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• Setting up MongoDB in High Performance Computing LSF linux cluster

  - by Dnaiel

  I am trying to run mongo in a LSF cluster computing environment where I have no admin control. Our sysadmin installed mongodb, but it is not running. Any ideas on what should I ask the server admin to do for it to run? Or if I could run it locally? [node1382]allelix> mongod --dbpath /users/dnaiel/ma/mongodb/ Tue Oct 2 21:33:48 [initandlisten] MongoDB starting : pid=22436 port=27017 dbpath=/seq/epigenome01/allelix/ma/mongodb/ 64-bit host=node1382 Tue Oct 2 21:33:48 [initandlisten] Tue Oct 2 21:33:48 [initandlisten] ** WARNING: You are running on a NUMA machine. Tue Oct 2 21:33:48 [initandlisten] ** We suggest launching mongod like this to avoid performance problems: Tue Oct 2 21:33:48 [initandlisten] ** numactl --interleave=all mongod [other options] Tue Oct 2 21:33:48 [initandlisten] Tue Oct 2 21:33:48 [initandlisten] db version v2.2.0, pdfile version 4.5 Tue Oct 2 21:33:48 [initandlisten] git version: f5e83eae9cfbec7fb7a071321928f00d1b0c5207 Tue Oct 2 21:33:48 [initandlisten] build info: Linux ip-10-2-29-40 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64 BOOST_LIB_VERSION=1_49 Tue Oct 2 21:33:48 [initandlisten] options: { dbpath: "/users/dnaiel/ma/mongodb/" } Tue Oct 2 21:33:48 [initandlisten] journal dir=users/dnaiel/ma/mongodb/journal Tue Oct 2 21:33:48 [initandlisten] recover begin Tue Oct 2 21:33:48 [initandlisten] info no lsn file in journal/ directory Tue Oct 2 21:33:48 [initandlisten] recover lsn: 0 Tue Oct 2 21:33:48 [initandlisten] recover /seq/epigenome01/allelix/ma/mongodb/journal/j._0 Tue Oct 2 21:33:48 [initandlisten] recover cleaning up Tue Oct 2 21:33:48 [initandlisten] removeJournalFiles Tue Oct 2 21:33:48 [initandlisten] recover done Tue Oct 2 21:33:48 [websvr] admin web console waiting for connections on port 28017 Tue Oct 2 21:33:48 [initandlisten] waiting for connections on port 27017 It basically waits forever and cannot start mongodb. These servers are not webservers but they do have network access, it's a cloud computing LSF environment system. Any advice would be welcome, thanks in advance.

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• Incomplete upgrade 12.04 to 12.10

  - by David

  Everything was running smoothly. Everything had been downloaded from Internet, packages had been installed and a prompt asked for some obsolete programs/files to be removed or kept. After that the computer crashed and and to manually force a shutdown. I turned it on again and surprise I was on 12.10! Still the upgrade was not finished! How can I properly finish that upgrade? Here's the output I got in the command line after following posted instructions: i astrill - Astrill VPN client software i dayjournal - Simple, minimal, digital journal. i gambas2-gb-form - A gambas native form component i gambas2-gb-gtk - The Gambas gtk component i gambas2-gb-gtk-ext - The Gambas extended gtk GUI component i gambas2-gb-gui - The graphical toolkit selector component i gambas2-gb-qt - The Gambas Qt GUI component i gambas2-gb-settings - Gambas utilities class i A gambas2-runtime - The Gambas runtime i google-chrome-stable - The web browser from Google i google-talkplugin - Google Talk Plugin i indicator-keylock - Indicator for Lock Keys i indicator-ubuntuone - Indicator for Ubuntu One synchronization s i A language-pack-kde-zh-hans - KDE translation updates for language Simpl i language-pack-kde-zh-hans-base - KDE translations for language Simplified C i libapt-inst1.4 - deb package format runtime library idA libattica0.3 - a Qt library that implements the Open Coll idA libbabl-0.0-0 - Dynamic, any to any, pixel format conversi idA libboost-filesystem1.46.1 - filesystem operations (portable paths, ite idA libboost-program-options1.46.1 - program options library for C++ idA libboost-python1.46.1 - Boost.Python Library idA libboost-regex1.46.1 - regular expression library for C++ i libboost-serialization1.46.1 - serialization library for C++ idA libboost-signals1.46.1 - managed signals and slots library for C++ idA libboost-system1.46.1 - Operating system (e.g. diagnostics support idA libboost-thread1.46.1 - portable C++ multi-threading i libcamel-1.2-29 - Evolution MIME message handling library i libcmis-0.2-0 - CMIS protocol client library i libcupsdriver1 - Common UNIX Printing System(tm) - Driver l i libdconf0 - simple configuration storage system - runt i libdvdcss2 - Simple foundation for reading DVDs - runti i libebackend-1.2-1 - Utility library for evolution data servers i libecal-1.2-10 - Client library for evolution calendars i libedata-cal-1.2-13 - Backend library for evolution calendars i libedataserver-1.2-15 - Utility library for evolution data servers i libexiv2-11 - EXIF/IPTC metadata manipulation library i libgdu-gtk0 - GTK+ standard dialog library for libgdu i libgdu0 - GObject based Disk Utility Library idA libgegl-0.0-0 - Generic Graphics Library idA libglew1.5 - The OpenGL Extension Wrangler - runtime en i libglew1.6 - OpenGL Extension Wrangler - runtime enviro i libglewmx1.6 - OpenGL Extension Wrangler - runtime enviro i libgnome-bluetooth8 - GNOME Bluetooth tools - support library i libgnomekbd7 - GNOME library to manage keyboard configura idA libgsoap1 - Runtime libraries for gSOAP i libgweather-3-0 - GWeather shared library i libimobiledevice2 - Library for communicating with the iPhone i libkdcraw20 - RAW picture decoding library i libkexiv2-10 - Qt like interface for the libexiv2 library i libkipi8 - library for apps that want to use kipi-plu i libkpathsea5 - TeX Live: path search library for TeX (run i libmagickcore4 - low-level image manipulation library i libmagickwand4 - image manipulation library i libmarblewidget13 - Marble globe widget library idA libmusicbrainz4-3 - Library to access the MusicBrainz.org data i libnepomukdatamanagement4 - Basic Nepomuk data manipulation interface i libnux-2.0-0 - Visual rendering toolkit for real-time app i libnux-2.0-common - Visual rendering toolkit for real-time app i libpoppler19 - PDF rendering library i libqt3-mt - Qt GUI Library (Threaded runtime version), i librhythmbox-core5 - support library for the rhythmbox music pl i libusbmuxd1 - USB multiplexor daemon for iPhone and iPod i libutouch-evemu1 - KernelInput Event Device Emulation Library i libutouch-frame1 - Touch Frame Library i libutouch-geis1 - Gesture engine interface support i libutouch-grail1 - Gesture Recognition And Instantiation Libr idA libx264-120 - x264 video coding library i libyajl1 - Yet Another JSON Library i linux-headers-3.2.0-29 - Header files related to Linux kernel versi i linux-headers-3.2.0-29-generic - Linux kernel headers for version 3.2.0 on i linux-image-3.2.0-29-generic - Linux kernel image for version 3.2.0 on 64 i mplayerthumbs - video thumbnail generator using mplayer i myunity - Unity configurator i A openoffice.org-calc - office productivity suite -- spreadsheet i A openoffice.org-writer - office productivity suite -- word processo i python-brlapi - Python bindings for BrlAPI i python-louis - Python bindings for liblouis i rts-bpp-dkms - rts-bpp driver in DKMS format. i system76-driver - Universal driver for System76 computers. i systemconfigurator - Unified Configuration API for Linux Instal i systemimager-client - Utilities for creating an image and upgrad i systemimager-common - Utilities and libraries common to both the i systemimager-initrd-template-am - SystemImager initrd template for amd64 cli i touchpad-indicator - An indicator for the touchpad i ubuntu-tweak - Ubuntu Tweak i A unity-lens-utilities - Unity Utilities lens i A unity-scope-calculator - Calculator engine i unity-scope-cities - Cities engine i unity-scope-rottentomatoes - Unity Scope Rottentomatoes

