High Performance Computing

Jun-2018

• Hardware

  • No news

• Software

  • Updated packages
    • Key: intel/2018.1
      Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
    • Key: pgi/17.10
      Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
    • Key: pgi/18.1
      Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2018

• Hardware

  • No news

• Software

  • Updated packages
    • Key: ansys/18.1
      Description: The ANSYS software suites include Fluent, CFX and ANSYS Mechanical. It's only available to LSU users.
    • Key: impi/2017.3.196/intel64
      Description: This is an intel MPI implementation. It is included in the Intel-2017.4 compiler. It is a good compiler for MPI programming on Xeon Phi.
    • Key: impi/2018.0.128/intel64
      Description: This is an intel MPI implementation. It is included in the Intel-2018.0 compiler. It is a good compiler for MPI programming on Xeon Phi.
    • Key: python/3.6.2-anaconda-tensorflow
      Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Oct-2017

• Hardware

  • no news

• Software

  • Updated packages
    • Key: amber/16/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: cuda/8.0
      Description: Compute Unified Device Architecture (CUDA) is a parallel computing architecture developed by Nvidia for graphics processing
    • Key: fftw/3.3.6/INTEL-140-MVAPICH2-2.0
      Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
    • Key: gromacs/5.1.4/INTEL-140-MVAPICH2-2.0
      Description: GROMACS (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular dynamics with Plumed installed.
    • Key: intel/2016.3
      Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
    • Key: intel/2017.4
      Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
    • Key: intel/2018.0
      Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jul-2017

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: pigz/2.3.4
      Description: pigz is parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
    • Key: remora/1.8
      Description: Resource Monitoring for Remote Applications
    • Key: xdinfo/1.3-1
      Description: Adds XSEDE Information Services Think Client (xdinfo) tool to paths remove-path PATH /usr/local/packages/xsede/xdinfo-1.3-1/bin
  • Updated packages
    • Key: matlab/r2017a
      Description:
    • Key: python/2.7.13-anaconda-tensorflow
      Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -
    • Key: gateway-usage-reporting/2.0
      Description: adds gateway-submit_attributes tool to paths in the login shell environment remove-path PATH /etc/globus/gateway_submit_attributes-2.0
    • Key: xdusage/2.0-3
      Description: adds XSEDE xdusage tool to paths in the login shell environment remove-path PATH /usr/local/packages/xsede/xdusage/xdusage-2.0-3/bin

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Mar-2017

• Hardware

  • A "single" queue is added to the queuing system, whereas ppn is allowed to be set as 1, 2, 4, 6 and 8 cores
  • The "bigmem" queue has 3 nodes with 256GB RAM each

• Software

  • Newly installed packages
    • Key: gnuparallel/20170122
      Description: GNU parallel is a shell tool for executing jobs in parallel using one or more computers
    • Key: swift/0.96.2
      Description: Swift is a simple scripting language for executing many instances of ordinary application programs on distributed and parallel resources.
  • Updated packages
    • Key: cuda/7.5
      Description: Compute Unified Device Architecture (CUDA) is a parallel computing architecture developed by Nvidia for graphics processing
  • Retired packages
    • Key: globus/globus-gram5-xsede.module
      

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • At the moment, Intel Xeon Phi cards support native and offload mode, but the symmetric mode is not working properly

Jan-2017

• OS Update

• Upgraded to RHEL 6.8 with the latest security patches

• Hardware

  • Bigmem Queue (3 big memory nodes) is added: Each node has 28 cores, 256GB Ram, 1TB HD

• Software

  • No Change

• Maintenance Scheduled

  • Downtime to replace batteries on Tuesday Jan 31

• Known Problems

  • At the moment, Intel Xeon Phi cards support native and offload mode, but the symmetric mode is not working properly. We are working on it.

