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• GUID Partition Table & Linux

  - by Zac

  (1) Is it true that the new GUID Partition Table scheme allows a user to partition a drive however he/she like, outside of the traditional MBR "4 primaries or 3 primaries + 1 extension" paradigm? If so, are there any limitations to the GPT? If my assumption is wrong, what are its advantages over the MBR model? (2) I'm getting a new laptop this week and will be installing Ubuntu (and, more generally, Linux) for the first time ever. Does Ubunutu come pre-configured with MBR as a default? If so, how do I get Ubuntu w/ GPT? If not, how do I specify GPT over MBR? Thanks!

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• Is there a difference between starting a WebLogic Admin Server through the command-line or through t

  - by lindelof

  I have WebLogic 11g installed on my machine under /srv/wls, and I start Node manager on it with /srv/wls/wlserver_10.3/server/bin/startNodeManager.sh. I create my domain with config.sh, and then I want to start the Admin Server of that domain with Node Manager. So I open a WLST session and do the following: > nmConnect(...) > nmStart('AdminServer') But when I then visit localhost:7001/console, and login, the screen on the browser remains blank and the server logs tell me the server has run out of PermGen space. I don't encounter this problem when starting the Admin Server through the shell script under $DOMAIN/startWebLogic.sh. Then it works fine. Any idea what I am doing wrong? I couldn't find anything in Google nor on the Oracle forums...

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• Optimizing Python code with many attribute and dictionary lookups

  - by gotgenes

  I have written a program in Python which spends a large amount of time looking up attributes of objects and values from dictionary keys. I would like to know if there's any way I can optimize these lookup times, potentially with a C extension, to reduce the time of execution, or if I need to simply re-implement the program in a compiled language. The program implements some algorithms using a graph. It runs prohibitively slowly on our data sets, so I profiled the code with cProfile using a reduced data set that could actually complete. The vast majority of the time is being burned in one function, and specifically in two statements, generator expressions, within the function: The generator expression at line 202 is neighbors_in_selected_nodes = (neighbor for neighbor in node_neighbors if neighbor in selected_nodes) and the generator expression at line 204 is neighbor_z_scores = (interaction_graph.node[neighbor]['weight'] for neighbor in neighbors_in_selected_nodes) The source code for this function of context provided below. selected_nodes is a set of nodes in the interaction_graph, which is a NetworkX Graph instance. node_neighbors is an iterator from Graph.neighbors_iter(). Graph itself uses dictionaries for storing nodes and edges. Its Graph.node attribute is a dictionary which stores nodes and their attributes (e.g., 'weight') in dictionaries belonging to each node. Each of these lookups should be amortized constant time (i.e., O(1)), however, I am still paying a large penalty for the lookups. Is there some way which I can speed up these lookups (e.g., by writing parts of this as a C extension), or do I need to move the program to a compiled language? Below is the full source code for the function that provides the context; the vast majority of execution time is spent within this function. def calculate_node_z_prime( node, interaction_graph, selected_nodes ): """Calculates a z'-score for a given node. The z'-score is based on the z-scores (weights) of the neighbors of the given node, and proportional to the z-score (weight) of the given node. Specifically, we find the maximum z-score of all neighbors of the given node that are also members of the given set of selected nodes, multiply this z-score by the z-score of the given node, and return this value as the z'-score for the given node. If the given node has no neighbors in the interaction graph, the z'-score is defined as zero. Returns the z'-score as zero or a positive floating point value. :Parameters: - `node`: the node for which to compute the z-prime score - `interaction_graph`: graph containing the gene-gene or gene product-gene product interactions - `selected_nodes`: a `set` of nodes fitting some criterion of interest (e.g., annotated with a term of interest) """ node_neighbors = interaction_graph.neighbors_iter(node) neighbors_in_selected_nodes = (neighbor for neighbor in node_neighbors if neighbor in selected_nodes) neighbor_z_scores = (interaction_graph.node[neighbor]['weight'] for neighbor in neighbors_in_selected_nodes) try: max_z_score = max(neighbor_z_scores) # max() throws a ValueError if its argument has no elements; in this # case, we need to set the max_z_score to zero except ValueError, e: # Check to make certain max() raised this error if 'max()' in e.args[0]: max_z_score = 0 else: raise e z_prime = interaction_graph.node[node]['weight'] * max_z_score return z_prime Here are the top couple of calls according to cProfiler, sorted by time. ncalls tottime percall cumtime percall filename:lineno(function) 156067701 352.313 0.000 642.072 0.000 bpln_contextual.py:204(<genexpr>) 156067701 289.759 0.000 289.759 0.000 bpln_contextual.py:202(<genexpr>) 13963893 174.047 0.000 816.119 0.000 {max} 13963885 69.804 0.000 936.754 0.000 bpln_contextual.py:171(calculate_node_z_prime) 7116883 61.982 0.000 61.982 0.000 {method 'update' of 'set' objects}

