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• Configuration management in support of scientific computing

  - by Sharpie

  For the past few years I have been involved with developing and maintaining a system for forecasting near-shore waves. Our team has just received a significant grant for further development and as a result we are taking the opportunity to refactor many components of the old system. We will also be receiving a new server to run the model and so I am taking this opportunity to consider how we set up the system. Basically, the steps that need to happen are: Some standard packages and libraries such as compilers and databases need to be downloaded and installed. Some custom scientific models need to be downloaded and compiled from source as they are not commonly provided as packages. New users need to be created to manage the databases and run the models. A suite of scripts that manage model-database interaction needs to be checked out from source code control and installed. Crontabs need to be set up to run the scripts at regular intervals in order to generate forecasts. I have been pondering applying tools such as Puppet, Capistrano or Fabric to automate the above steps. It seems perfectly possible to implement most of the above functionality except there are a couple usage cases that I am wondering about: During my preliminary research, I have found few examples and little discussion on how to use these systems to abstract and automate the process of building custom components from source. We may have to deploy on machines that are isolated from the Internet- i.e. all configuration and set up files will have to come in on a USB key that can be inserted into a terminal that can connect to the server that will run the models. I see this as an opportunity to learn a new tool that will help me automate my workflow, but I am unsure which tool I should start with. If any member of the community could suggest a tool that would support the above workflow and the issues specific to scientific computing, I would be very grateful. Our production server will be running Linux, but support for OS X would be a bonus as it would allow the development team to setup test installations outside of VirtualBox.

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• Add group rwx permissions to a folder

  - by Jasie

  I have a folder named docs, how do I add rwx permissions for group devs to docs? I tried: chmod -R g+rwx docs but I don't know where to specify that it's the devs group I want to grant permissions for.

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• Git - post-receive hook with git pull "Failed to find a valid git directory"

  - by ludicco

  It's very weird but when setting a git repository and creating a post-receive hook with: echo "--initializing hook--" cd ~/websites/testing echo "--prepare update--" git pull echo "--update completed--" the hook runs indeed, but it never manage to run git pull properly: 6bfa32c..71c3d2a master -> master --initializing hook-- --prepare update-- fatal: Not a git repository: '.' Failed to find a valid git directory. --update completed-- so I'm asking myself now, how it's possible to make the hook update the clone with post-receive? in this case the user running the processes is the same, and its everything inside the user folder so I really don't understand...because if if I go manually into cd ~/websites/testing git pull it works without any problem... any help on that would be pretty much appreciated Thanks a lot

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• failed to enable x11 forwarding

  - by Hunt

  I am trying to enable X11 forwarding on my server which is running on FreeBSD 7.1. I have a putty installed in my windows in which i have enabled X11 forwarding by checking on Enable X11 forwarding and specifying following parameter X display location localhost:0 after that i run putty and checked whether X11 is enabled or not by typing following command echo "$DISPLAY" or echo $DISPLAY but i am getting following error DISPLAY: Undefined variable. Even i have installed XManager but in that also i am getting following error The X11 forwarding request was rejected ! To solve this problem, please turn on the X11 forwarding features of the remote SSH server can anyone suggest me how to get rid off this ?

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• How are PID's generated?

  - by Helltone

  On *nix, PIDs are unique identifiers for running processes. How are PID's generated? Is it just an integer which gets incremented or a more complex structure such as a list? How do they get recycled? By recycling I mean that, when a process terminates, it's PID will eventually be reused by another process.

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• How to configure sudoers with path wildcards?

  - by C. Lee

  Hi, I need sudo for a command for any path under a particular area. Example: sudo mycommand /opt/apps/myapp/... What is the sudoers syntax to allow this command to run in any path that falls under /opt/apps/myapp? This is Solaris 10 sudo. Thanks.