Jun-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: amos/3.1.0/INTEL-14.0.2
      Description: The AMOS consortium is committed to the development of open-source whole genome assembly software -
    • Key: blat/0.35/INTEL-14.0.2
      Description: Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. Blat is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line Blat on their own Linux server. -
    • Key: bwa/0.7.4/INTEL-14.0.2
      Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. -
    • Key: expat/2.1.0/INTEL-14.0.2
      Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) -
    • Key: ray/2.3.1/INTEL-140-MVAPICH2-2.0
      Description: Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. -
    • Key: rnnotator/3.4.0
      Description: Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. The contigs produced by Rnnotator are highly accurate and reconstruct full-length genes when transcripts are sequenced sufficiently deep, roughly 30X for a given transcript. Rnnotator was designed to assemble Illumina single or paired-end reads. Rnnotator is also able to incorporate strand-specific RNA-Seq reads into the assembly in order to further improve the assembly. -
    • Key: sparsehash/2.0.2/INTEL-14.0.2
      Description: An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. -
  • Updated packages
    • Key: abyss/1.9.0/INTEL-140-MVAPICH2-2.0
      Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -
    • Key: ansys/17.0
      Description: The ANSYS software suites include Fluent, CFX and ANSYS Mechanical. It's only available to LSU users.
    • Key: gromacs/5.0.7/INTEL-140-OPENMPI-1.8.4
      Description: GROMACS (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular dynamics.
    • Key: wq/272
      Description: WQ is a support tool that creates supports a dispatcher/worker model of distributed computing. Serial, multi-thread OpenMP, and small multi-process MPI are supported. Tasks are defined by input file names, or other command line strings, contained in an input file - one line per task.
  • Retired packages
    • Key: openmpi/1.8.1/INTEL-14.0.2
      

• Maintenance Scheduled

  • System will be offline for file system update. Downtime might last for a couple of weeks. Details are coming soon

• Known Problems

  • No impact on users

Apr-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: bbcp/15.02.03
      Description: BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. -
    • Key: wq/264
      Description: WQ is a support tool that creates supports a dispatcher/worker model of distributed computing. Serial, multi-thread OpenMP, and small multi-process MPI are supported. Tasks are defined by input file names, or other command line strings, contained in an input file - one line per task.
  • Updated packages
    • Key: pgi/15.10
      Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
    • Key: globus/5.7-8
      Description: globus gram5 xsede 5.7-8
    • Key: globus/globus-gram5-xsede.module
      Description: globus gram5 xsede 5.7-8
  • Retired packages
    • Key: globus/5.7-6
      

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2016

• Hardware

  • no news

• 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
      

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Aug-2015

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: amber/14/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: boost/1.55.0/INTEL-14.0.2
      Description: Boost provides free peer-reviewed portable C++ source libraries. -
    • Key: boost/1.55.0/INTEL-14.0.2-mic
      Description: Boost provides free peer-reviewed portable C++ source libraries. Intel Xeon Phi version (mic) - URL: http://www.boost.org/
    • Key: espresso/5.1.2/INTEL-140-OPENMPI-1.8.4
      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: hpx/0.9.10/impi-4.1.3.048-intel64
      Description: HPX is a general purpose C++ runtime system for parallel and distributed applications of any scale. - Built with Intel MPI for CPU only
    • Key: hpx/0.9.10/impi-4.1.3.048-intel64-mic
      Description: HPX is a general purpose C++ runtime system for parallel and distributed applications of any scale. - Intel Xeon Phi (mic) version built with impi
    • Key: hpx/0.9.10/mvapich2-2.0-INTEL-14.0.2
      Description: HPX is a general purpose C++ runtime system for parallel and distributed applications of any scale. - Build with MVAPICH2
    • Key: paraview/4.3.1/GCC-4.9.0
      Description: An open-source, multi-platform data analysis and visualization application. -
    • Key: paraview/4.3.1/INTEL-140-MVAPICH2-2.0
      Description: An open-source, multi-platform data analysis and visualization application. -
    • Key: siesta/3.2/INTEL-140-OPENMPI-1.8.4
      Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
  • Updated packages
    • Key: blast/2.2.31/INTEL-14.0.2
      Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm
    • Key: pgi/14.10
      Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
    • Key: pgi/15.4
      Description: The Portland Group compilers for C, C++ and Fortran. It also supports OpenACC. http://www.pgroup.com/resources/docs.htm
    • Key: globus/6.0
      Description: globus client xsede 6.0-1

