Tag Archives: IO

Linux

First Open Chemistry Beta Release

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We are pleased to announce the first beta release of the Open Chemistry suite of cross platform, open-source, BSD-licensed tools and libraries – Avogadro 2, MoleQueue and MongoChem. They are being released in beta, before all planned features are complete, to get feedback from the community following the open-source mantra of “release early, release often”. We will be making regular releases over the coming months, as well as automatically generating nightly binaries. A Source article from 2011 introduced the project, slides from FOSDEM describe it more recently, and the 0.5.0 release binaries can be downloaded here.

These three desktop applications can each be used independently, but also have the capability of working together. Avogadro 2 is a rewrite of Avogadro that addresses many of the limitations we saw. This includes things such as the rendering code, scalability, scriptability, and increased flexibility, enabling us to effectively address the current and upcoming challenges in computational chemistry and related fields. MoleQueue provides desktop services for executing standalone programs both locally and on remote batch schedulers, such as Sun Grid Engine, PBS and SLURM. MongoChem provides chemically-aware search, storage, and informatics visualization using MongoDB and VTK.

Avogadro 2

Avogadro 2 is a rewrite of Avogadro; please see the recently-published paper for more details on Avogadro 1. Avogadro has been very successful over the years, and we would like to thank all of our contributors and supporters, including the core development team: Geoff Hutchison, Donald Curtis, David Lonie, Tim Vandermeersch, Benoit Jacob, Carsten Niehaus, and Marcus Hanwell. We also recently obtained permission from almost all authors to relicense the existing code under the 3-clause BSD license, which will make migration of code to the new architecture much easier.

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

Avogadro is not yet feature complete, but we invite you to try it out along with the suite of applications as we continue to improve it. The new Avogadro libraries feature much finer granularity; whereas before we provided a single library with all API, there is now a layered API in multiple libraries. The Core and IO libraries have minimal dependencies, with the rendering library adding a dependence on OpenGL, and the Qt libraries adding Qt 4 dependencies. This allows us to reuse the code in many more places than was possible before, with rendering possible on a server

From: http://blog.cryos.net/archives/265-First-Open-Chemistry-Beta-Release.html

Business, Finance, Occupation & Industry

PIMCO High Income Fund Announces Elimination of a Non-Fundamental Investment Policy

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By Business Wirevia The Motley Fool

Filed under:

PIMCO High Income Fund Announces Elimination of a Non-Fundamental Investment Policy

NEW YORK–(BUSINESS WIRE)– PIMCO High Income Fund (NYS: PHK) (the “Fund”) announced that its Board of Trustees has approved the elimination of its non-fundamental investment policy which provides that the Fund will not invest in interest-only (“IO“) or principal-only (“PO“) securities or inverse floating rate (“inverse floater”) securities. The change takes effect immediately, such that the Fund may now invest in these instruments.

The Fund’s management team believes the Fund would benefit from the ability to utilize these instruments in targeted situations in current and future market conditions, including to react to changes in interest rates or the rate of principal payments (including pre-payments) on underlying mortgage assets and to better capitalize on the management team’s views on the housing and mortgage markets.

IOs are a class of debt security, typically representing an interest in a pool of mortgage-related or other asset-backed securities, which receives all of the interest from the asset pool, while the PO class of the security receives all of the principal. The value of (i.e. the yield to maturity and price) an IO or PO class is extremely sensitive to the rate of principal payments (including prepayments) on the related, underlying mortgages or other assets. For example, a rapid rate of principal payments may have a material adverse effect on the value of IO securities, while a slower than expected rate of principal payments may have a material adverse effect on a PO class security’s value. If the underlying mortgage or other assets experience greater or slower than anticipated prepayments of principal, the Fund may fail to recoup some or all of its initial investment in IOs or POs, even if the security is in one of the highest rating categories.

An inverse floater is a type of debt instrument that bears a floating or variable interest rate that moves in the opposite direction to interest rates generally or the interest rate on another security or index. Changes in interest rates generally, or the interest rate of the other security or index, inversely affect the interest rate paid on the inverse floater, with the result that the inverse floater’s price will be considerably more volatile than that of a fixed-rate instrument of similar credit quality. The market prices of inverse floaters may be highly sensitive to changes in interest rates and prepayment rates on the underlying securities, and may decrease significantly when interest rates increase or prepayment rates change.