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• Attempting to set up xampp and zend server on the same machine

  - by umbregachoong

  I am attempting to set up the zend server and xampp on the same machine but I am running into problems. I came across documentation on the zend site that said you cannot do this. However the folks over at apachefriends said you can. I have since discovered that I can run some of the zendframework examples within xampp by downloading the zendframework2 library and the skeleton app from git and I am doing this right now. However, I would like to know how to set them both up without having any conflicts both for the apache2 server and phpmyadmin. (One of the frustrating things is trying to load phpmyadmin in the deployment dialog by using the zpk tool in Zend). What I did in trying to set up both servers on windows 7 is as follows: First I have tried to set up the httpd conf files separately for each server, xampp running on port 8082 , and zend running on port 8088. At the time xampp would work, but zend server would not. This is after setting up the virtual host files separately for each server. Question 1: Where are the zend server error logs? Earlier, I was able to get both of them running configuring the xampp server httpd-conf file alone, however, I experienced problems with phpmyadmin even after configuring phpmyadmin on xampp to work on a different port other than 3306. Second question here: how to set up the two mysql phpmyadmin instances so they do not conflict with each other? Here is the xampp virtual host section: ##ServerAdmin [email protected] DocumentRoot "C:/xampp/htdocs/" ServerName localhost 8082 ##ServerAlias www.dummy-host.example.com ##ErrorLog "logs/dummy-host.example.com-error.log" ##CustomLog "logs/dummy-host.example.com-access.log" common Here is the zend virtual host section: DocumentRoot "C:\Program Files (x86)\Zend\Apache2/htdocs" ServerName localhost:8088 </VirtualHost> I have looked at this httpd.apache.org/docs/2.2/vhosts/ and this http://survivethedeepend.com/zendframeworkbook/en/1.0/creating.a.local.domain.using.apache.virtual.hosts but I am obviously doing something wrong here. I also have the java sdk running on this machine with tomcat and apache and I have no conflicts- too bad this is not the case for zend server and xampp Thanks umbre gachoong

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• Can't pin modified shortcuts to the Windows 7 task bar

  - by Coder

  I have a shortcut to a .bat file which I pin to the task bar using a workaround by using another icon and this seems to work. Now I make a copy of that shortcut, point it to a different .bat file, rename it, and I can't pin this one to the task bar. I have to find some other new unused icon to pin, pin it, then modify it manually. The other problem this causes is that windows seems to track which icons were pinned even if they are modified after the fact. As such, if I use media player as my dummy icon, pin it, then alter it's name and shortcut to point to a .bat file, I can't re-pin windows media player and if I select unpin from the windows media player, it unpins my shortcut to my .bat file. I can't believe how ridiculous this is. Is there a way to pin anything I want to the taskbar (ie. .bat file in my case) that does not cause problems like this? Is there an easy way I can copy an existing shortcut and modify it and re-pin it to the taskbar? The reason I want to copy it is because I start a .bat file (in particular git bash) and I set properties on the window like quick edit, increase the screen buffer and set it's position and size manually. I don't want to have to do this to every single icon I want to pin since they will be identical aside from the shortcut url.