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Feb 2015

• Software

  • Updated
    • NAMD version 2.10b2 with Xeon Phi support installed.
      Module: namd/2.10b2/INTEL-14.0.2-ibverbs-mic
    • LAMMPS 21Jan15 with Xeon Phi support installed.
      Module: lammps/21Jan15/INTEL-14.0.2-impi-4.1.3.048-mic
    • Matlab version r2013a
      Module: matlab/r2013a
    • Mathematica version 10.0
      Module: mathematica/10.0
  • Retired
    • Module: namd/2.10b2/INTEL-14.0.2-ibverbs
    • Module: namd/2.10b2/INTEL-14.0.2-ibverbs-mic
  • Benchmark Results
    

    NAMD APOA1 Benchmark:
    
    NumberOfNodes   CPUonly  CPU+Phi  Speedup
    1  0.621938 days/ns  0.254949 days/ns  2.44
    2  0.471777 days/ns  0.142642 days/ns  3.31
    4  0.310066 days/ns  0.0823795 days/ns  3.76
    8  0.220733 days/ns  0.0601484 days/ns  3.67
    
    NAMD STMV Benchmark:
    
    NumberOfNodes   CPUonly  CPU+Phi  Speedup
    1  6.22028 days/ns  2.42398 days/ns  2.57
    2  3.35414 days/ns  1.37301 days/ns  2.44
    4  1.96454 days/ns  0.858824 days/ns  2.29
    8  1.28667 days/ns  0.510283 days/ns  2.51
    16  0.652524 days/ns  0.360255 days/ns  1.81
    
    LAMMPS Rhodopsin Benchmark:
    
    Number of Nodes;Without package (Baseline);OMP package;
       INTEL+OMP;Offload to Phi-Auto Balance;Offload to Phi-Fixed Balance
    1 node	Loop time (sec)	28.5529	24.1188	20.7227	13.6826	12.7717
    32 node	Loop time (sec)	34.8826	30.0743	25.7038	18.0796	17.5099
    1 node	Speedup	1	1.18	1.38	2.09	2.24
    32 node	Speedup	1	1.16	1.36	1.93	1.99
    
    LAMMPS Liquid Crystal Benchmark:
    1 node	Loop time (sec)	26.9558	26.4598	6.80273	4.97776	4.64265
    32 node	Loop time (sec)	26.9836	26.4459	7.7801	6.27055	7.63933
    1 node	Speedup	1	1.02	3.96	5.42	5.81
    32 node	Speedup	1	1.02	3.47	4.30	3.53
    

• Maintenance Scheduled

  • None scheduled.

