[LA-SiGMA] LSU HPC/LONI system updates
Wei P Feinstein
wfeinstein at lsu.edu
Tue Jan 19 10:46:25 CST 2016
Dear HPC/LONI users:
********* HPC/LONI SYSTEM UPDATES<http://www.hpc.lsu.edu/sysnews/index.php> (January 2016)********
<http://www.hpc.lsu.edu/sysnews/index.php>
CONTENTS:
LONI HPC
QB2
Eric
LSU HPC
SuperMIC
SuperMike2
Pandora
Philip
*******************************************************************
I LONI QB2--Nvidia GPU
Software
Updated packages
Key: amber/14/CUDA-65-INTEL-140-MVAPICH2-2.0
Description: "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
Key: cmake/3.4.1/INTEL-14.0.2
Description: Description: CMake, the cross-platform, open-source build system.
Key: espresso/5.2.1/INTEL-14.0.2-mvapich-2.0
Description: Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Key: geant4/10.01/GCC-4.9.0
Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
Key: intel/15.0.0
Description: Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
Retired packages
Key: clhep/2.1.4.2/GCC-4.4.7
Key: geant4/10.00.p02/GCC-4.4.7
*******************************************************************
II LONI Eric
No changes
*******************************************************************
III LSU HPC SuperMIC--Intel Xeon Phi
Software
Newly installed packages
Key: gaussian/g09-d01
Description:
Key: octave/3.8.2/INTEL-14.0.2
Description: Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. -
Key: pcre/8.36/INTEL-14.0.2
Description: Description:
Key: vtune/2015.3.0
Description: This is an intel VTune Amplifier XE for parallel_studio-2015u3
Key: gateway-usage-reporting/1.0
Description: adds gateway-usage-reporting tool to paths in the login shell environment
Updated packages
Key: ansys/16.0
Description: Description:
Key: espresso/5.2.1/INTEL-14.0.2-mvapich-2.0
Description: Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Key: impi/5.0.1.035/intel64
Description: This is an intel MPI implementation. It is included in the Intel-15.0.1 compiler. It is a good compiler for MPI programming on Xeon Phi.
Key: mathematica/10.1
Description: Description:
Key: matlab/r2015b
Description: Description:
Key: python/2.7.10-mkl-mic
Description: Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Within this version, the numpy/scipy packages are linked to Intel Math Kernel Library (MKL), so that they can be accelerated with Xeon Phi. -
Key: globus/5.7-6
Description: globus gram5 xsede 6.0-1
Key: perl/5.22.0
Description: Description: Larry Wall's Practical Extraction and Report Language -
Key: xsede/1.1
Description:
Retired packages
Key: mathematica/10.0
*******************************************************************
IV LSU HPC SuperMike2
Software
Newly installed packages
Key: +jdk-1.7.0_79
Description: The JDK is a development environment for building applications, applets, and components using the Java programming language.
Key: +matlab-r2015b
Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
*******************************************************************
V LSU HPC Pandora
Hardware
Pandora will be decommissioned on Friday, 22 Jan 2016. At that time, the cluster will stop running jobs and queued jobs will be deleted. Login access to Pandora will continue for a short period after January 22nd so that users can back up their files.
Maintenance Scheduled
Decommissioning: Friday, 22 Jan 2016
*******************************************************************
VI LSU HPC Philip ( SOFTENV is replaced by MODULE)
Software
Newly installed packages
Key: a5_pipeline/20150522
Description: Description: A5 is a pipeline for assembling DNA sequence data
Key: abyss/1.9.0/INTEL-150-MPICH-3.1.4
Description: Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -
Key: amos/3.1.0/INTEL-15.0.3
Description: Description: The AMOS consortium is committed to the development of open-source whole genome assembly software -
Key: beagle_lib/2.1.2/INTEL-15.0.3
Description: Description: beagle-lib is a high-performance library that can perform the core
Key: beast/2.1.3
Description: Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
Key: blast/2.2.22
Description: Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm
Key: blast/2.2.31/INTEL-15.0.3
Description: Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm
Key: bowtie/1.1.1/INTEL-15.0.3
Description: Description: Bowtie is an ultrafast, memory-efficient short read aligner.