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• Vim: Custom Folding function done, custom highlighting required

  - by sixtyfootersdude

  I have defined a function in vim to properly indent folds. Ie so they look like this: Unfolded this is text also text indented text indented text not indented text folded with default function this is text also text +-- 2 lines: indented text ---------------------------- not indented text folded with my new function this is text also text ++- 2 lines: indented text ---------------------------- not indented text The only problem is the the highlighting is still like this: folded with my new function (highlighting shown with tag) this is text also text <hi> ++- 2 lines: indented text ----------------------------</hi> not indented text I would like the highlighting to start at the ++ and not at the beginning of the line. I have looked in the vim manual but could not find anything like that. One so-so solution I found was to make the background black. highlight Folded ctermbg=black ctermfg=white cterm=bold But this make folds less visible. I have tried several variations of: syn keyword Folded lines syn region Folded ... But I don't think that this is the way that folds are selected. Can anyone offer a suggestion? By the way this is my function to indent the folds: set foldmethod=indent function! MyFoldText() let lines = 1 + v:foldend - v:foldstart let ind = indent(v:foldstart) let spaces = '' let i = 0 while i < ind let i = i+1 let spaces = spaces . ' ' endwhile let linestxt = 'lines' if lines == 1 linestxt = 'line' endif return spaces . '+' . v:folddashes . ' '. lines . ' ' . linestxt . ': ' . getline(v:foldstaendfunction endfunction au BufWinEnter,BufRead,BufNewFile * set foldtext=MyFoldText() By the way thanks to njd for helping me get this function setup.

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• Automating the choice between JPEG and PNG with a script

  - by MHC

  Choosing the right format to save your images in is crucial for preserving image quality and reducing artifacts. Different formats follow different compression methods and come with their own set of advantages and disadvantages. JPG, for instance is suited for real life photographs that are rich in color gradients. The lossless PNG, on the other hand, is far superior when it comes to schematic figures: Picking the right format can be a chore when working with a large number of files. That's why I would love to find a way to automate it. A little bit of background on my particular use case: I am working on a number of handouts for a series of lectures at my unversity. The handouts are rich in figures, which I have to extract from PDF-formatted slides. Extracting these images gives me lossless PNGs, which are needlessly large at times. Converting these particular files to JPEG can reduce their size to up to less than 20% of their original file size, while maintaining the same quality. This is important as working with hundreds of large images in word processors is pretty crash-prone. Batch converting all extracted PNGs to JPEGs is not an option I am willing to follow, as many if not most images are better suited to be formatted as PNGs. Converting these would result in insignificant size reductions and sometimes even increases in filesize - that's at least what my test runs showed. What we can take from this is that file size after compression can serve as an indicator on what format is suited best for a particular image. It's not a particularly accurate predictor, but works well enough. So why not use it in form of a script: I included inotifywait because I would prefer for the script be executed automatically as soon as I drag an extracted image into a folder. This is a simpler version of the script that I've been using for the last couple of weeks: #!/bin/bash inotifywait -m --format "%w%f" --exclude '.jpg' -r -e create -e moved_to --fromfile '/home/MHC/.scripts/Workflow/Conversion/include_inotifywait' | while read file; do mogrify -format jpg -quality 92 "$file" done The advanced version of the script would have to be able to handle spaces in file names and directory names preserve the original file names flatten PNG images if an alpha value is set compare the file size between the temporary converted image and its original determine if the difference is greater than a given precentage act accordingly The actual conversion could be done with imagemagick tools: convert -quality 92 -flatten -background white file.png file.jpg Unfortunately, my bash skills aren't even close to advanced enough to convert the scheme above into an actual script, but I am sure many of you can. My reputation points on here are pretty low, but I will gladly award the most helpful answer with the highest bounty I can set. References: http://www.formortals.com/introducing-cnb-imageguide/, http://www.turnkeylinux.org/blog/png-vs-jpg Edit: Also see my comments below for some more information on why I think this script would be the best solution to the problem I am facing.

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• How to restore infrared support in Windows XP?