• Known Problems

  • None impacting users

Jun-2018

• Hardware

  • No news

• Software

  • Newly installed packages
    • Key: a5_pipeline/20160825
      Description: A5 is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. -
    • Key: abyss/1.9.0/INTEL-180-MVAPICH2-2.2
      Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -
    • Key: agalma/2.0.0
      Description: Agalma is a set of analysis pipelines for transcriptome assembly and analysis, phylogenetic analysis, expression analysis (including phylogenetic analysis of gene expression data).
    • Key: amber/16/INTEL-180-MVAPICH2-2.2
      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: amos/3.1.0/INTEL-18.0.0
      Description: The AMOS consortium is committed to the development of open-source whole genome assembly software -
    • Key: ansys/18.1
      Description: The ANSYS software suites include Fluent, CFX and ANSYS Mechanical. It's only available to LSU users.
    • Key: autodock/4.2.5.1/INTEL-18.0.0
      Description: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. -
    • Key: autodock_vina/1.1.2
      Description: AutoDock Vina is an open-source program for doing molecular docking. -
    • Key: autogrid/4.2.5.1/INTEL-18.0.0
      Description: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. -
    • Key: bbcp/12.01.30.00.0
      Description: BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp -
    • Key: beagle_lib/2.1.2/INTEL-18.0.0
      Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. -
    • Key: beast/1.8.4
      Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -
    • Key: beast2/2.4.6
      Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -
    • Key: bedtools/2.26.0/INTEL-18.0.0
      Description: 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. -
    • Key: blast/2.2.28/INTEL-18.0.0
      Description: 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. -
    • Key: blast+/2.7.1/INTEL-18.0.0
      Description: 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. -
    • Key: boost/1.55.0/INTEL-18.0.0
      Description: Boost provides free peer-reviewed portable C++ source libraries. -
    • Key: boost/1.63.0/INTEL-18.0.0
      Description: Boost provides free peer-reviewed portable C++ source libraries. -
    • Key: bowtie/1.2.2/INTEL-18.0.0
      Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. -
    • Key: bowtie2/2.3.4.1/INTEL-18.0.0
      Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. -
    • Key: bzip2/1.0.6/INTEL-18.0.0
      Description: bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. -
    • Key: cap3/20071221
      Description: CAP3 assembly program -
    • Key: cd-hit/4.6.6/INTEL-18.0.0
      Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. -
    • Key: clhep/2.3.1.1/GCC-6.4.0
      Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. -
    • Key: clonalframe/1.2/INTEL-18.0.0
      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-18.0.0
      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: cmake/3.7.2/INTEL-18.0.0
      Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. -
    • Key: cmg/2017.10
      Description: CMG provides reservoir simulation software, including thermal, compositional, black oil and enhanced oil recovery processes.
    • Key: cuda/9.0.176
      Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. -
    • Key: cufflinks/2.2.1/INTEL-18.0.0
      Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq -
    • Key: curl/7.49.1/INTEL-18.0.0
      Description: libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. -
    • Key: dendropy/4.4.0
      Description: DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. -
    • Key: dmtcp/2.5.1
      Description: DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc. -
    • Key: eigen/3.2.3/INTEL-18.0.0
      Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. -
    • Key: exabayes/1.5/INTEL-180-MVAPICH2-2.2
      Description: ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters. -
    • Key: expat/2.2.0/INTEL-18.0.0
      Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) -
    • Key: fasttree/2.1.10/INTEL-18.0.0
      Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
    • Key: fastx_toolkit/0.0.13.2/INTEL-18.0.0
      Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. -
    • Key: fftw/3.3.3/INTEL-180-MVAPICH2-2.2
      Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. -
    • Key: freeglut/3.0.0/INTEL-18.0.0
      Description: freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. -
    • Key: gatk/4.0.2.1
      Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. -
    • Key: gaussian/g09-d01
      Description: Gaussian 09 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling.
    • Key: gaussview/5.0.8
      Description: A graphical user interface designed to help prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces.