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• Linux file permissions not being preserved

  - by yellavon

  I am deploying some custom software as root (a necessity for this situation). I set the owner/group to user1:user1 and set all the files to 644 beforehand in shell, then copy and deploy with ant. However, when files get copied over from the deployment directory, the ownership changes back to root and all the files install with 666 permissions. This seems to occur whether the file is overwritten or newly created. I believe there is a way to set an option in cp, mv commands to preserve permissions, but that would be a lot of commands to change. How can I fix this? Is there some setting I can change temporarily for root so the install always preserves the file permissions?

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• Xdebug 2.0.5 with Zend Server CE PHP5.2.12 possible?

  - by notbrain

  I'm using Zend Server CE with PHP 5.2.12 on OSX Snow Leopard and want to use Xdebug. I've turned off Zend Data Cache, Zend Optimizer+, and Zend Debugger in the console. When I run $ cd ~/Downloads/xdebug-2.0.5 $ /usr/local/zend/bin/phpize I get Configuring for: PHP Api Version: 20041225 Zend Module Api No: 20060613 Zend Extension Api No: 220060519 The PHP API Version, 20041225, seems to be off from the documentation (aka wrong). When I continue installation with $ ./configure ---with-php-config=/usr/local/zend/bin/php-config $ make $ sudo make install The installed xdebug.so seems to be the wrong one. Which version of xdebug do I need for this PHP API version? The Zend API numbers are ok. I'm just confused at why the PHP API Version doesn't match. PHP Warning: PHP Startup: Unable to load dynamic library '/usr/local/zend/lib/php_extensions/xdebug.so' - (null) in Unknown on line 0 PHP 5.2.12 (cli) (built: Feb 17 2010 13:39:36)

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• Postfix - How to configure to send these emails?

  - by Jon

  I want my mailserver to send mail from my local application "from" any user supplied email address "to" my own address, say "[email protected]". The MX records for "mysite.com" actually point to a different server, even though the outgoing mainserver is running with mydomain set as "mysite.com". Perhaps this is part of the problem? postfix is currently causing a SMTPRecipientsRefused error within the python application. Can anyone point me to what to change in the configuration? Thanks postconf -n: alias_database = hash:/etc/aliases alias_maps = hash:/etc/aliases append_dot_mydomain = no biff = no config_directory = /etc/postfix inet_interfaces = all mailbox_command = procmail -a "$EXTENSION" mailbox_size_limit = 0 mydestination = mysite.com, localhost.com, , localhost, * myhostname = mysite.com mynetworks = 127.0.0.0/8 [::ffff:127.0.0.0]/104 [::1]/128 myorigin = /etc/mailname readme_directory = no recipient_delimiter = + relayhost = smtp_tls_session_cache_database = btree:${data_directory}/smtp_scache smtpd_banner = $myhostname ESMTP $mail_name (Debian/GNU) smtpd_tls_cert_file = /etc/ssl/certs/ssl-cert-snakeoil.pem smtpd_tls_key_file = /etc/ssl/private/ssl-cert-snakeoil.key smtpd_tls_session_cache_database = btree:${data_directory}/smtpd_scache smtpd_use_tls = yes

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• pip install very slow through virtual box