Investment in IOs, POs and inverse …read more
Source: FULL ARTICLE at DailyFinance

News, Politics, Government

Conferences.IO Solves One Of The Biggest Problems That Happens At Events

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By Amit Chowdhry, Contributor

Remember when you were a kid and it was very easy to ask your teachers a question just by raising your hand?  A few years ago, I was taking an economics class at Michigan State University (MSU) that had 600 students.  Students in that class rarely ever asked a question because six-hundred pairs of eyes would suddenly focus on them, which can put on a lot of pressure.  Conferences.IO and GoSoapBox co-founders John Pytel and Dave Mulder are working on solving this issue today. …read more
Source: FULL ARTICLE at Forbes Latest

Linux

Solaris for a Red Hat admin

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By abohmeed

Hello Solaris gurus
Recently I was assigned to work on the company’s Oracle Solaris 10 servers. Actually this is the first time I lay eyes on a Solaris machine… like ever! I’ve spent my career dealing with Red Hat run servers (I am an RHCE). I’ve also worked for a while on IBM AIX.
The question is, simply, where to start? I’ve already downloaded the entire Solaris 10 information library from Oracle. It’s huge reading resource (> 1GB) that is going to take some time to go through. So is there another source of information not for newbies but for a Linux guy like me?
To narrow things down a little my manager has asked me to handle the performance degradation problem on those servers as a first priority, so what exactly should I be looking at? I already checked the CPU, memory and disk IO but they all look normal. So any more ideas?
Thanks a lot in advance

…read more
Source: FULL ARTICLE at The UNIX and Linux Forums

Linux

BusyTasks 12.7 (Plasmoid Script)

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Thumbnail

BusyTasks 12.7
(Plasmoid Script)
UPDATE: Altered plasmoid configuration (own method createUserInterface) for new KDE versions.
Please read at least section REQUIREMENTS before installation

DOCUMENTATION:
Isn’t everything some kind of process? At least on a computer it is. So let’s keep an eye on them.
This plasmoid initially was a clumsy spin-off from Dmitry Makovey‘s tail plasmoid, but after I got more and more used to python and the program got more and more complex I cut everything superfluous and eventually separated it from tail.
This plasmoid uses several programs to get its input. The collected data is neither unique nor new, but the idea to clearly sum it up in one single program is. This task monitor displays up to four different tasks, each with different priority.

CPU intensive task:
Name and the percentage of the most CPU intensive task. The underlying top daemon is very efficient and does not really affect CPU, it is piped to shared memory.
Used backend: http://linux.die.net/man/1/top

Memory intensive task:
Name of the most memory intensive task, combined with a measure of size (absolute value or percentage to total available memory).
The implementation is the same as for the task above.

IO intensive task:
The task that currently asks for IO.
The software package includes an own version of iotop that sends data via shared memory.
Original version: http://guichaz.free.fr/iotop/

NET intensive task:
The task that eats up your bandwidth.
You will be prompted for an administrator password when starting nethogs.
Like the one of iotop, this is a modified nethogs daemon that uses IPC.
Original version: http://nethogs.sourceforge.net

Additionally, the configurable update interval plays a crucial role in resource consumption. The smaller it is set, the more resources are needed.
There should be slightly less resource consumption (in terms of IO as well as overall) since release 8.0. Release 10.0 eventually cut out all IO.

The plasmoid is highly configurable to fit most desktop designs.
It supports highlighting of processes, either through a simple colour change after a certain limit of per cents or via colour gradient. For the statisticians among you, you can even log output. BusyTasks is only useful if it is always visible (e.g. residing on a panel) If you’d have got to minize windows or show the desktop to have a glance on it you could equally start the system monitor.

REQUIREMENTS: (and installation instructions)
The program was tested under several different distributions and is considered stable.(read below). Some of the used daemons may require additional libraries, however.
For full functionality, you need to meet the following requirements:

  • Installation of top in your command-line interpeter. This usually is the case on UNIX OSs.
  • Proper value of $HOME variable in the shell environment. Verify with “echo $HOME“.
  • Python version 2.
    On new systems version 3 may …read more
    Source: FULL ARTICLE at KDE Apps
    • Video Gaming

    Hitman: Absolution Infographic Breaks Down Player Kill Stats

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    Hitman: Absolution studio IO Interactive has released a handy infographic featuring some stats pulled from both the Hitman Sniper Challenge and Absolution’s asynchronous multiplayer mode, Contracts.

    Contracts Mode, according to IO, has proven to be a hit across the globe. The most-played Contract on each platform exceeds 500,000 plays and counting. The infographic also reveals players have collectively earned over 1.3 trillion dollars in Contracts so far and tend to favour 47’s pistols above other firearms.