    • Key: gcc/6.4.0
      Description: 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,...). -
    • Key: geant4/10.4.2/GCC-6.4.0
      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: geant4/10.4.2/INTEL-18.0.0
      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: git/2.17
      Description: Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. -
    • Key: gnuparallel/20180222/INTEL-18.0.0
      Description: GNU parallel: Build and execute shell commands in parallel -
    • Key: gnuplot/5.0.7/INTEL-18.0.0
      Description: Portable interactive, function plotting utility -
    • Key: gromacs/2016.5/INTEL-180-MVAPICH2-2.2
      Description: 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 CPU only build, containing both MPI and threadMPI builds. -
    • Key: gsl/2.4/GCC-6.4.0
      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: gsl/2.4/INTEL-18.0.0
      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: hdf5/1.8.18/INTEL-180-MVAPICH2-2.2
      Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. -
    • Key: hisat2/2.1.0
      Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). -
    • Key: hmmer/3.1b2/INTEL-18.0.0
      Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. -
    • Key: hwloc/1.11.5/INTEL-18.0.0
      Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. -
    • Key: hypre/2.12.1/INTEL-180-MVAPICH2-2.2
      Description: Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. -
    • Key: idba/1.1.3/INTEL-18.0.0
      Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. -
    • Key: imagemagick/7.0.7_28/INTEL-18.0.0
      Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images -
    • Key: impi/2018.0.128
      Description: Intel MPI -
    • Key: intel/18.0.0
      Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL -
    • Key: jdk/1.8.0_161
      Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. -
    • Key: jellyfish/2.2.7/GCC-6.4.0
      Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. -
    • Key: lammps/16Mar18/INTEL-180-MVAPICH2-2.2
      Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
    • Key: last/869/INTEL-18.0.0
      Description: LAST finds similar regions between sequences. The main difference between LAST and similar tools (e.g. BLAT, LASTZ) is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. -
    • Key: libgtextutils/0.6.1/INTEL-18.0.0
      Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream -
    • Key: lmdb/0.9.21/INTEL-18.0.0
      Description: OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. -
    • Key: lucy/1.20/INTEL-18.0.0
      Description: Lucy is used to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers. -
    • Key: mafft/7.245/INTEL-18.0.0
      Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. -
    • Key: mathematica/11.0
      Description: Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics. It's only available to LSU users.
    • Key: matlab/r2017a
      Description: MATLAB is a high-level language and interactive environment developed by Mathworks. It is widely u sed in science and engineering across industry and academia. Parallel Computing Toolbox is available. Due to license restriction, MATLAB is only available to LSU users.
    • Key: mauve/20150213
      Description: Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics. -
    • Key: metis/5.1.0/INTEL-18.0.0
      Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. -
    • Key: mira/4.0.2
      Description: MIRA is the swiss army knife of sequence assembly that I've used and developed during the past 16 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it. -
    • Key: mothur/1.36.1/INTEL-180-MVAPICH2-2.2
      Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. -
    • Key: mpich/3.2/INTEL-18.0.0
      Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). -
    • Key: mrbayes/3.2.6/INTEL-180-MVAPICH2-2.2
      Description: MrBayes is a program for the Bayesian estimation of phylogeny. -
    • Key: mummer/3.23/INTEL-18.0.0
      Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. -
    • Key: mummer4/4.0.0beta2/INTEL-18.0.0
      Description: MUMmer is a versatil alignment tool for DNA and protein sequences. -
    • Key: muscle/3.8.31/INTEL-18.0.0
      Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. -
    • Key: mvapich2/2.2/INTEL-18.0.0
      Description: This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. -
    • Key: namd/2.12/INTEL-180-MVAPICH2-2.2
      Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. -
    • Key: netcdf/4.4.1.1/INTEL-180-MVAPICH2-2.2
      Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
    • Key: netcdf_c++/4.3.0/INTEL-18.0.0
      Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
    • Key: netcdf_fortran/4.4.4/INTEL-18.0.0
      Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -
