Oakley

HOWTO: Use NFSv4 ACL

This document shows you how to use the NFSv4 ACL permissions system. An ACL is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certian file or directory by user or group. NFSv4 ACLs provide more specific options than typical POSIX read/write/execute permissions used in most systems.

Understanding NFSv4 ACL

This is an example of an NFSv4 ACL

HOWTO: Reduce Disk Space Usage

This "how to" will demonstrate how to lower ones' disk space usage.  The following procedures can be applied to all of OSC's file systems.

We recommend users regularly check their data usage and clean out old data that is no longer needed.

Users who need assistance lowering their data usage can contact OSC Help.

LAMMPS 14May16 too-many-threads known issue fixed

Date: 
Wednesday, November 30, 2016 - 3:45pm
Supercomputer: 

The LAMMPS 14May16 known issue wherein parallel lammps spawned too many threads has been fixed on all clusters.  No user action is required; if a user had applied the OMP_NUM_THREADS workaround then it may be removed, but it will not cause probems if left in place. The corrected executables were made the defaults for module lammps/14may16 at these times:

Spark Documentation

Apache Spark is an open source cluster-computing framework originally developed in the AMPLab at University of California, Berkeley but was later donated to the Apache Software Foundation where it remains today. In contrast to Hadoop's disk-based analytics paradigm, Spark has multi-stage in-memory analytics. Spark can run programs upto 100x faster than Hadoop’s MapReduce in memory or 10x faster on disk. Spark support applications written in python, java, scala and R

Changes of Default Memory Limits

Problem Description

Our current GPFS file system is a distributed process with significant interactions between the clients. As the compute nodes being GPFS flle system clients, a certain amount of memory of each node needs to be reserved for these interactions. As a result, the maximum physical memory of each node allowed to be used by users' jobs are reduced, in order to keep the healthy performance of the file system. In addition, using swap memory is not allowed anymore. 

WARP3D

From WARP3D's webpage:

WARP3D is under continuing development as a research code for the solution of large-scale, 3-Dsolid models subjected to static and dynamic loads. The capabilities of the code focus on 
fatigue & fracture analyses primarily in metals. WARP3D runs on laptops-to-supercomputers and can analyze models with several million nodes and elements. 

Availability and Restrictions

Versions

The following versions of WARP3D are available on OSC clusters:

Amber 16 now available

Date: 
Friday, July 29, 2016 - 4:15pm
Supercomputer: 

Amber 16 has been installed on the OSC clusters; usage is via the module amber/16. For information on available executables and installation details see the software page for Amber or the output of the module help command, e.g.: module help amber/16.  On August 15, 2016 Amber 16 will be made the default amber module.

R

R is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques, and is highly extensible.

Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

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