    Speaking of firearms: never get in front of a Spaniard with a sniper rifle. Players from Spain are far and away the game’s most efficient snipers.

    Check out the rest of the stats below.

    Continue reading…

    …read more
    Source: FULL ARTICLE at IGN Video Games

    Linux

    Physical disk IO size smaller than fragment block filesystem size ?

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    By rarino2

    Hello,
    in one default UFS filesystem we have 8K block size (bsize) and 1K fragmentsize (fsize). At this scenary I thought all “FileSytem IO” will be 8K (or greater) but never smaller than the fragment size (1K). If a UFS fragment/blocksize is allwasy several ADJACENTS sectors on disk (in a disk with sector=515B), all “physical disk IO” it will allways, like “Filesystem IO“, greater than 1K.

    But with dtrace script from DTrace Toolkit (bitesize.d) I can see IOs with 512B size.

    ¿What is wrong in my assumptions or what is the explanation?

    Thank you very much in advance!!

    …read more
    Source: FULL ARTICLE at The UNIX and Linux Forums

    Linux

    How get program name that produced an IO error redirected to a LOG in a nohup command?

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    By enriquegm82

    Good afternoon,

    I’m have program that executes in background another programs. The main program would be programA and the programs executed by the main one, would be program1a, program1b and program1c.

    I need the programs to continue the execution no matter if the shell connection is lost, so I’m using the NOHUP command.

    However, each program has its own LOG file, like follows.-

    programA –> logfileA.txt
    program1a –> logfile1a.txt
    program1b –> logfile1b.txt
    program1c –> logfile1c.txt

    When an error occurs in one of the child programs, the error message is displayed in the LOG file corresponding to the main program.

    Example.-

    1) The programA is invoked from another routine.-

    nohup nice -10 programA 2>&1 > logfileA.txt

    2) Inside programA it invokes the other 3 programs.-

    nohup nice -10 program1a 2>&1 > logfile1a.txt
    nohup nice -10 program1b 2>&1 > logfile1b.txt
    nohup nice -10 program1c 2>&1 > logfile1c.txt

    When an error occurs, it is showed or displayed in the logfileA.txt, instead of being displayed in the logfile1a.txt or logfile1b.txt or logfile1c.txt

    How can I know what program produced the error that it is displayed in the main program’s LOG file?

    Thanks in advance for your responses.

    Source: FULL ARTICLE at The UNIX and Linux Forums

    Business, Finance, Occupation & Industry

    Top Buys by Directors: Lapeyre Jr.'s $174.5K Bet on IO

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    By DividendChannel.com The directors of a company tend to have a unique inside view into the business, so when directors make major buys, investors are wise to take notice. Presumably the only reason a director of a company would choose to take their hard-earned cash and use it to buy stock in the open market, is that they expect to make money ? maybe they find the stock very undervalued, or maybe they see exciting progress within the company, or maybe both. So in this series we look at the largest insider buys by company directors over the trailing six month period, one of which was a total of $174.5K by James M. Lapeyre Jr., Director at ION Geophysical Corp (NYSE: IO).
    Source: FULL ARTICLE at Forbes Markets

    Linux

    Classpath of JAVA

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    By yifangt

    Hello,
    ABC question as I could not get a direct answer: How to locate the default IO class of JAVA? My question was triggered by the row in most java program

    Code:
    import java.io.*

    as I am very curious where the io class is located in my Mint14 (Ubuntu12.10). I am aware it is similar to use DBI in PERL, or #include in C++, where I could locate the packages/libraries in certain directories:

    Code:
    /usr/lib/perl5/DBI.pm
    /usr/include/c++/4.7/iostream

    but I could not locate any file name (io.class, or io.jre) for this io class in java? Have checked my system for the libraries:

    Code:
    /usr/lib/jvm/java-7-openjdk-amd64/lib/
    /usr/lib/jvm/java-7-openjdk-common/jre/lib/
    /home/kevin/downloadsoftware/jre1.7.0_10/lib/
    /usr/lib/eclipse/plugins/

    Also checked Oracle website, where there is:

    Code:
    package java.io

    but I could not find this file in my system, and the java program works fine. Can anybody give me some explanantion about the “default IO, file, string, date & time, etc classes” of java1.7.x when it was installed. My java is:

    Code:
    $java -version
    java version "1.7.0_09"
    OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.10.1)
    OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

    Thanks a lot!

    Source: FULL ARTICLE at The UNIX and Linux Forums