  - by AJP

  pip install --exists-action=w -r requirements.txt is very very slow through virtual box. Any suggests of how to diagnose and fix? Would seeing the VagrantFile be useful? VirtualBox 4.2.12 (can't upgrade to .14 as it doesn't work.) Vagrant 1.0.7 Host machine: ProductName: Mac OS X ProductVersion: 10.7.5 BuildVersion: 11G63b VagrantFile contains: Vagrant::Config.run do |config| config.vm.box = "precise64" config.vm.customize ["modifyvm", :id, "--memory", 2048] config.vm.box_url = "http://files.vagrantup.com/precise64.box" config.vm.network :hostonly, "33.33.33.21" config.vm.forward_port 5000, 5000 config.vm.forward_port 5555, 5555 config.vm.share_folder "v-root", "/vagrant", "./" Vagrant::Config.run do |config| config.vm.provision :shell, :inline => "VENV=/usr/local/venv bash /vagrant/setup_env.sh" end end Normal download speed is only about 5 times slower at 0.8 Mb per second versus 4 MB per second (as judged by curling a 50 Mb file from S3). But pip install is taking about 20 times longer from Mac (i.e. about 40 minutes) versus 2.

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• How to use my computer to control a lamp?

  - by nona urbiz

  I've been researching computer automation systems, but everything I've found has been overkill for what I'm interested in. Can anyone help me control a lamp that is on my desk, plugged in the wall beneath the desk, with my computer (also on the desk, usually). What got me thinking is that I have the lamp plugged into a Belkin extension cord/surge protector that came with a wireless switch that toggles the power going to 6 of the eight sockets. Can I somehow hook my computer into this? I'm not too afraid to get into some wiring type thing, but do have a somewhat limited budget. It'd also be cool to get a dimmer in the loop too. thanks aha. after more research, i have realized what i'm looking for is instructions for a DIY version of this that won't look so ugly, and that i can build a UI for rather than shortcuts.

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• How to troubleshoot a remote wmi query/access failure?

  - by Roman

  I'm using Powershell to query a remote computer in a domain for a wmi object, eg: "gwmi -computer test -class win32_bios". I get this error message: Value does not fall within the expected range Executing the query local under the same user works fine. It seems to happen on both windows 2003 and also 2008 systems. The user that runs the shell has admin rights on the local and remote server. I checked wmi and dcom permissions as far as I know how to do this, they seem to be the same on a server where it works, and another where it does not. I think it is not a network issue, all ports are open that are needed, and it also happens within the same subnet. When sniffing the traffic we see the following errors: RPC: c/o Alter Cont Resp: Call=0x2 Assoc Grp=0x4E4E Xmit=0x16D0 Recv=0x16D0 Warning: GssAPIMechanism is not found, either caused by not reassembled, conversation off or filtering. And an errormessage from Kerberos: Kerberos: KRB_ERROR - KDC_ERR_BADOPTION (13) The option code in the packet is 0x40830000 Any idea what I should look into?

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• Firewalling a Cisco ASA Split tunnel

  - by dunxd

  I have a Cisco ASA 5510 at head office, and Cisco ASA 5505 in remote offices. The remote offices are connected over a split tunnelled VPN - the ASA 5505s use "Easy VPN" Client type VPN in Network Extension Mode (NEM). I'd like to set firewall rules for the non-tunnelled traffic only. Traffic over the VPN to head office should not have any firewall rules applied. I might want to apply different firewall rules to different remote offices. All the documentation I have been able to find assumes the Client VPN is a software endpoint, and all the configuration is done at the 5510. When using a Cisco 5505 as the VPN client, is it possible to configure any firewalling at the Client end, or does it all have to come from the 5510? Are there any other issues to look out for when split-tunnelling a VPN by this method?

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• How do I open a pdf file with PDF X-Change Viewer so that I can still modify the pdf source?