Key: bowtie2/2.1.0/INTEL-15.0.3
Description: Description: Bowtie 2 is an ultrafast and memory-efficient tool
Key: cap3/20071221
Description: Description: CAP3 assembly program -
Key: cd-hit/4.6.1/INTEL-15.0.3
Description: Description: CD-HIT is a very widely used program for clustering and
Key: clonalframe/1.2/INTEL-15.0.3
Description: Description: ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data. ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. -
Key: clonalorigin/1.0/INTEL-15.0.3
Description: Description: ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. -
Key: cufflinks/2.2.1/INTEL-15.0.3
Description: Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq -
Key: dendropy/3.12.0/GCC-4.9.0-python-2.7.10
Description: Description: A Python library for phylogenetics and phylogenetic computing:
Key: eigen/3.2.3/INTEL-15.0.3
Description: Description: Eigen is a C++ template library for linear algebra:
Key: expat/2.1.0/INTEL-15.0.3
Description: Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application
Key: fastx_toolkit/0.0.13.2/INTEL-15.0.3
Description: Description: The FASTX-Toolkit is a collection of command line tools
Key: hmmer/3.1b1/INTEL-15.0.3
Description: Description: HMMER is used for searching sequence databases for homologs of protein sequences,
Key: idba_ud/1.1.1/INTEL-15.0.3
Description: Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads
Key: jellyfish/2.1.3/GCC-4.9.0
Description: Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. -
Key: last/604/INTEL-15.0.3
Description: Description: MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 32 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data. -
Key: libgtextutils/0.6.1/INTEL-15.0.3
Description: Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream -
Key: lucy/1.20/INTEL-15.0.3
Description: Description: Mothur is a single piece of open-source, expandable software
Key: mafft/7.245/GCC-4.9.0
Description: Description: MAFFT is a multiple sequence alignment program
Key: mauve/20150213
Description: Description: Mauve is a system for constructing multiple genome
Key: mercurial/2.5.2/GCC-4.9.0-python-2.7.10
Description: Description: Mercurial is a free, distributed source control management tool.
Key: mira/4.0.2/GCC-4.9.0
Description: Description: MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 32 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data. -
Key: mothur/1.36.1/INTEL-150-MPICH-3.1.4
Description: Description: Mothur is a single piece of open-source, expandable software
Key: mummer/3.23/INTEL-15.0.3
Description: Description: MUMmer is a system for rapidly aligning entire genomes,
Key: muscle/3.8.31/INTEL-15.0.3
Description: Description: MUSCLE is one of the best-performing multiple alignment programs
Key: oases/0.2.08/INTEL-15.0.3
Description: Description: Oases is a de novo transcriptome assembler designed to produce transcripts from
Key: parmetis/3.2.0/INTEL-150-MPICH-3.1.4
Description: Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs,
Key: pcre/8.36/INTEL-15.0.3
Description: Description:
Key: qiime/1.9.1-python-2.7.10-anaconda
Description: Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation.
Key: quake/0.3.5/INTEL-15.0.3
Description: Description: Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken. -
Key: raxml/8.2.3/INTEL-15.0.3-mt-sse3
Description: Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. -
Key: repet/2.2
Description: Description: The REPET package ( Flutre et al, 2011 ) integrates
Key: rum/2.0.5_06
Description: Description: RUM is an alignment, junction calling,
Key: samtools/0.1.19/INTEL-15.0.3
Description: Description: SAM Tools provide various utilities for manipulating alignments in the SAM format,
Key: samtools/1.1/INTEL-15.0.3
Description: Description: SAM Tools provide various utilities for manipulating alignments in the SAM format,
Key: sina/1.2.11
Description: Description: SINA will align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. -
Key: soapdenovo2/r240/INTEL-15.0.3
Description: Description: SOAPdenovo is a novel short-read assembly method that can build a
Key: soapdenovotrans/1.0.4/INTEL-15.0.3
Description: Description: SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets. -
Key: sparsehash/2.0.2/INTEL-15.0.3
Description: Description: An extremely memory-efficient hash_map
Key: sspace/3.0
Description: Description: SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format. -
Key: szip/2.1/GCC-4.9.0
Description: Description: Szip compression software, providing lossless compression of scientific data -
Key: t_coffee/11.00
Description: Description: T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment. -
Key: tophat/2.1.0
Description: Description: TopHat is a fast splice junction mapper for RNA-Seq reads. -
Key: trinity/2.1.0/INTEL-15.0.3
Description: Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation.