    • Key: nwchem/6.8/INTEL-180-MVAPICH2-2.2
      Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. This version enables MRCC methods.
    • Key: oases/0.2.08/INTEL-18.0.0
      Description: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. -
    • Key: openmpi/3.1.0/INTEL-18.0.0
      Description: The Open MPI Project is an open source MPI-2 implementation. -
    • Key: orthofinder/2.2.6/INTEL-18.0.0
      Description: OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.
    • Key: parallel_netcdf/1.9.0/INTEL-180-MVAPICH
      Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. -
    • Key: parmetis/4.0.3/INTEL-180-MVAPICH2-2.2
      Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. -
    • Key: pcre/8.36/INTEL-18.0.0
      Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. -
    • Key: perl/5.24.0/INTEL-18.0.0
      Description: Larry Wall's Practical Extraction and Report Language -
    • Key: petsc/3.9.2/INTEL-180-MVAPICH2-2.2
      Description: Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. This version is with real scalar.
    • Key: pgi/18.1
      Description: PGI compilers for C/C++, Fortran, OpenACC and CUDA Fortran -
    • Key: phylobayes_mpi/20161021/INTEL-180-MVAPI
      Description: A Bayesian software for phylogenetic reconstruction using mixture models -
    • Key: prottest/3.4.2
      Description: ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand.
    • Key: python/2.7.14-anaconda
      Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. -
    • Key: python/3.6.4-anaconda
      Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. -
    • Key: qiime2/2018.4
      Description: QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
    • Key: quantumespresso/6.2.1/INTEL-180-MVAPICH
      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: quorum/1.1.1/INTEL-18.0.0
      Description: QuorUM is an error corrector for Illumina reads -
    • Key: r/3.4.3/INTEL-18.0.0
      Description: R is a free software environment for statistical computing and graphics. -
    • Key: raxml/8.2.11/INTEL-18.0.0-mt-sse3
      Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. -
    • Key: repet/2.5
      Description: The REPET package ( Flutre et al, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale. Its two main pipelines are dedicated to the detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs). -
    • Key: root/6.10.08/GCC-6.4.0
      Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. -
    • Key: ruby/2.5.0/INTEL-18.0.0
      Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. -
    • Key: rum/2.0.5_06
      Description: RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. -
    • Key: samtools/0.1.19/INTEL-18.0.0
      Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. -
    • Key: samtools/1.1/INTEL-18.0.0
      Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. -
    • Key: sina/1.2.11
      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-18.0.0
      Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. -
    • Key: soapdenovotrans/1.0.4/INTEL-18.0.0
      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-18.0.0
      Description: An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. -
    • Key: sprng/2.0b/INTEL-180-MVAPICH2-2.2
      Description: Scalable Parallel Pseudo Random Number Generators Library -
    • Key: sspace/3.0
      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: stringtie/1.3.3/INTEL-18.0.0
      Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. -
    • Key: szip/2.1/INTEL-18.0.0
      Description: Szip compression software, providing lossless compression of scientific data -
    • Key: t_coffee/11.00
      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: TopHat is a fast splice junction mapper for RNA-Seq reads. -
    • Key: totalview/8.12.0
      Description: TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It's available to LSU users only. -
    • Key: transabyss/2.0.1
      Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. -
    • Key: trinity/2.6.6/INTEL-18.0.0
      Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. -
    • Key: valgrind/3.11.0/INTEL-180-MVAPICH2-2.2
      Description: Valgrind: Debugging and profiling tools -
    • Key: vcftools/0.1.14/INTEL-18.0.0
      Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. -
    • Key: velvet/1.2.10/INTEL-18.0.0
      Description: Sequence assembler for very short reads -
    • Key: vmatch/2.3.0
      Description: Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks. -
    • Key: wannier90/2.0.1/INTEL-180-MVAPICH2-2.2
      Description: A tool for obtaining maximally-localised Wannier functions -
    • Key: xz/5.2.2/INTEL-18.0.0
      Description: xz: XZ utilities -
    • Key: zlib/1.2.11
      Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. -