  - by ltcomdata

  Whenever I open a pdf file with PDF X-Change Viewer it locks up the source pdf file to edits. Is there a way to open the pdf (with PDF X-Change Viewer) so that it doesn't lock-up the source file --- perhaps as a shell command with an option? The background: I use LaTeX to edit my pdf files, and preview the result with PDF X-Change Viewer. I must first close PDF X-Change Viewer before I can preview any changes I make in the LaTeX source. It would be nice if PDF X-Change Viewer did not lock-up the pdf source so that I could modify it without first closing PDF X-Change Viewer.

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• No sounds played in google chrome tabs

  - by shtolik

  I have somehow muted all the tabs in my google chrome. Youtube and other flash players are playing video, but there is no sound. In Window 7 Volume mixer I can see Google chrome icon and it has muted icon there. But clicking that icon unmute sounds just for a second and then it's muted back on. Seems that chrome itself or some of it extensions are turning mute... Update: How do I mute certain tabs in Chrome? question seems related, but I don't have MuteTab extension installed in Chrome.

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• Where do you find the Bash source files of programs in Linux/Mac OSX?

  - by AndrewKS

  I am currently writing some convenience methods for my terminal in my bash_profile and am sure if what I am writing is "the best way". I figure a good way to verify whether what I'm doing is right or not would be to find some source code of more established programs and see how they do it. My question then is, where can I find this code on my Mac? An example is, with Macports installed, where is the source code that opens the port interactive console when I type nothing but "port" in my shell? (I added Linux in the title even though I am on a Mac because I assume the answer would be the same for both) Edit: The answer I am looking for is in terms of which directory relative to the programs will I find their unix scripts.

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• Lesser known Ubuntu desktop applications

  - by becomingGuru

  So, this Ubuntu software center comes with 100s of applications of all types. In this version they have disabled rating, making it hard to find how good it is. I found gnome-shell today, that seemed awesome. There are other ones, less well known, For eg, Abiword is far better than Open Office Org Word processor in many ways. (Altho' I dont like word processors themselves.) What are the other less well known applications that you use and like. One application per answer.

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• Recommended way to restrict Apache users

  - by Dor

  Following on why should we restrict Apache users, another two questions arises: What is the recommended method of restricting the places Apache users can traverse & read in the file system? What to do against fork bombs and other shell scripting problems? (bash scripting is allowed) My possible solutions (I prefer to know which solution you choose and why): chroot OR mod_chroot disable bash OR use Restricted BASH Please offer another solutions if you find appropriate. (perhaps selinux is?) Current status: Users are allowed to executed bash scripts (via PHP for example) suexec is active Apache requested are served with FastCGI for PHP

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• Ctrl W s not splitting windows in vim

  - by rajan sthapit

  I am trying to use Ctrl+ws to split a window in vim. However it is not working in my case. I opened a file using vim filename. Then I pressed Ctrl+ws. But as soon as I press just Ctrl+w it clears the viewport and I could see my shell display before vim opened the file. I mean the view port is replaced by the content just before the file was opened. However, I am still editing the file with vim. Suggestions?

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• Trying to find a duplicate version of PHP on my system. Where is it?

  - by macek

  I have having a helluva time trying to track down which php binary my apache is using. locate bin/php returns this list /usr/bin/php /usr/bin/php-cgi /usr/bin/php-config /usr/bin/phpize /usr/local/bin/php /usr/local/bin/php-cgi /usr/local/bin/php-config /usr/local/bin/php-shell.sh /usr/local/bin/phpize Let's see the versions: /usr/bin/php -v shows 5.3.2 /usr/bin/local/php -v shows 5.3.2 What about which? [macek ~]$ which php /usr/bin/php The problem phpinfo(); when executed by apache shows 5.2.11 Where is this phantom 5.2.11 on my system?

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• How do I reattach to Ubuntu Server's 'do-release-upgrade' process?