  - by Emil Rasmussen

  My infrared port is not working on my Windows XP SP 3 (Thinkpad X60). I can see it Device Manager, and it's status is, that it is working probably. The problem manifests in several ways. Originally I was trying to transfer data from my Polar RS800CX watch, and the Polar ProTrainer 5 software gave me the this error message: "Communication port couldn't be opened". Then I tried to connect the watch to another computer, and the infrared connection was established immediately. I then tried to connect the other computer to my Thinkpad X60. The other computer again immediately showed the Wireless Link icon "'computername' is in range" in the notification area. But nothing is shown on the Thinkpad, and a file transfer to the Thinkpad is unsuccessful with an error message that reports that "the target machine actively refused it [the connection]". This brings me to conclude that the infrared support in Windows on the Thinkpad is somehow broken. This is further supported by the fact that I can't find the "Wireless Link" icon in the Control Panel and when I try to run the irprops.cpl nothing happens. So the question is, how to reinstall the infrared support? Some of the solutions that I have explored is: I have tried to disable/enable the infrared in the BIOS - to trick a re-installation. The IR modules settings on the other computer that can get a successful IR connection is an exact match to the ThinkPad that can't get a connection. The was a problem in Windows XP SP 2 with the Wireless Link icon - MS KB article - but that hotfix can't be applied on SP 3 installation. I also guess that the hotfix is included in SP 3. Any other suggestions?

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• How can I kill and wait for background processes to finish in a shell script when I Ctrl+C it?

  - by slipheed

  I'm trying to set up a shell script so that it runs background processes, and when I ctrl+C the shell script, it kills the children, then exits. The best that I've managed to come up with is this. It appears that kill 0 -INT also kills the script before the wait happens, so the shell script dies before the children complete. Any ideas on how I can make this shell script wait for the children to die after sending INT? #!/bin/bash trap 'killall' INT killall() { echo **** Shutting down... **** kill 0 -INT wait # Why doesn't this wait?? echo DONE } process1 & process2 & process3 & cat # wait forever

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• Bash: Reset and Clear Commands

  - by sixtyfootersdude

  I have been using the command: reset to clear my terminal. Although I am pretty sure this is not what I should be doing. Reset, as the name suggests resets your entire terminal (changes lots of stuff). Here is what I want: I basically want to use the command clear. However if you clear and then scroll up you still get tonnes of stuff from before. In general this is not a problem however I am looking at gross logs that are long and I want to make sure that I am just viewing the most recent one. I know that I could use more or something like that but I prefer this approach.

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• Laptop choice for development: MacBook Pro 17 vs Dell Studio XPS 16 vs HP Envy 15

  - by Shalan

  Hey! First things first - let me state that I am not intending to play games on this - I have narrowed down to these 3 purely based on specs and its individual brand reliability in the market. I intend to primarily use: Visual Studio 2008 Pro a lot (develop and deploy on Windows platforms) SQL Server 2005 Oracle 10g Adobe Photoshop CS4 Microsoft Expression Studio Google Sketchup I currently use a desktop PC (Core2Duo 2.66Ghz with 3GB DDRII memory) running Vista Business 32-bit - and I have to admit that, especially for Visual Studio, its quite sluggish to a point where it affects productivity. Furthermore, I intend to only use the notebook on a table - with a cooled surface, like granite :) - so I would appreciate people's input with regard to heat issues. Im aware that the Dell's primary exhaust gets blocked by the lid when open, but some reviews don't seem to place extraordinary emphasis on heat issues resulting from this. My options for the Dell/Alienware: Core i7 720QM 4GB DDRIII memory ATI mobility 3670 (512) 128GB Solid State Drive 16-inch Full HD RGB-LED LCD display (1080p) 3-year next-business-day support My configuration for the Apple MBP: Core2Duo 2.8Ghz (Im assuming the T9600) 4GB DDRIII memory 128GB Solid State Drive standard 1 year support The one advantage I think of with the MBP is that I can have the addition of OSX (though Im unsure what I would use it for, but purely to play around with a much-boasted-about OS) What are your thoughts on this, especially regarding build-quality, heat, performance and battery-life? Much thanks! ~shalan

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• Unzip individual files from multiple zip files and extract those individual files to home directory

  - by James P.