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2018

• Hardware

  • No news

• Software

  • Newly installed packages
    • Key: +beast-2.4.7
      Description: A cross-platform program for Bayesian analysis of molecular sequences using MCMC
  • Updated packages
    • Key: +gcc-4.9.2
      Description: Free compilers from GNU
    • Key: +Intel-18.0.0
      Description: The C/C++ and Fortran compiler suite from Intel.

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Oct-2017

• Hardware

  • no news

• Software

  • no news

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jul-2017

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: +bedtools-2.26.0
      Description: Bedtools is a powerful toolset for genome arithmetic
    • Key: +pigz-2.3.4
      Description: A parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data
    • Key: +remora-1.8
      Description: Resource Monitoring for Remote Applications
    • Key: +vcftools
      Description: vcftoolsA is a set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  • Updated packages
    • Key: +Intel-16.0.3
      Description: The C/C++ and Fortran compiler suite from Intel.
    • Key: +Intel-17.0.4
      Description: The C/C++ and Fortran compiler suite from Intel.
    • Key: +impi-17.3.196-Intel-17.0.4
      Description: Intel MPI implementation.
    • Key: +impi-5.1.3.210-Intel-16.0.3
      Description: Intel MPI implementation.
    • Key: +matlab-r2017a
      Description: MATLAB is a high-level language and interactive environment developed by Mathworks. It is widely u sed in science and engineering across industry and academia. Parallel Computing Toolbox is available.
    • Key: +mvapich2-2.2-Intel-16.0.3
      Description: An MPI-2 implementation (conforming to MPI 3.0 standard) .
    • Key: +mvapich2-2.2-Intel-17.0.4
      Description: An MPI-2 implementation (conforming to MPI 3.0 standard) .
    • Key: +portland-15.10
      Description: Portland Group's high-performance compilers and tools.
    • Key: +R-3.3.3-gcc-4.7.2
      Description:
  • Retired packages
    • Key: +ddt-3.2
      

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Mar-2017

• Hardware

  • A new queue called "shelob" is added to the queuing system

• Software

  • No changes

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2017

• OS Update

• Upgraded to RHEL 6.8 with the latest security patches

• Software

  • Newly installed packages
    • Key: +CP2K-3.0-impi-4.1.3-Intel-13.0.0
      Description: quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems
    • Key: +CP2K-3.0-mvapich2-2.0.1-Intel-14.0.2
      Description: quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems
    • Key: +gnuparallel-20161022-gcc-4.4.6
      Description: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
    • Key: +lsuhpctools
      Description: The jobc is a bash utility that allows users and sysadmins to track all job charge information on the LSU HPC and LONI clusters. This tool is still under internal testing and will be made available to users soon.
    • Key: +swift-0.96.2
      Description: Swift is a simple scripting language for executing many instances of ordinary application programs on distributed and parallel resources.
    • Key: +wannier90-2.0.1-Intel-13.0.0
      Description: program for calculating maximally-localised Wannier functions

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jun-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: +ansys-17.0
      Description: The ANSYS software suites include Fluent, CFX and ANSYS Mechanical.
    • Key: +mathematica-10.4
      Description: Mathematica seamlessly integrates a numeric and symbolic computational engine, graphics system, programming language, documentation system, and advanced connectivity to other applications.
    • Key: +Paraview-4.4.0-Intel-13.0.0-openmpi-1.6.2
      Description: ParaView is an open-source, multi-platform data analysis and visualization application.
    • Key: +espresso-5.3.0-Intel-13.0-openmpi-1.6.2
      Description: 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) .

• Maintenance Scheduled

  • System will be offline for storage maintenance on Monday, June 6

• Known Problems

  • No impact on users

Apr-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: +autodock_vina-1.1.2
      Description: an open-source program for doing molecular docking
    • Key: +bbcp-15.02.03
      Description: BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP.
    • Key: +gromacs-5.0.7-Intel-13.0.0-mvapich2-1.9
      Description: An opne-source, molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
    • Key: +gromacs-5.0.7-Intel-13.0.0-openmpi-1.6.5
      Description: An opne-source, molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
    • Key: +gromacs-5.0.7-Intel-14.0.2
      Description: An opne-source, molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
    • 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.
    • Key: +wq-264
      Description: WQ (WorkQueuing) provides a task dispatcher-worker service. To use, you'll need the PBS template ($WQ_PBS_TEMPLATE). Just make a copy and edit to fit your application needs. A sample task script ($WQ_EXAMPLE_TASK) and user documentation ($WQ_DOC) are also available.

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2016

• Hardware

  • no news

• 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.

