Provozní změny MetaCentra a CERIT-SC: podpora paralelních/distribuovaných výpočtů v Matlabu + nový SW

Provozní změny MetaCentra a CERIT-SC: podpora paralelních/distribuovaných výpočtů v Matlabu + nový SW

Představujeme Vám další pravidelnou informaci o provozních novinkách infrastruktur MetaCentrum a CERIT-SC:

1. Podpora paralelních/distribuovaných výpočtů v Matlabu -- zjednodušení práce s přípravou paralelního/distribuovaného poolu workerů:


2. Nově instalovaný/pořízený SW:

Pozn.: Bližší informace o instalovaných aplikacích jsou k dispozici na stránce aplikací:


Wien2k (wien2k-13.1)

* allpathslg (ver. 48203)  - short read genome assembler from the Computational Research and Development group at the Broad Institute
* atlas (ver. 3.10.1, compiled by gcc4.4.5 and gcc4.7.0)  - The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance.
* cm5pac (ver. 2013)  - a package to carry out a calculation of CM5 partial atomic charges using Hirshfeld atomic charges from Gaussian 09's output file (calculations performed in Revision D.01 of Gaussian 09 may produce wrong CM5 charges in certain cases)
* damask (ver. 2689)  - flexible and hierarchically structured model of material point behavior for the solution of (thermo-) elastoplastic boundary value problems
* fastq_illumina_filter (ver. 0.1)  - Illumina's CASAVA pipeline produces FASTQ files with both reads that pass filtering and reads that don't
* fftw (ver. 3.3, variants: double, omp, ompdouble)  - C subroutine library for computing the discrete Fourier transform
* gmap (ver. 2013-11-27)  - A Genomic Mapping and Alignment Program for mRNA and EST Sequences, Genomic Short-read Nucleotide Alignment Program
* gnuplot (ver. 4.6.4)  - a portable command-line driven graphing utility allowing to visualize mathematical functions and data
* grace (ver. 5.1.23)  - a WYSIWYG tool to make two-dimensional plots of numerical data
* lammps (ver. dec2013)  - Large-scale Atomic/Molecular Massively Parallel Simulator
* maker (ver. 2.28)  - Genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
* masurca (ver. 2.1.0)  - MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches.
* metaVelvet (ver. 1.2)  - a short read assember for metagenomics
* numpy (ver. 1.8.0 for Python 2.6, compiled with gcc and Intel)  - a Python language extension defining the numerical array and matrix type and basic operations over them (compiled with Intel MKL libraries support for faster performance) * NWChem (ver. 6.3.2)  - an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality
* openmpi (ver. 1.6.5, gcc + pgi + intel)  - an implementation of MPI
* orca (ver. 3.0.1)  - modern electronic structure program package
* paramiko (ver. 1.12)  - a Python module that implements the SSH2 protocol for secure (encrypted and authenticated) connections to remote machines
* pycrypto (ver. 2.6.1)  - a collection of both secure hash functions (such as SHA256 and RIPEMD160) and various encryption algorithms (AES, DES, RSA, ElGamal, etc.)
* SOAPdenovo2   - a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes (includes SOAPec, GapCloser, Data prepare and Error Correction modules)
* sRNAworkbench3.0   - a suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices
* ugene (ver. 1.13)  - a free open-source cross-platform bioinformatics software
* vcftools (ver. 0.1.11)  - an ultrafast, memory-efficient short read aligner of short DNA sequences
* vtk (ver. 5.4.2)  - freely available software system for 3D computer graphics, image processing and visualization
* xmgrace (ver. 5.1.23)  - a WYSIWYG tool to make two-dimensional plots of numerical data


S pozdravem Tomáš Rebok,
MetaCentrum + CERIT-SC.

Tom Rebok, 20. 2. 2014