[LA-SiGMA] LSU HPC/LONI Cluster System Update
Wei P Feinstein
wfeinstein at lsu.edu
Mon Jun 6 09:05:13 CDT 2016
********** <http://www.hpc.lsu.edu/sysnews/index.php> HPC/LONI SYSTEM UPDATES (June 2016) ********
CONTENTS:
LONI HPC
QB2
Eric
LSU HPC
SuperMIC
SuperMike2
Philip
The latest information of software stack can be found at http://www.hpc.lsu.edu/docs/guides/index.php
*******************************************************************
I LONI QB2--Nvidia GPU
Hardware
no news
Software
Newly installed packages
Key: mothur/1.36.1/INTEL-140-MVAPICH2-2.0
Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. -
Key: qiime/1.9.1-python-2.7.10-anaconda
Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). -
Updated packages
Key: python/2.7.10-anaconda
Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. -
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.
Maintenance Scheduled
Not scheduled
Known Problems
No impact on users
*******************************************************************
II LONI Eric
No changes
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III LSU HPC SuperMIC--Intel Xeon Phi
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 on Monday, July 11. Downtime may last for a couple of weeks. Details are coming soon
Known Problems
No impact on users
*******************************************************************
IV LSU HPC SuperMike2
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
*******************************************************************
V LSU HPC Philip
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
*******************************************************************
Thank you,
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>
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