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• Mac OS X : Open up 3 terminals, run different commands from all for each of them, to set up a develo

  - by taelor

  I'm a Ruby on Rails Web Developer and there is a lot of repetition I go through to start up my development environment. I was wondering if there is any way that I can remove some of this repetition by writing a script, or using a program (like quicksilver) or something to get my work environment going. I know how to use quicksilver to open up terminal, and I even have a saved window group to get my 3 or 4 panes open. The next thing I would love to automatically happen is getting all three to goto a certain directory, and each run different commands. One will start the local server, and in another tab, start a background process. the other would open text mate, and then start a console session, while the last one runs a svn(or git) status. Oh yah, and I would love to go ahead and open firefox, and a few tabs going to a couple of locations. Does anyone have any suggestions on how I could make all this happen in once quicksilver command, or a double click on some type of script on my Desktop?

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• Cannot properly read files on the local server

  - by Andrew Bestic

  I'm running a RedHat 6.2 Amazon EC2 instance using stock Apache and IUS PHP53u+MySQL (+mbstring, +mysqli, +mcrypt), and phpMyAdmin from git. All configuration is near-vanilla, assuming the described installation procedure. I've been trying to import SQL files into the database using phpMyAdmin to read them from a directory on my server. phpMyAdmin lists the files fine in the drop down, but returns a "File could not be read" error when actually trying to import. Furthermore, when trying to execute file_get_contents(); on the file, it also returns a "failed to open stream: Permission denied" error. In fact, when my brother was attempting to import the SQL files using MySQL "SOURCE" as an authenticated MySQL user with ALL PRIVILEGES, he was getting an error reading the file. It seems that we are unable to read/import these files with ANY method other than root under SSH (although I can't say I've tried every possible method). I have never had this issue under regular CentOS (5, 6, 6.2) installations with the same LAMP stack configuration. Some things I've tried after searching Google and StackExchange: CHMOD 0777 both directory and files, CHOWN root, apache (only two users I can think of that PHP would use), Importing SQL files with total size under both upload_max_filesize and post_max_size, PHP open_basedir commented out, or = "/var/www" (my sites are using Apache VirtualHosts within that directory, and all the SQL files are deep within that directory), PHP safe mode is OFF (it was never ON) At the moment I have solved this issue with the smaller files by using the FILE UPLOAD method directly to phpMyAdmin, but this will not be suitable for uploading my 200+ MiB SQL files as I don't have a stable Internet connection. Any light you could shed on this situation would be greatly appreciated. I'm fair with Linux, and for the things that do stump me, Google usually has an answer. Not this time, though!

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• Managing disk in a VM

  - by dst

  I'm replacing my two old rack servers with a new one that has plenty of power to take over the functionality my current servers. The server is a 4U rack mount with 16 3.5" SAS drive bays, two 2.5" bays, a Xeon E3-1230v2 CPU and 32GB of ECC RAM. My issue is the following. I would like to have a FreeBSD file server with ZFS managing disks. However, I need other VMs for e.g. a shell/git server, mail server etc. I'm wondering how to deal with the following issues: I want ZFS to fully manage the disks, so I'm not using any hardware RAID. Should I pass the SAS controller directly to the FreeBSD system as passthrough PCI? I want to maximize the reliability of the setup. On what disks should I install the hypervsor and keep server system disks? For (2) I have the option of having a RAID setup on the SAS controller and using that as system disk to store the hypervisor as well as VM images. However, this makes PCI passthrough to the file server impossible. Another option is using the two 2.5" bays. In terms of reliability how are SSDs compared to e.g. WD RE4 disks? Would it make sense to have two SSDs in software RAID as boot disks for the hypervisor or should I just go with e.g. WD RE4 disks in a software RAID setup. I also need to think about where to store the mails for the mail server, but this could be done over NFS between the VMs. BTW, this is for home use, so the load is not really that big. What I'm looking for is best practices for splitting up a server.

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• disks not ready in array causes mdadm to force initramfs shell