  - by Alex Leach

  I accidentally pressed Ctrl+C during Ubuntu Server's do-release-upgrade process. I'd dropped to a shell to compare a .conf file in /etc/. When I pressed Ctrl-C, it asked whether I wanted to try to reattach to the upgrade process, but it failed to do so. So I quit, and now there's a hanging dpkg process which is holding onto the apt lock. This is a virtualised server with no GUI frontend... Is it possible to recover the upgrade process, or do I have to kill the dpkg process and start again? UPDATE:- AFAICT, there was no way to reattach to the upgrade process. However, it wasn't a disaster at all. I killed the hanging dpkg process, and then ran dpkg --configure -a. This walks you through reconfiguring all packages already installed on the system, tidying up any problems whilst it does so. After that, I used aptitude to upgrade the remaining packages, which had already been downloaded, but hadn't been installed or configured.

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• My site was recently attacked. What do I do?

  - by ChrisH

  This is a first for me. One of the sites I run was recently attacked. Not at all an intelligent attack - pure brute force - hit every page and every non-page with every extension possible. Posted with garbage data to every form and tried to post to some random urls too. All tod, 16000 requests in one hour. What should I do to prevent/alert this kind of behavior? Is there a way to limit the request/hr for a given ip/client? Is there a place I should be reporting the user to? They appear to be from China and did leave what seems like a valid e-mail.

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• IRC "proxy" for persistent connection between several computers

  - by Zeta Two

  I'm looking for a program that enables me to stay connected to one or more IRC networks and be able to view the log even though I connect from several different computers. I'm thinking about something like a proxy running on a server who always is connected to the servers/channels I want and to which I connect from whichever client I want to use. Does anyone know of a program like this? Edit: Apparently I could be running a IRC session in a shell on a server and connect to this but I would like something more GUI:ish.

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• Secure Apache Virtual Hosts?

  - by Dr Hydralisk

  I am going to host a few small sites on VPS, and each of them are going to run my own custom PHP scripts. I am fairly certain that they are secure (did everything in the book, plus some of which is not in the book) to make sure they can't be exploited. But just to be safe I want to know how I could secure each of the virtual hosts so that they can't escape from there virtual host (if a hacker uploaded a shell they could not go above the www folder a legitimate user can't do in ftp no matter how many times they click ..) folder on Debian and Apache.

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• Odd domain switching behavior in Firefox and Chrome

  - by Jeremy Detrempe

  We have different development severs and a production server. Testing is done in the development servers. As a QA engineer, I'm switching between these servers quite often throughout the day. In Chrome, sometimes I need to reload a page a few times to get it to pull from the newly switched server. In Firefox, sometimes I need to quit the browser in order to get it to pull from the newly switched server. (We have small tags that indicate which server you are pulling from, which is how I know in-browser.) Why does that happen? I'd love to know how that happens (maybe what it's called?) and what the best way to deal with it is. (I know that Firefox has an extension for domain switching; is that the best solution?)

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• cannot run CMD script from Vista windows explorer

  - by jamesvista

  I am running Vista Home Premium. I tried to write a script to do some simple automation.... it does not work! even the most simple script like: @echo ON dir . does not get executed and only an empty CMD shell pops open when started from explorer. From the cmd windows there is no problem. This is really weird and I have never seen this before (but wrote many CMD scripts before) ftype cmdfile and batfile are unchanged from "%1" %* virusscan done - no problems Is there a policy setting that might have changed? Any ideas?

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• How do you determine the OWNER of an Oracle Database

  - by Kwang Mark Eleven

  When you install an Oracle database in a Unix server, the Unix user id you use for the installation becomes the OWNER of the database. What is the most reliable and general way of determining in a shell script which Unix user is the owner of an Oracle installation? I mean, can you perform a grep on a file created by the installation to find this information or shall I resort to use the ls command on a specific file on a specific directory. If the name of the file to be checked is also variable, I would need to have a way of determining the name and path to the file. Thanks in advance for your time

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• Is the 4pin atx power plug required [closed]

  - by rockinthesixstring

  I know the answer is probably a resounding YES, but I just wanted to double check. I just purchased a new chassis for my PC and now my 4pin cpu power plug doesn't reach. I'm wondering if the 4 pins are required for operation, or can I get by for the weekend without it until I can go get an extension? EDIT: Looks like it is mandatory with my Mobo. I tried to post without it and i just got a blank screen. Looks like I'm getting a new adapter asap.

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