  I would like to unzip individual files. These files have a .txt extension. These files also live within multiple zipped files. Here is the command I'm trying to use. unzip -jn /path/to/zipped/files/zipArchiveFile2011\*.zip /path/to/specific/individual/files/myfiles2011*.txt -d /path/to/home/directory/for/extract/ From my understanding, the -j option excludes directories and will extract only the txt files The -n option will not overwrite a file if it has already been extracted. I've also learned that the forward slash in /path/to/zipped/files/zipArchiveFile2011\*.zip is necessary to escape the wildcard (*) character. Here is sample of error messages I'm coming accross: Archive: /path/to/zipped/files/zipArchiveFile20110808.zip caution: filename not matched: /path/to/specific/individual/files/myfiles20110807.txt caution: filename not matched: /path/to/specific/individual/files/myfiles20110808.txt Archive: /path/to/zipped/files/zipArchiveFile20110809.zip caution: filename not matched: /path/to/specific/individual/files/myfiles20110810.txt caution: filename not matched: /path/to/specific/individual/files/myfiles20110809.txt I feel that I'm missing something very simple. I've tried using single quotes (') and double quotes (") around directory paths. But no luck.

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• Learning Linux screencasts

  - by Dmitriy Nagirnyak

  Hi, I am trying to get started with Linux. There are number of books (many of which are just man pages), some of them provide good overview so I can dig deeper online then. What I would like is to find number of screencasts that would cover basics of Linux commands, server administration, commonly performed tasks etc (no GUI, only terminal). I want to watch the screencasts to "get it quicker" and then use a book or online resources to "dig it deeper". Any recommendations? Thanks, Dmitriy.

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• Probelm After Changing password in ubuntu

  - by Narendra

  Hi All, I am using ubuntu system which uses openldap for user login authentication. For changing my login password i used "$sudo passwd" and changed it. (of course the password given is same as old one). Then onwards when i trying to run "apt" command it showing command not found. and for some other programs it showing segmentation fault. Can any one tell me why I am facing issue and how to solve this.

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• OSX: Python packages fail to install, error message "/usr/local/bin: File Exists"

  - by kylehotchkiss

  I keep trying to install django and other python packages, and I keep getting the exact same error message: Installing django-admin.py script to /usr/local/bin error: /usr/local/bin: File exists So I look to make sure that my /usr/local folder is okay. At first glance it appears okay, until I try cd-ing into my bin. It says it can't because it's not a directory. Peculiar, I thought, so then I tried a Anchorage:local khotchkiss$ ls -a -l total 26168 drwxr-xr-x 6 root wheel 204 Dec 26 20:18 . drwxr-xr-x@ 14 root wheel 476 Feb 24 12:54 .. -rwxr-xr-x@ 1 root wheel 13395080 Oct 22 23:04 bin drwxr-xr-x 8 root wheel 272 Dec 26 20:18 git drwxr-xr-x 4 root wheel 136 Dec 18 11:31 include drwxr-xr-x 12 root wheel 408 Dec 18 11:31 lib And haven't a clue of what the 'bin' is, why its so large, and why its preventing me from installing python packages. Any clue?

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• Good ways to restart all the computers in a remote cluster?

  - by vgm64

  I have a cluster that I manage and from time to time I get emails from each node (and head node) begging to be restarted after an automatic upgrade. Currently, my best solution so far is a shell script like: $> cat cluster_reboot.sh ssh [email protected] reboot ssh [email protected] reboot ssh [email protected] reboot ssh [email protected] reboot ssh [email protected] reboot ssh [email protected] reboot I end up just typing the root password six times, but it works, I guess. Is there a better way? Can I force the head node to reboot the computers for me?

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• Prevent scp from copying local files?

  - by ashcatch

  I just read the Linux scp command issue question and it reminded me that I regularily forget to specify the colon in the host part of a scp command, and thus copying a file locally instead of copying to a remote host, e.g. I do scp foo host instead of scp foo host: But I never use scp to copy a file locally. So I wonder if there is a way to make scp fail if both (the source and destination) arguments refer to local files.