  - by RaidPinata

  Okay, this is starting to get pretty frustrating. I've read most of the other answers on this site that have anything to do with this issue but I'm still not getting anywhere. I have a RAID 6 array with 10 devices and 1 spare. The OS is on a completely separate device. At boot only three of the 10 devices in the raid are available, the others become available later in the boot process. Currently, unless I go through initramfs I can't get the system to boot - it just hangs with a blank screen. When I do boot through recovery (initramfs), I get a message asking if I want to assemble the degraded array. If I say no and then exit initramfs the system boots fine and my array is mounted exactly where I intend it to. Here are the pertinent files as near as I can tell. Ask me if you want to see anything else. # mdadm.conf # # Please refer to mdadm.conf(5) for information about this file. # # by default (built-in), scan all partitions (/proc/partitions) and all # containers for MD superblocks. alternatively, specify devices to scan, using # wildcards if desired. #DEVICE partitions containers # auto-create devices with Debian standard permissions # CREATE owner=root group=disk mode=0660 auto=yes # automatically tag new arrays as belonging to the local system HOMEHOST <system> # instruct the monitoring daemon where to send mail alerts MAILADDR root # definitions of existing MD arrays # This file was auto-generated on Tue, 13 Nov 2012 13:50:41 -0700 # by mkconf $Id$ ARRAY /dev/md0 level=raid6 num-devices=10 metadata=1.2 spares=1 name=Craggenmore:data UUID=37eea980:24df7b7a:f11a1226:afaf53ae Here is fstab # /etc/fstab: static file system information. # # Use 'blkid' to print the universally unique identifier for a # device; this may be used with UUID= as a more robust way to name devices # that works even if disks are added and removed. See fstab(5). # # <file system> <mount point> <type> <options> <dump> <pass> # / was on /dev/sdc2 during installation UUID=3fa1e73f-3d83-4afe-9415-6285d432c133 / ext4 errors=remount-ro 0 1 # swap was on /dev/sdc3 during installation UUID=c4988662-67f3-4069-a16e-db740e054727 none swap sw 0 0 # mount large raid device on /data /dev/md0 /data ext4 defaults,nofail,noatime,nobootwait 0 0 output of cat /proc/mdstat Personalities : [linear] [multipath] [raid0] [raid1] [raid6] [raid5] [raid4] [raid10] md0 : active raid6 sda[0] sdd[10](S) sdl[9] sdk[8] sdj[7] sdi[6] sdh[5] sdg[4] sdf[3] sde[2] sdb[1] 23441080320 blocks super 1.2 level 6, 512k chunk, algorithm 2 [10/10] [UUUUUUUUUU] unused devices: <none> Here is the output of mdadm --detail --scan --verbose ARRAY /dev/md0 level=raid6 num-devices=10 metadata=1.2 spares=1 name=Craggenmore:data UUID=37eea980:24df7b7a:f11a1226:afaf53ae devices=/dev/sda,/dev/sdb,/dev/sde,/dev/sdf,/dev/sdg,/dev/sdh,/dev/sdi,/dev/sdj,/dev/sdk,/dev/sdl,/dev/sdd Please let me know if there is anything else you think might be useful in troubleshooting this... I just can't seem to figure out how to change the boot process so that mdadm waits until the drives are ready to build the array. Everything works just fine if the drives are given enough time to come online. edit: changed title to properly reflect situation

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• Are my iptables secure?

  - by Patricia

  I have this in my rc.local on my new Ubuntu server: iptables -F iptables -A INPUT -i eth0 -p tcp --sport 22 -m state --state ESTABLISHED -j ACCEPT iptables -A OUTPUT -o eth0 -p tcp --dport 22 -m state --state NEW,ESTABLISHED -j ACCEPT iptables -A INPUT -i eth0 -p tcp --dport 22 -m state --state NEW,ESTABLISHED -j ACCEPT iptables -A OUTPUT -o eth0 -p tcp --sport 22 -m state --state ESTABLISHED -j ACCEPT iptables -A OUTPUT -o eth0 -p tcp --dport 9418 -m state --state NEW,ESTABLISHED -j ACCEPT iptables -A INPUT -i eth0 -p tcp --sport 9418 -m state --state ESTABLISHED -j ACCEPT iptables -A OUTPUT -o eth0 -p tcp --dport 5000 -m state --state NEW,ESTABLISHED -j ACCEPT # Heroku iptables -A INPUT -i eth0 -p tcp --sport 5000 -m state --state ESTABLISHED -j ACCEPT # Heroku iptables -A INPUT -p udp -s 74.207.242.5/32 --source-port 53 -d 0/0 --destination-port 1024:65535 -j ACCEPT iptables -A INPUT -p udp -s 74.207.241.5/32 --source-port 53 -d 0/0 --destination-port 1024:65535 -j ACCEPT iptables -A OUTPUT -o eth0 -p tcp --dport 443 -m state --state NEW,ESTABLISHED -j ACCEPT iptables -A INPUT -i eth0 -p tcp --sport 443 -m state --state ESTABLISHED -j ACCEPT iptables -P INPUT DROP iptables -P FORWARD DROP 9418 is Git's port. 5000 is a port used to manage Heroku apps. And 74.207.242.5 and 74.207.241.5 are our DNS servers. Do you think that this is secure? Can you see any holes here? Update: Why is it important to block OUTPUT? This machine will be used only by me.

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• What's needed in a complete ASP.NET environment?

  - by Christian W

  We have a ASP3.0 application with a few ASP.NET (2.0) dittys mixed in. (Our longtime goal is to migrate everything to ASP.NET but that's not important for this issue) Our current test/deploy workflow is like this: 1 Use notepad++ or VS2008 to fix a bug/feature (depending on what I have open) 2 Open my virtual test-server 3 Copy the fixed file over, either with explorer, or if I can be bothered to open it, WinMerge 4 Test that the fix works 5 Close the virtual test-server 6 Connect to our host with VPN 7 Use WinMerge to update the files necessary 8 Pray to higher powers that the production environment is not so different that something bombs. To make things worse, only I have access to my "test-server". So I'm the only one testing it. I really want to make this a bit more robust, I even have a subversion setup running. But I always forget to commit changes... And I don't even work in my checked out folder, but a copy of what is currently in production... Can someone recommend some good reading on deploying, testing, staging and stuff like that. I currently use VS2008 and want to use subversion or GIT (or any other free VCS). Since I'm the only developer, teamsystem is not really an option (cost-related). I have found myself developing an "improved" feature, only to find a bug in the same feature in the production system. And since my "improved" feature incorporated deleting some old functionality, I have to fix bugs directly in production... That's not a fun feeling... (I have inherited this system recently... So it's not directly my fault that it is like this ;) )

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• How can I avoid a few seconds of blank video when using -vcodec copy?

