Changes between Version 34 and Version 35 of WikiStart


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Timestamp:
Jun 3, 2019, 4:36:21 PM (5 years ago)
Author:
Mikael Brandström Durling
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  • WikiStart

    v34 v35  
    1 == Welcome to the Mykopat Grid Wiki ==
    2 [Old Wiki page]https://my-mgrid.mykopat.slu.se/trac/grid/wiki/oldwiki
     1== What is the Mykopat Computing Grid? ==
     2The computing grid has been setup for users to be able to analyse large genetic data sets, and other analysis requiring long computing times on Linux systems. A grid of computers is essentially a number of computers linked together by a common grid management software. The management software manages how job requests should be spread across the computer resources and most importantly makes sure the resources are shared in a fair manner.
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    4 == What is the Mykopat Computing Grid? ==
    5 The computing grid has been setup for users to be able to analyse very large genetic data sets, and other analysis requiring long computing times on Linux systems. A grid of computers is essentially a number of computers linked together by a common grid management software. The management software delegates how the job requests should be handled by the computer resources and most importantly makes sure the resources are shared in a fair manner.
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    7 Currently our grid consists of five computers available around the clock for long running high-resource jobs. These provide 40 cpu cores and 296GB ram. In addition to this we are also adding normal desktop computers as a part of the grid during non-office hours. Currently this adds somewhat more than 33 extra cores for short-running low-memory tasks.
     4Before you can use the system, you need to ask for grid access from Les.
    85
    96== [wiki:Software Available Software] ==
     7Here we  have a list of installed [wiki:Software]. Please check the list before asking to have software installed. If you miss anything specific. Create an issue here where you specify what you need or drop a mail to the department IT staff (help att mykopat.slu.se).
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    11 Here we  have a list of installed [wiki:Software]. Please check the list before asking to have software installed. If you miss anything specific. Create an issue here where you specify what you need.
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    13 
    14 
    15 == How to log in: There are several ways to access the grid:==
    16 
     9== How to log in: There are several ways to access the grid: ==
    1710 1. From Macs and other unix-like computers you can login using the ssh-command in the terminal. You will then interact with the grid though commands in the terminal.
    1811 1. From Windows computers, you can login using Putty to login to a terminal session. You will then interact with the grid though commands in the terminal.
    19  1. There is also an option to start a Remote Desktop on the grid login node.
    2012
    21 Don't forget to run your jobs through the [GridEngine grid engine], otherwise they might just be stopped by the system when the default resource limits are exceeded.
     13The hostname to connect to is: `my-grid.mykopat.slu.se`
     14
     15Don't forget to run your jobs through the [wiki:GridEngine grid engine], otherwise they might just be stopped by the system when the default resource limits are exceeded.
    2216
    2317== Running commands ==
    24 Once you have logged in to my-mgrid you will encounter a Linux system. (It is a Debian GNU/Linux system, quite similar to Ubuntu, but with some customisations to make it more suitable to act in a grid environment. If you are unfamiliar with work in a unix shell, you should consult som unix shell tutorial. We have a small Unix CheatSheet or quick reference that might be useful. You should also check the GridEngine pages for information on how to run long-running analysis.
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     18Once you have logged in you will encounter a Linux system. It is a Debian GNU/Linux system, quite similar to Ubuntu, but with some customisations to make it more suitable to act in a grid environment. If you are unfamiliar with work in a unix shell, you should consult som unix shell tutorial. We have a small Unix CheatSheet or quick reference that might be useful. You should also check the GridEngine pages for information on how to run long-running jobs.
    2619
    2720== Projects ==
     
    3932For each project a number of WebServices are available to use. These include:
    4033
    41  * [ProjectWebFolder Project web folder]
    42  * [ProjectSubversion Subversion for version control of project files]
    43  * [ProjectTrac Trac for project documentation (includes a wiki like this, issue handling and a nice browser for subversion)]
     34 * [wiki:ProjectWebFolder Project web folder]
     35 * [wiki:ProjectSubversion Subversion for version control of project files]
     36 * [wiki:ProjectTrac Trac for project documentation (includes a wiki like this, issue handling and a nice browser for subversion)]
    4437
    4538== '''[wiki:FrequentlyAskedQuestions Frequently Asked Questions]''' ==
    4639Go here to find out information about common problems (for example: installing software in your local folder)
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    48 
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    5041Technical documentation for Administrators is found in the [[Admin]] section of the wiki.