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Aug-2015

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: +gsl-1.9-gcc-4.7.2
      Description:
  • Key: +mrbayes-3.2.5-Intel-13.0.0-openmpi-1.6.2
    Description: MrBayes is a free software program which performs Bayesian inference of phylogeny MrBayes is a free software program which performs Bayesian inference of phylogeny
  • Key: +mrbayes-3.2.5-Intel-13.0.0-openmpi-1.6.2-CUDA-4.2.9
    Description: MrBayes is a free software program which performs Bayesian inference of phylogeny
  • Key: +mvapich2-2.1-pgi-15.4
    Description: An MPI-2 implementation (conforming to MPI 2.2 standard) which includes all MPI-1 features.
  • Key: +openmpi-1.6.2-pgi-15.4
    Description:
  • Key: +portland-14.10
    Description: Portland Group's high-performance compilers and tools.
  • Key: +portland-15.4
    Description: Portland Group's high-performance compilers and tools.
  • Key: +R-3.2.0-gcc-4.7.2
    Description:
  • Key: +subversion-1.8.13
    Description: Subversion is an open source version control system
  • Retired packages
    • Key: +portland-11.5
      Description: Portland Group's high-performance compilers and tools.
    • Key: +portland-13.7
      Description: Portland Group's high-performance compilers and tools.

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Feb 2015

• System Updates

  • The bigmem queue maximum walltime has been increased from 48 to 168 hours.

• Software

  • New packages installed.
    • CLHEP (Class Library for High Energy Physics) - CERN high energy physics tools.
      Softenv Key: +clhep-2.1.4.2-gcc-4.4.6
    • GEANT4 - CERN particle radiation transport physics.
      Softenv Key: +geant-4.10.00.p02-gcc-4.4.6
    • ROOT - CERN object-oriented framework for particle physics.
      Softenv Key: +root-5.34.23-gcc-4.4.6
    • GATE - Use GEANT4 for tomography.
      Softenv Key: +gate-7.0-gcc-4.4.6
  • Software Updates
    • The Intel compiler has been upgraded to version 14.0.2.
      Softenv Key: +Intel-14.0.2
    • MVAPICH2 2.0.1 has been installed.
      Softenv Key: +mvapich2-2.0.1-Intel-14.0.2
    • Matlabr2012b has been installed.
      Softenv Key: +matlab-r2012b
    • Mathematica-10.0 has been installed.
      Softenv Key: +mathematica-10.0

• Maintenance Scheduled

  • None scheduled.

• Known Problems

  • None impacting users

Oct-2017

• Hardware

  • no news

• Software

  • no news

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jul-2017

• Hardware

  • no news

• Software

  • Updated packages
    • Key: matlab/r2017a
      Description:

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2017

• OS Update

• Upgraded to RHEL 6.8 with the latest security patches

• Software

  • Updated packages
    • Key: ansys/17.2
      Description: The ANSYS software suites include Fluent and ANSYS Mechanical. It's only available to LSU users.

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jun-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: ddt/6.0.5
      Description: A proprietary debugger for C/C++ and Fortran code. It also supports debugging on GPU (with CUDA and OpenACC) a nd Intel Xeon Phi co-processor. It's only available to LSU users.

• Maintenance Scheduled

  • System will be offline for storage maintenance on Monday, June 6

• Known Problems

  • No impact on users

Apr-2016

• Hardware

  • no news

• Software

  • Newly installed packages
    • Key: bbcp/15.02.03
      Description: BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. -

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2016

• Hardware

  • no news

• 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
      

• Maintenance Scheduled

  • Not scheduled

• Known Problems

  • No impact on users

Jan-2016

• 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.

• Software

  • Newly installed packages
    • No items
  • Updated
    • No items
  • Retired
    • No items

• Maintenance Scheduled

  • Decommissioning: Friday, 22 Jan 2016

• Known Problems

  • No impact on users