  - by arlomedia

  I'm processing user-uploaded videos on a CentOS web server with ffmpeg. I need to convert each video to a standard size and format, then extract a 30-second sample clip from each video. I want to use the "-vcodec copy" flag in the extraction command to avoid encoding a second time. This command works for my initial conversion: ffmpeg -i uploaded.mov -f mp4 -vcodec libx264 -vpre medium -acodec libfaac -r 15 -b 360k -ab 48k -ar 22050 -s 480x320 formatted.mp4 And this sometimes works for the extraction: ffmpeg -i formatted.mp4 -vcodec copy -acodec copy -ss 0 -t 30 formatted_sample.mp4 However, when I run the extraction command on some videos, the extracted sample clip starts with several seconds of blank video. The audio starts right away but the video doesn't start for 3-6 seconds. To demonstrate the problem, I've uploaded two video clips and run the above commands on them. I created the first clip in Final Cut Express and encoded it with Handbrake before uploading to the web server: 1a) uploaded clip 1b) converted with first command 1c) extracted with second command, missing first six seconds By comparison, this second clip comes from Apple's website and does not show the problem: 2a) uploaded clip 2b) converted with first command 2c) extracted with second command, no problem Can anyone see what's different about the two source clips? And if so, is there anything I can do in my conversion command so that when the extraction command runs, the clip is set up to avoid the missing video? By the way, I initially had the problem with ffmpeg 0.6.1 installed from yum, but I upgraded to the latest git version and the problem remains.

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• Sync desktop Mac environment to laptop

  - by Andrew Vit

  I spend the majority of my time working at my desktop Mac, which I have configured for my web development environment. My spouse has a MacBook for casual use, and I occasionally steal it back when I need to work off-site, or when travelling. The question is how to best synchronize the two so I can switch between them more readily. I've solved a few obvious things by using online services: Email is hosted on IMAP. Working files are in Dropbox. Source code is managed in git. However, the following are things I always miss when jumping on the laptop: Installed Applications (current versions) Installed libraries & utilities (/usr/local) Apache VirtualHosts & other configurations (/etc) Disk image files for VMs My current method is to connect the MacBook via Firewire target mode and rsync the /Users/me home directory, and then cherry-pick the other items I need from Applications, /etc and /usr/local. The problem with this method is that it can be very time consuming due to things like my virtual machine image files, cached emails, etc. How can I make this faster & easier? Can you recommend a solution for configuration management (so I can repeatably install & configure the same software on both), or synchronization (so I can bring the MacBook up to date nightly, over our home network)?

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• MongoDB data directory transfer and upgrade

  - by KPL

  I just transferred my data directory (of Mongo 1.6.5) to a new server and installed Mongo 2.0 on it. I set the data directory path and did sudo server mongod restart. It failed, and the log file output says this - ***** SERVER RESTARTED ***** Sun Oct 9 07:51:47 [initandlisten] MongoDB starting : pid=8224 port=27017 dbpath=/database/mongodb 64-bit host=domU-12-31-39-09-35-81 Sun Oct 9 07:51:47 [initandlisten] db version v2.0.0, pdfile version 4.5 Sun Oct 9 07:51:47 [initandlisten] git version: 695c67dff0ffc361b8568a13366f027caa406222 Sun Oct 9 07:51:47 [initandlisten] build info: Linux bs-linux64.10gen.cc 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64 BOOST_LIB_VERSION=1_41 Sun Oct 9 07:51:47 [initandlisten] options: { auth: "true", config: "/etc/mongod.conf", dbpath: "/database/mongodb", fork: "true", logappend: "true", logpath: "/var/log/mongo/mongod.log", nojournal: "true" } Sun Oct 9 07:51:47 [initandlisten] couldn't open /database/mongodb/local.ns errno:1 Operation not permitted Sun Oct 9 07:51:47 [initandlisten] error couldn't open file /database/mongodb/local.ns terminating Sun Oct 9 07:51:47 dbexit: Sun Oct 9 07:51:47 [initandlisten] shutdown: going to close listening sockets... Sun Oct 9 07:51:47 [initandlisten] shutdown: going to flush diaglog... Sun Oct 9 07:51:47 [initandlisten] shutdown: going to close sockets... Sun Oct 9 07:51:47 [initandlisten] shutdown: waiting for fs preallocator... Sun Oct 9 07:51:47 [initandlisten] shutdown: closing all files... Sun Oct 9 07:51:47 [initandlisten] closeAllFiles() finished Sun Oct 9 07:51:47 [initandlisten] shutdown: removing fs lock... Sun Oct 9 07:51:47 dbexit: really exiting now I have already run it with --upgrade once.

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• Technology mash: is this possible?

  - by Jon Story

  I'm in the process of setting up my own DNS+hosting on a couple of VPS and my home machines, mostly for academic/learning purposes, but also for convenient accessing of my files, hosting my personal websites, private git repositories etc. I've got a main web server with DNS, and a slave DNS server. I've also got a couple of machines at home doing file hosting, video streaming and all that fun stuff. I'm intending to use my VPS's to provide myself with a dynamic DNS system so that I can point mydomain.com at my DNS servers, with home.mydomain.com going into my home network via a raspberry pi. HOWEVER.... I've not got access to the network infrastructure at home (rented accommodation with managed internet), so I can't forward the ports on the router to my own machines. As such, I'm wondering if it's possible to route all the traffic via an SSH/HTTP tunnel through one of the VPS? My plan is to have the raspberry pi provide a VPN into my home network. The raspberry pi uses SSH to connect to the VPS, and the VPS forwards any traffic to home.mydomain.com via the tunnel to the raspberry pi. Is this even possible, and how do I go about it? I don't mind getting my hands dirty with coding and low level tools, I'm just not sure where to start or what the best way to go about it is.

