freeware

PyYAML
A full-featured YAML framework for the Python programming language
https://pyyaml.org/

0.1.5 Propietario Freeware

MPI IntelMPI
A multifabric message-passing library that implements the open-source MPICH specification
https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html

3.1.4 3.3 Propietario Freeware

MPI OpenMPI
A Message Passing Interface library project combining technologies and resources from several other projects
https://www.open-mpi.org/

1.8.4, 2.0.2 Propietario Freeware

Aplicaciones

Nombre

Versión

Licencia

MPI mpich
A freely available, portable implementation of MPI, a standard for message-passing for distributed-memory applications used in parallel computing
www.mpich.org/

0.3.2.1 Open source

Allinea DDT
Graphical Debugger for parallel programming
https://developer.nvidia.com/allinea-ddt

5.0.1 Propietario

SCM AMS
Amsterdam Modeling Suite
www.scm.com/

2019.303 Propietario
Licencia hasta 2024

atom
pseudopotential generation program
http://bohr.inesc-mn.pt/~jlm/pseudo.html

4.2.7 Uso académico

bowtie2
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

2.2.9 Open Source GPL_3

cp2k
CP2K is a freely available quantum chemistry and solid state physics program package
www.cp2k.org/

3.0 Open Source GPL

cplex
IBM ILOG CPLEX Optimization Studio is an optimization software package
www.ibm.com/analytics/cplex-optimizer

12.4 Propietario

createLammpsInput
https://github.com/esemble/simpy/blob/master/tools/caltech/
createLammpsInput.pl

8.0_191 Propietario

Cufflinks
Transcriptome assembly and differential expression analysis for RNA-Seq
https://cole-trapnell-lab.github.io/cufflinks/

2.2.2

Open Source

DFTB+
a fast and efficient versatile quantum mechanical simulation software package
www.dftbplus.org/

18.2 Open Source LGPL

Ea-utils
Command-line tools for processing biological sequencing data
https://expressionanalysis.github.io/ea-utils/

r805 Open Source

Quantum ESPRESSO
an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
www.quantum-espresso.org/

5.0.2, 5.0.2, 5.2.0, 6.5.0 Open Source GPL

FastQC
Provides a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines
www.bioinformatics.babraham.ac.uk/projects/fastqc/

0.11.5 Open Source GPL3+

GAMESS
General Atomic and Molecular Electronic Structure System is computer software for computational chemistry program
https://www.msg.chem.iastate.edu/gamess/

2018-R3 Propietario Freeware

GPAW
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE)
https://wiki.fysik.dtu.dk/gpaw/

1.5.2 Open Source GPL3+

GROMACS
GROningen MAchine for Chemical Simulations is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids
www.gromacs.org/

2016.3 Open Source LGPL

Hadoop
Apache Hadoop is a collection of open-source software utilities that facilitate using a network of many computers to solve problems involving massive amounts of data and computation
https://hadoop.apache.org/

2.7.1

Open Source AL 2.0

LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator is a molecular dynamics program from Sandia National Laboratories
https://lammps.sandia.gov/

2017.8.11, 2018.12.12 Open Source GPL

MOPAC
A computer program designed to implement semi-empirical quantum chemistry algorithms
http://openmopac.net/

7.1.11 Dominio público

NWChem
NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality
https://nwchemgit.github.io/

6.6 Open Source ECL 2.0

OpenMX
A program for extended structural equation modeling
www.openmx-square.org/

3.9 Open Source AL 2.0

ORCA
An ab initio quantum chemistry program package that contains modern electronic structure methods
www.faccts.de/orca/

4.0.1 Propietario uso académico

PLUMED
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations
www.plumed.org/

2.3.2 Open Source LGPL

QCEIMS
Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) is a program for the prediction of mass spectra from first principles
www.chemie.uni-bonn.de/pctc/mulliken-center/software/movies_grimme/qceims

3.6, 3.75 ,4.0  

QUAST
Quality Assessment Tool for Genome Assemblies. Tools for genome assemblies evaluation and comparison
http://quast.sourceforge.net/

4.4 Open Source GPL2

Samtools
A suite of programs for interacting with high-throughput sequencing data
www.htslib.org/

0.1.19 MIT

Schrödinger Computational Platform
Molecular modeling programs
www.schrodinger.com/

2019.4,2020.2 Propietario
Licencia hasta 2022

Siesta
Spanish Initiative for Electronic Simulations with Thousands of Atoms.  A method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
www.uam.es/siesta

4.0.1,4.1-b3 Open Source GPL3

soapdenovo2
a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes
https://github.com/aquaskyline/SOAPdenovo2

2.04

Open Source GPL3

Apache Spark
A fast and general cluster computing system for Big Data
https://spark.apache.org/

1.6.0,1.6.1 Open Source AL 2.0

TopHat
a fast splice junction mapper for RNA-Seq reads
http://ccb.jhu.edu/software/tophat/index.shtml

2.1.1 BSL 1.0

Turbomole
An ab initio computational chemistry program that implements various quantum chemistry methods
www.turbomole.org/

7.3 Propietario

QuantumATK
Atomic-Scale Modeling for Semiconductor & Materials Research
www.synopsys.com/silicon/quantumatk.html

2016.3, 2016.4, 2017.0, 2018.06, 2019.03 Propietario

 

Lenguajes de programación

Nombre

Versión

Licencia

Clang
A compiler front end for the C, C++, Objective-C and Objective-C++ programming languages
https://clang.llvm.org/

3.6.0 Open source

GCC
The GNU Compiler Collection is a compiler system produced by the GNU Project supporting various programming languages
https://gcc.gnu.org/

4.8.2, 4.9.2, 6.3.0, 7.2.0, 8.3.0 Open Source GPLv3+

Intel C Compiler
A group of C and C++ compilers from Intel
https://software.intel.com/content/www/us/en/develop/tools/
compilers.html

16.0.0 Propietario

Java
www.java.com/en/

1.8.0_31 Propietario

Mathematica
A modern technical computing system spanning most areas of technical computing
www.wolfram.com/mathematica/

11.3 Propietario

Matlab
A multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks
www.mathworks.com/products/matlab.html

R2018b Propietario

Oracle JDK
The Java Development Kit is an implementation of either one of the Java Platform
www.oracle.com/technetwork/java/javase/overview/index.html

11.0.1 Propietario

Oracle JRE
Java Runtime Environment (JRE)
www.oracle.com/java/

8.0_191 Propietario

Maude
A high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications
http://maude.cs.illinois.edu/w/index.php/The_Maude_System

2.7.1,alpha110 Open Source GPLv2

Python
An interpreted, high-level, general-purpose programming language
https://www.python.org/

2.7.10, 2.7.11, 3.4.3, 3.7 Open Source PSFL

R
A programming language and free software environment for statistical computing and graphics
www.r-project.org/

3.2.0, 3.3.0 Open Source AL 2.0

Scala
A general-purpose programming language providing support for both object-oriented programming and functional programming
www.scala-lang.org/

2.11.8 Open Source AL 2.0

Tcl
A high-level, general-purpose, interpreted, dynamic programming language
https://www.tcl-lang.org/

8.5.19 Open source BSD-style