Key: valgrind/3.9.0/GCC-4.9.0
Description: Description: Valgrind: Debugging and profiling tools -
Key: velvet/1.2.10/INTEL-15.0.3
Description: Description: Sequence assembler for very short reads -
Key: vmatch/2.2.4
Description: Description: Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks. -
Key: EasyBuild/1.13.0
Description: Description: EasyBuild is a software build and installation framework
Key: GCC/4.9.0
Description: Description: GNU compiler for C, C++ and Fortran -
Key: INTEL/15.0.3
Description: Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, and Intel MKL -
Key: INTEL-150-MPICH/3.1.4
Description: Description: Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers and MPICH. -
Updated packages
Key: ansys/16.0
Description: Description:
Key: boost/1.55.0/INTEL-15.0.3
Description: Description: Boost provides free peer-reviewed portable C++ source libraries. -
Key: boost/1.58.0/INTEL-15.0.3
Description: Description: Boost provides free peer-reviewed portable C++ source libraries. -
Key: cmake/2.8.12/INTEL-15.0.3
Description: Description: CMake, the cross-platform, open-source build system.
Key: cmake/3.2.3/INTEL-15.0.3
Description: Description: CMake, the cross-platform, open-source build system.
Key: fftw/3.3.3/INTEL-15.0.3
Description: Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
Key: gcc/4.9.0
Description: Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
Key: gsl/1.16/INTEL-15.0.3
Description: Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. -
Key: hdf5/1.8.12/INTEL-15.0.3
Description: Description: HDF5 is a unique technology suite that makes possible the management of
Key: intel/15.0.3
Description: Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
Key: mathematica/10.2
Description: Description:
Key: matlab/r2015b
Description: Description:
Key: metis/5.1.0/INTEL-15.0.3
Description: Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes,
Key: mpich/3.1.4/GCC-4.9.0
Description: Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation.
Key: mpich/3.1.4/INTEL-15.0.3
Description: Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation.
Key: mrbayes/3.2.5/INTEL-150-MPICH-3.1.4
Description: Description: MrBayes is a program for the Bayesian estimation of phylogeny. -
Key: netcdf/4.2.1.1/INTEL-15.0.3
Description: Description: NetCDF (network Common Data Form) is a set of software libraries
Key: octave/3.8.2/INTEL-15.0.3
Description: Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. -
Key: perl/5.20.0/INTEL-15.0.3
Description: Description: Larry Wall's Practical Extraction and Report Language -
Key: python/2.7.10-anaconda
Description: Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -
Key: python/2.7.7/GCC-4.9.0
Description: Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -
Key: r/3.1.3/INTEL-15.0.3
Description: Description: R is a free software environment for statistical computing and graphics. -
Retired packages
Key: +amber-11-intel-11.1-mpich-1.2.7p1
Key: +ansys-lsdyna-11.0
Key: +apache_ant-1.7.1
Key: +arpack-96-intel-11.1
Key: +atlas-3.8.2-intel-11.1
Key: +blacs-1.1-intel-11.1-mpich-1.2.7p1
Key: +boost-1.37.0-intel-11.1
Key: +boostjam-3.1.17-intel-11.1
Key: +cmake-2.8.9-gcc-4.1.2
Key: +condor-7.2.0
Key: +cuda-4.0.17
Key: +cuda-4.2.9
Key: +ddt-2.6
Key: +fftw-2.1.5-intel-11.1
Key: +fftw-2.1.5-intel-11.1-mpich-1.2.7p1