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• How to know whether mongodb is running on 64 bit mode or 32 bit mode

  - by Jim Thio

  My programmer install mongodb. Then somehow it doesn't work. I run C:\mongod\bin>mongod mongod --help for help and startup options Sat Aug 11 22:57:50 Sat Aug 11 22:57:50 warning: 32-bit servers don't have journaling enabled by def ault. Please use --journal if you want durability. Sat Aug 11 22:57:50 Sat Aug 11 22:57:50 [initandlisten] MongoDB starting : pid=3800 port=27017 dbpat h=/data/db 32-bit host=haryantoi5 Sat Aug 11 22:57:50 [initandlisten] Sat Aug 11 22:57:50 [initandlisten] ** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data Sat Aug 11 22:57:50 [initandlisten] ** see http://blog.mongodb.org/post/13 7788967/32-bit-limitations Sat Aug 11 22:57:50 [initandlisten] ** with --journal, the limit is lower Sat Aug 11 22:57:50 [initandlisten] Sat Aug 11 22:57:50 [initandlisten] db version v2.0.7-rc1, pdfile version 4.5 Sat Aug 11 22:57:50 [initandlisten] git version: 9efe4cce272373b52b96de1309c1fbf 0c984305f Sat Aug 11 22:57:50 [initandlisten] build info: windows sys.getwindowsversion(ma jor=6, minor=0, build=6002, platform=2, service_pack='Service Pack 2') BOOST_LIB _VERSION=1_42 Sat Aug 11 22:57:50 [initandlisten] options: {} ************** Unclean shutdown detected. Please visit http://dochub.mongodb.org/core/repair for recovery instructions. ************* Sat Aug 11 22:57:50 [initandlisten] exception in initAndListen: 12596 old lock f ile, terminating Sat Aug 11 22:57:50 dbexit: Sat Aug 11 22:57:50 [initandlisten] shutdown: going to close listening sockets.. . Sat Aug 11 22:57:50 [initandlisten] shutdown: going to flush diaglog... Sat Aug 11 22:57:50 [initandlisten] shutdown: going to close sockets... Sat Aug 11 22:57:50 [initandlisten] shutdown: waiting for fs preallocator... Sat Aug 11 22:57:50 [initandlisten] shutdown: closing all files... Sat Aug 11 22:57:50 [initandlisten] closeAllFiles() finished Sat Aug 11 22:57:50 dbexit: really exiting now It seems that mongod is running on 32 bit. I have a 64 bit computer and I want to run mongodb in 64 bit enviroment. How do I do so?

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• should i and how do i backup my database for a webapp that is hosted on amazon ec2 server?

  - by user8184

  I set up an amazon ec2 instance using ubuntu server edition. I install LAMP stack on it. I did up a php web app running on mysql. I have not officially launched, but I need to know this before launching. Should I backup my database data? If so, how should I do it as cost effective as possible? Previously for another web app, i wrote a perl or bash script (cannot remember) that will be executed by cron on a daily basis. The script will then backup the database into a single .sql file and send as email attachment to my gmail account. That web app was on shared hosting hence, I was quite sure i needed to do backup of my database. My files are on git repo so I am not worried about that. Please advise. I am totally unfamiliar with AWS. Only know as much as setting up an account. That is all. Thank you.

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• Which revision control system for single user

  - by G. Bach

  I'm looking to set up a revision control system with me as a single user. I'd like to have access (read and write) protected using SSL, little overhead, and preferrably a simple setup. I'm looking to do this on my own server, so I don't want to use the option of registering with some professional provider of such a service (I like having direct control over my data; also, I'd like to know how to set up something like that). As far as I'm aware, what kind of project I want to subject to revision control doesn't really matter, but just for completeness' sake, I'm planning on using this for Java project, some html/css/php stuff, and in the future possibly as a synchronizing tool for small data bases (ignore that later one if it doesn't fit in with the paradigm of revision control). My questions primarily arise from the fact that I only ever used Subversion from Eclipse, so I don't have thorough knowledge of what's out there, what fits better for which needs, etc. So far I've heard of Subversion, Git, Mercurial, but I'm open to any system that's widely used and well supported. My server is running Ubuntu 11.10. Which system should I choose, what are the advantages of the respective systems, and if you know of any particularly useful ones, are there tutorials regarding the setup of the system I should choose that you could recommend?

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• OpenVPN-based VPN server on same system it's "protecting": feasible?

  - by Johnny Utahh

  Scenario: hosted machine (typically a VPS) serving wiki, svn, git, forums, email lists (eg: GNU mailman), Bugzilla (etc) privately to < 20 people. People not on team not allowed access. Seeking VPN-restricted access to said server. Have good user experience with OpenVPN-based servers/clients, but have yet to server-admin such systems. Otherwise, experienced Linux sysadmin. Target system: Ubuntu, probably 12.04. Seeking to put an OpenVPN process on above server to "protect" all the above-mentioned services, enabling only OpenVPN-authorized clients/processes to access above services. (Can easily acquire additional IP address(es) as needed for this setup.) Option: if absolutely needed, can employ an additional, dedicated, "VPN server" VPS simply to be my VPN server "front end." But prefer to have all server processes (VPN server plus other server apps) all running on same machine, if possible. Will consider further if dedicated-VPN-machine setup enables 1. easier installation/administration, 2. better/easier end-user experience, and/or 3. makes system significantly more secure. Any of above feasible? The main intention: create a VPN from purely-hosted resources, and not spend all the effort to make a non-VPN, secure site--which typically means "SSL wrapping" + all the continual webserver-application-update management. Let the VPN server deal with access security, and spend list time pushing said security "down" in the other apps/Apache.