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• how can i edit .bashrc file

  - by Tulu

  i am working for cisco. I want to edit that .bashrc file.So can any body suggest what I will do?

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• Mount an sshfs via macfuse at boot

  - by dag729

  I want to mount an sshfs folder at boot under Mac OSX: I'm using Macfusion right now, that is a GUI for MacFUSE, but I have to mount the folder manually. How can I achieve that? Thanks

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• With a username passed to a script, find the user's home directory

  - by Clinton Blackmore

  I am writing a script that gets called when a user logs in and check if a certain folder exists or is a broken symlink. (This is on a Mac OS X system, but the question is purely bash). It is not elegant, and it is not working, but right now it looks like this: #!/bin/bash # Often users have a messed up cache folder -- one that was redirected # but now is just a broken symlink. This script checks to see if # the cache folder is all right, and if not, deletes it # so that the system can recreate it. USERNAME=$3 if [ "$USERNAME" == "" ] ; then echo "This script must be run at login!" >&2 exit 1 fi DIR="~$USERNAME/Library/Caches" cd $DIR || rm $DIR && echo "Removed misdirected Cache folder" && exit 0 echo "Cache folder was fine." The crux of the problem is that the tilde expansion is not working as I'd like. Let us say that I have a user named george, and that his home folder is /a/path/to/georges_home. If, at a shell, I type: cd ~george it takes me to the appropriate directory. If I type: HOME_DIR=~george echo $HOME_DIR It gives me: /a/path/to/georges_home However, if I try to use a variable, it does not work: USERNAME="george" cd ~$USERNAME -bash: cd: ~george: No such file or directory I've tried using quotes and backticks, but can't figure out how to make it expand properly. How do I make this work?

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• Alternatives to native LDAP

  - by Matt

  We've implemented an LDAP to NIS solution and have begun transitioning some systems to native LDAP binding for authentication and automount maps. Unfortunately we have a very mixed environment with more than 20 *nix environments. The setup for each variant is of course unique and has required various workarounds to get full functionality. We're now at the point where we're willing to revisit the solution and possibly migrate toward something like Likewise (http://www.likewise.org), but would like to know what others are using to solve this problem.

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• NIS: which mechanism hides shadow.byname for unpriviledged users?

  - by Mark Salzer

  On some Linux box (SLES 11.1) which is a NIS client I can do as root: ypcat shadow.byname and get output, i.e. some lines with the encrypted passwords, amongst other information. On the same Linux box, if I run the same command as unpriviledged user, I get No such map shadow.byname. Reason: No such map in server's domain Now I am surprised. My good old knowlege says that shadow passwords in NIS are absurd because there is no access control or authentication in the protocol and thus every (unpriviledged) user can access the shadow map and thereby obtain the encrypted passwords. Obviously we have a different picture here. Unfortunately I don't have access to the NIS server to figure out what is happening. My only guess is that the NIS master gives the map only to clients conection from a priviledged port (1024), but this is only an uneducated guess. What mechanisms are there in current NIS implementations to lead to a behavior like the above? How "secure" are they? Can the be circumvented easily? Or are shadow passwords in NIS as secure as the good old shadow files?

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• Expanding globs in xargs

  - by Craig

  I have a directory like this mkdir test cd test touch file{0,1}.txt otherfile{0,1}.txt stuff{0,1}.txt I want to run some command such as ls on certain types of files in the directory and have the * (glob) expand to all possibilities for the filename. echo 'file otherfile' | tr ' ' '\n' | xargs -I % ls %*.txt This command does not expand the glob and tries to look for the literal 'file*.txt' How do I write a similar command that expands the globs? (I want to use xargs so the command can be run in parallel)

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• bash vs sh | What is the difference

  - by Saif Bechan

  In using i see 2 types of code #!/usr/bin/sh and #!/user/bin/bash I have Googled this and the opinions vary a lot. The explanation I have seen on most websites is that sh is older than bash, and that there is no real difference. Does someone know the difference between these and can give a practical example when to use either one of them. I highly doubt that there is no real difference, because then having to things that do the exact same thing would be just

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