Key: +fftw-3.2-intel-11.1-mpich-1.2.7p1
Key: +fluent
Key: +fluent-public
Key: +fluent-13.0
Key: +fluent-13.0-public
Key: +ansys-14.5
Key: +ansys-15.0
Key: +ansys-16.0
Key: +gamess-12Jan2009R1-intel-11.1
Key: +gaussian-03
Key: +gaussian-09
Key: +gaussian-09-C01
Key: +gaussian-09-D01
Key: +gcc-4.3.2
Key: +git-1.6.1.3-intel-11.1
Key: +globus-4.0.8
Key: +globus-4.2.1
Key: +gnuplot-4.2.4-intel-11.1
Key: +graphviz-2.20.3-gcc-4.3.2
Key: +gromacs-4.0.2-intel-11.1-mpich-1.2.7p1
Key: +gromacs-4.5.4-intel-11.1-openmpi-1.4.3
Key: +gromacs-4.5.4-intel-11.1-openmpi-1.4.3-cuda-4.0.17
Key: +gsl-1.9-intel-11.1-mpich-1.2.7p1
Key: +hdf5-1.8.2-intel-11.1-mpich-1.2.7p1
Key: +hypre-2.4.0b-intel-11.1-mpich-1.2.7p1
Key: +ImageMagick-6.4.6.9-intel-11.1
Key: +intel-cc-10.1
Key: +intel-fc-10.1
Key: +intel-mkl-10.1
Key: +intel-mkl-10.2
Key: +intel-cc-11.1
Key: +intel-fc-11.1
Key: +intel-12.1
Key: +intel-13.1.0
Key: +jdk-1.6.0
Key: +lammps-17Sep11-intel-11.1-openmpi-1.4.3
Key: +lapack-3.2-intel-11.1
Key: +lapack-3.2-intel-11.1-mpich-1.2.7p1
Key: +lapack-3.4.0-gcc-4.1.2
Key: +lapack-3.4.0-gcc-4.3.2
Key: +lapack-3.4.0-intel-11.1
Key: +lapack-3.4.0-pgi-12.8
Key: +maple-11
Key: +mathematica-10.0
Key: +mathematica-8.0
Key: +mathematica-9.0
Key: +matlab-r2011b
Key: +matlab-r2007b
Key: +maya
Key: +metis-4.0-intel-11.1
Key: +migrate-3.3.2-gcc-4.3.2-openmpi-1.6.1
Key: +mpich-1.2.7p1-intel-11.1
Key: +mpich2-1.3.2p1-intel-11.1
Key: +mpich2-1.4.1p1-gcc-4.3.2
Key: +mpich2-1.4.1p1-intel-11.1
Key: +mpiP-3.1.2-intel-11.1-mpich-1.2.7p1
Key: +mrbayes-3.2.1-gcc-4.3.2-openmpi-1.6.1
Key: +namd-2.7-intel-11.1-mpich2-1.3.2p1
Key: +namd-2.7-mpich-1.2.7p1-intel-11.1
Key: +namd-2.8-intel-11.1-mpich2-1.3.2p1
Key: +namd-2.8-intel-11.1-mpich2-1.3.2p1-cuda-4.0.17
Key: +netcdf-4.0-intel-11.1
Key: +next_gen_sequencing_tools
Key: +octave-3.0.3-intel-11.1
Key: +octave-3.0.4-intel-11.1
Key: +openmpi-1.4.3-intel-11.1
Key: +openmpi-1.6.1-gcc-4.1.2
Key: +openmpi-1.6.1-gcc-4.3.2
Key: +openmpi-1.6.1-Intel-12.1.4
Key: +openmpi-1.6.1-pgi-12.8
Key: +orca-2.8.0-openmpi-1.4.3
Key: +ParMetis-3.1.1-intel-11.1-mpich-1.2.7p1
Key: +parpack-96-intel-11.1-mpich-1.2.7p1
Key: +paup-4.0
Key: +pdtoolkit-3.14.1-intel-11.1
Key: +perl-5.10.1
Key: +perl-5.16.0
Key: +perl-5.16.2
Key: +petsc-3.0.0.p3-intel-11.1-mpich-1.2.7p1
Key: +portland-11.5
Key: +portland-12.8
Key: +tapir-1.0-python-2.7.3-gcc-4.3.2
Key: +python-2.6.4-intel-11.1
Key: +python-2.7.3-gcc-4.3.2
Key: +R-2.8.1-gcc-4.3.2
Key: +R-3.0.0-gcc-4.3.2
Key: +scalapack-1.8.0-intel-11.1-mpich-1.2.7p1
Key: +scons-1.2.0
Key: +sprng-2.0b-intel-11.1-mpich-1.2.7p1
Key: +SuperLU_DIST-2.3-intel-11.1-mpich-1.2.7p1
Key: +tau-2.18-intel-11.1-mpich-1.2.7p1
Key: +tau-2.19.2-intel-11.1-mpich-1.2.7p1
Key: +tcl-8.5.9-intel-11.1
Key: +totalview-8.3.0.1
Key: +totalview-8.8.0
Key: +visit-1.11.1
Key: +visit-1.12.1
Key: +visit-2.3.2
Key: +visit-2.4.0
The latest software stack information can be found at http://www.hpc.lsu.edu/docs/guides/index.php
Wei Feinstein, Ph.D.
High Performance Computing
Information Technology Services
Louisiana State University
337 Frey Computing Services Center
Baton Rouge, LA 70803
Office 225-578-0582 | Mobile 251-599-3814
wfeinstein at lsu.edu<mailto:wfeinstein at lsu.edu> | lsu.edu<http://lsu.edu> | hpc.lsu.edu<http://hpc.lsu.edu>
<http://hpc.lsu.edu>
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