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• Puppet variables best practice, generalise or specialise?

  - by Andrei Serdeliuc

  I'm trying to figure out which things should be in git within the puppet manifest and which should be in env vars like FACTER_my_var and use that in the manifest instead. Scenario: you are deploying 3 php apps and you've already built all the layers up to the app in other manifests (base system, php extensions, users, etc), and all that's left is installing the correct app (from an apt repo) and creating a vhost. I'm tempted to have something along the lines of: apache::vhost { $::project_hostname: priority => '10', port => '80', docroot => $::project_document_root, logroot => "/var/log/apache2/${$::project_name}", serveradmin => '[email protected]', require => Package[httpd], ssl => false, override => 'all', setenv => ["APP_KERNEL dev"] } This would run on each server, and the FACTER_project_* vars would be set on a per server basis. An obvious restriction of this would be that you can't run more than one app with this specific example. Or would you rather have project_x.pp, project_y.pp which have hardcoded paths and names?

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• Issues Deploying Functional WAR to Elastic Beanstalk with Tomcat7

  - by BFar

  I am currently deploying OpenTripPlanner (http://github.com/OpenPlans/OpenTripPlanner.git) to Elastic Beanstalk. I'm able to successfully build and deploy opentripplanner with my own customized settings on an ec2. I have set it up so that the appropriate WAR file can be placed in the Tomcat/Webapps folder, and when Tomcat is started up, it will auto-deploy, and even download open trip planner's graph.obj from an S3. All of that works just fine, except when I try to deploy to Elastic Beanstalk. When I upload to Elastic Beanstalk, the log shows that my WAR file is successfully unpacked & successfully downloads the graph.obj from my S3. The only difference is that then nothing happens and I can't load the site in my browser. The health is RED, and I can't figure out what is going on. I've tried looking into ports and dns issues, but I can't determine what's wrong. Anyone have any ideas? Why would a WAR that works on tomcat7 outside of Beanstalk fail to be accessible?

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• Gnome-shell fails to load on 12.10

  - by Githlar

  I'm usually the one answering questions, but in this I'm throughly stumped! My Setup: Ubuntu 12.10 (Dist upgrade form 12.04) ATI M96 [Mobility Radeon HD 4650] Upon the first installation of 12.10 I had all kinds of issues getting the Legacy ATI drivers to install (I guess the source for the drivers isn't kosher with kernel 3.5). So, I added the repository ppa:makson96/fglrx - which has a version of the ATI source patched to work with kernel 3.5. After installation of fglrx-legacy from that PPA, gnome-shell and all my graphics work fine... until today. The Problem I unsuspended my computer today and the screen was black (not off, the black from the gnome lock screen). I'd move my mouse/hit a key and the background would flash and then it'd go back to black. Restarted via VT1 Logged into Gnome (gnome-shell) session, but no gnome-shell! Investigation: First, I went to VT1 and tried export DISPLAY=:0;gnome-shell --replace. It appeared to work fine, switch back to X and nothing. Went back to VT1 and saw this error message: JS ERROR: !!! Exception was: TypeError: Object 0x7fc748129c30 is not a subclass of (null), it's a xO JS ERROR: !!! message = '"Object 0x7fc748129c30 is not a subclass of (null), it's a xO"' JS ERROR: !!! fileName = '"/usr/share/gnome-shell/js/ui/tweener.js"' JS ERROR: !!! lineNumber = '218' JS ERROR: !!! stack = '"()@/usr/share/gnome-shell/js/ui/tweener.js:218 wrapper()@/usr/share/gjs-1.0/lang.js:204 ()@/usr/share/gjs-1.0/lang.js:145 ()@/usr/share/gjs-1.0/lang.js:239 init()@/usr/share/gnome-shell/js/ui/tweener.js:49 init()@/usr/share/gnome-shell/js/ui/environment.js:96 @<main>:1 "' Window manager warning: Log level 32: Execution of main.js threw exception: TypeError: Object 0x7fc748129c30 is not a subclass of (null), it's a xO Note: Everywhere it says "it's a xO", xO is actually garbled and changes every time (I'm thinking memory corruption?) This error is thrown by line 96 of /usr/share/gnome-shell/js/ui/environment.js: tweener.Init() Did a purge of fglrx-legacy, reboot, reinstall fglrx-legacy, reboot... same thing. Did a ppa-purge of ppa:gnome3-team/gnome3, and reinstalled gnome-shell and ubuntu-desktop from the standard repositores... same thing. I'm really at a loss here. I love gnome-shell and after using it for nearly a year now gnome classic just seems so archaic. Additional Information Apt log from the day I first suspended my machine (these are upgrades from the gnome3-team/gnome3 ppa and ubuntu-wine/ppa ppa): Start-Date: 2012-11-24 17:30:28 Commandline: aptdaemon role='role-commit-packages' sender=':1.618' Install: gkbd-capplet:amd64 (3.6.0-0ubuntu1), gnome-control-center-unity:amd64 (1.0-0ubuntu1~ubuntu12.10.1) Upgrade: nautilus:amd64 (3.6.2-0ubuntu0.1~quantal1, 3.6.3-0ubuntu2~ubuntu12.10.1), libgnome-control-center1:amd64 (3.4.2-0ubuntu19, 3.6.3-0ubuntu6~ubuntu12.10.1), wine1.5-i386:i386 (1.5.17-0ubuntu4, 1.5.18-0ubuntu1), wine1.5:amd64 (1.5.17-0ubuntu4, 1.5.18-0ubuntu1), gnome-settings-daemon:amd64 (3.4.2-0ubuntu14, 3.6.3-0ubuntu1~ubuntu12.10.1), gnome-control-center-data:amd64 (3.4.2-0ubuntu19, 3.6.3-0ubuntu6~ubuntu12.10.1), gnome-accessibility-themes:amd64 (3.6.0.2-0ubuntu1, 3.6.2-0ubuntu2~ubuntu12.10.1), gnome-themes-standard:amd64 (3.6.0.2-0ubuntu1, 3.6.2-0ubuntu2~ubuntu12.10.1), wine1.5-amd64:amd64 (1.5.17-0ubuntu4, 1.5.18-0ubuntu1), nautilus-data:amd64 (3.6.2-0ubuntu0.1~quantal1, 3.6.3-0ubuntu2~ubuntu12.10.1), gnome-control-center:amd64 (3.4.2-0ubuntu19, 3.6.3-0ubuntu6~ubuntu12.10.1), libnautilus-extension1a:amd64 (3.6.2-0ubuntu0.1~quantal1, 3.6.3-0ubuntu2~ubuntu12.10.1) End-Date: 2012-11-24 17:31:32 fglrxinfo (driver appears to be working): display: :0 screen: 0 OpenGL vendor string: Advanced Micro Devices, Inc. OpenGL renderer string: ATI Mobility Radeon HD 4650 OpenGL version string: 3.3.11653 Compatibility Profile Context Does anybody have any further ideas?

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• Strange ssh key issue

  - by user55714

  Scenario 1. I am doing this from /home/deploy directory I am trying to set up ssh with github for capistrano deployment. this has been an absolute nightmare. when I do ssh [email protected] as the deploy account I get Permission denied (publickey). so may be the key is not being found, so If I do a ssh-add /home/deploy/.ssh/id_rsa Could not open a connection to your authentication agent. (i did verify that the ssh-agent was running) If I do exec ssh-agent bash and then repeat the ssh-add then the key does get added and I can ssh into github. Now I exit from the ssh connection to my server and ssh back in and I can't ssh into github anymore! Scenario 2 if I login to my remote server and then cd into my .ssh directory and ssh into github then it all works fine I guess there is a problem with locating the key and for some reason the agent isn't funcitoning correctly. Any ideas? Her is a pastie with more details..my .bashrc, permissions etc. http://pastie.org/pastes/1190557/

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• Very slow context menu in Windows 8

  - by burzum

  I've installed Windows 8 Pro on a blank new SSD, the system is on c:\. I do not think this problem was existent when I started using Windows 8 but I think it started to happen after I've symlinked (mklink /D) a folder from another drive, a SATA drive, to c:\xampp\htdocs. When I right click a file or folder inside the symlinked folder it always takes at least ~5-10 seconds until the context menu comes up. This also happens sometimes, but not all the time for files and folder outside of the symlinked folder. Also when I delete folders the delete folder dialog seems to get locked and does not continue. When I delete a folder using rmdir from the command line it works fine and pretty fast. It appears to me like the file explorer in Windows 8 is pretty bad compared to any other Windows I've used before? Any idea how to get these problems solved? I've already removed a lot of context menu entries; the only ones left are the tortoise git context menus but I'm sure that's not the problem.

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• Disk doesn't contain a valid partition table

  - by Jeevan Dongre

  I was running a m1.small instance ec2 ubuntu instance. I was running out of disk space, so I upgraded my instance to medium. When I upgraded I actually got 429.5 GB of space and after that I added 10 gb of volume too. When I run the "sudo fdisk -l" command I got this results. Disk /dev/sda1: 8589 MB, 8589934592 bytes 255 heads, 63 sectors/track, 1044 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x00000000 Disk /dev/sda1 doesn't contain a valid partition table Disk /dev/sda2: 429.5 GB, 429461078016 bytes 255 heads, 63 sectors/track, 52212 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x00000000 Disk /dev/sda2 doesn't contain a valid partition table Disk /dev/sdf: 10.7 GB, 10737418240 bytes 255 heads, 63 sectors/track, 1305 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x00000000 sda1 is the primary parition and sda2 is what I got added upgrading my system to medium. But the problem persists, I am not able to pull the code from git, it is giving me this error. remote: Counting objects: 409, done. remote: Compressing objects: 100% (236/236), done. fatal: write error: No space left on device fatal: index-pack failed

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• Windows 2008 R2 file share - any way to "lock it down" outside of a 3rd party app?

  - by TheCleaner

  I have a 3rd party app that "makes a call" to write files to a file share on our network using the currently logged in credentials of the Windows domain user. Meaning the 3rd party app doesn't pass the apps credentials but simply issues a behind the scenes copy command to take a source file specified and copy/move it to the destination "repository" on the file share. The basic premise is that it keeps revisions/approvals for Document Control (think svn/git I guess, similar to this question: Lock down Windows folder to only be updatable by SVN). This all works fine...but here's my issue: I need a way to lock down the file share from being accessed/modified outside of using the 3rd party app (meaning prevent explorer/word/excel/etc from getting to that share). I know I can do the following: make the share a hidden share ($) - this definitely helps. Most users would have zero clue on how to get to such a share. Solves probably 95% of my issue. go one step further and set the "Hidden" attribute on the folders in the hidden share - this would go a little further in that even if a user knows the path to the hidden share like \\server\hidden$ they still won't see folders in that share without changing their explorer options to "show hidden files/folder Any other ideas on how I can lock this down? The users still need modify rights to this share/folders since the 3rd party app relies on their Windows permissions to that location when copying the files into it. I can't really use 3rd party tools to password protect the folder/share without causing the 3rd party app functions to fail.

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