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• Visualizing Undirected Graph That's Too Large for GraphViz?

  - by Gabe

  Hi Everyone, I was wondering if anyone has any advice for rendering an undirected graph with 178,000 nodes and 500,000 edges. I've tried Neato, Tulip, and Cytoscape. Neato doesn't even come remotely close, and Tulip and Cytoscape claim they can handle it but don't seem to be able to. (Tulip does nothing and Cytoscape claims to be working, and then just stops.) Does anyone have any ideas? I'd just like a vector format file (ps or pdf) with a remotely reasonable layout of the nodes. Thanks!

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• python union of 2 nested lists with index

  - by sbas

  I want to get the union of 2 nested lists plus an index to the common values. I have two lists like A = [[1,2,3],[4,5,6],[7,8,9]] and B = [[1,2,3,4],[3,3,5,7]] but the length of each list is about 100 000. To A belongs an index vector with len(A): I = [2,3,4] What I want is to find all sublists in B where the first 3 elements are equal to a sublist in A. In this example I want to get B[0] returned ([1,2,3,4]) because its first three elements are equal to A[0]. In addition, I also want the index to A[0] in this example, that is I[0]. I tried different things, but nothing worked so far :( First I tried this: Common = [] for i in range(len(B)): if B[i][:3] in A: id = [I[x] for x,y in enumerate(A) if y == B[i][:3]][0] ctdCommon.append([int(id)] + B[i]) But that takes ages, or never finishes Then I transformed A and B into sets and took the union from both, which was very quick, but then I don't know how to get the corresponding indices Does anyone have an idea?

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• VMWare ESX Updates - Which to Apply?

  - by Aaron Alton

  Wondering what more experienced ESX admins typically do... I just brought our ESX hosts up to 3.5 Update 5 (Yes, I know we're behind still). I then applied the "Critical Host Updates" baseline in VMWare update manager, and found that we're still short on 14 "critical updates". My question is, do most people go ahead and apply any update flagged as critical, or do they evaluate each update one-by-one to determine whether or not the issue that has been addressed is likely to affect them. In the SQL Server world (my alma mater, so to speak), we regularly apply service packs, and sometimes cumulative updates, but we only apply hotfixes when the issue that they are targeted towards affects us. Does the same logic hold fast in VMWare land?

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• url link in bibtex

  - by Tim

  Hi, I was wondering how to make a url link appear in Bibliography? For example, @misc{libsvm, abstract = {LIBSVM is an implbmentation of Support vector machine (SVM).}, author = {Chang, Chih-Chung}, keywords = {svm}, posted-at = {2010-04-08 00:05:04}, priority = {2}, title = {LIBSVM}, url = "http://www.csie.ntu.edu.tw/~cjlin/libsvm/", year = {2008} } will appear in Bibliography as [2] Chih-Chung Chang. Libsvm, 2008. But I hope the link "http://www.csie.ntu.edu.tw/~cjlin/libsvm/" could appear and the "Libsvm" could be all capital "LIBSVM". Honestly, I have no idea how a link should appear in Bibliography. What I think might be not professional. Please advise me how to put it in a professional way. Thanks and regards!

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• Build a RAID-5 USB Array or NAS?

  - by TK Kocheran

  I'm looking to build a RAID-5 or RAID-6 hard disk array to be used as a centralized backup location for my home network. I have a lot of 4-8GB DVD ISO files which I intend to serve over the network to my TV using DLNA or something similar. I need decent write times, fast read times, and preferably a way to connect this array to my network router over USB. I'll probably be using ext3/4 on it (I'd use btrfs if my router supported it :-[). Is there a way to build a RAID array that is accessible over USB? I'm kind of new to this and most guides assume you're running a RAID array inside your machine. I need at least 5TB of space, and I need redundancy, so I prefer RAID-6. How can I go about accomplishing this?

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• Apache 2.4.3 php-fpm mod_fast_cgi and mod_cache

  - by Anjia

  Did anybody successfully configured mod_cache in apache 2.4 with php-fpm and fastcgi? my cgi config: <IfModule mod_fastcgi.c> Alias /php5.fastcgi /var/www/fastcgi/php5.fastcgi AddHandler php-script .php FastCGIExternalServer /var/www/fastcgi/php5.fastcgi -socket /mnt/tmp/fast/php-fpm.sock -idle-timeout 1600 -pass-header Authorization Action php-script /php5.fastcgi virtual My php-fpm config is standard and I am loading mod_cache and mod_disk_cache in Apache. However the Apache does not seems to cache any content. The debug log file: Fri Sep 07 23:22:59.691333 2012] [cache:debug] [pid 35623:tid 123613201929984] mod_cache.c(161): [client 10.0.0.22:21938] AH00750: Adding CACHE_SAVE filter for /index.html [Fri Sep 07 23:22:59.691345 2012] [cache:debug] [pid 35623:tid 123613201929984] mod_cache.c(171): [client 10.0.0.22:21938] AH00751: Adding CACHE_REMOVE_URL filter for /index.html [Fri Sep 07 23:23:01.326598 2012] [cache:debug] [pid 35623:tid 123613185144576] cache_storage.c(626): [client 10.0.0.110:5414] AH00698: cache: Key for entity /index.html?(null) is `http://10.0.1.16:8080/index.html?`

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• Error when trying to create a faceted plot in ggplot2

  - by John Horton

  I am trying to make a faceted plot in ggplot2 of the coefficients on the regressors from two linear models with the same predictors. The data frame I constructed is this: r.together> reg coef se y 1 (Intercept) 5.068608671 0.6990873 Labels 2 goodTRUE 0.310575129 0.5228815 Labels 3 indiaTRUE -1.196868662 0.5192330 Labels 4 moneyTRUE -0.586451273 0.6011257 Labels 5 maleTRUE -0.157618168 0.5332040 Labels 6 (Intercept) 4.225580743 0.6010509 Bonus 7 goodTRUE 1.272760149 0.4524954 Bonus 8 indiaTRUE -0.829588862 0.4492838 Bonus 9 moneyTRUE -0.003571476 0.5175601 Bonus 10 maleTRUE 0.977011737 0.4602726 Bonus The "y" column is a label for the model, reg are the regressors and coef and se are what you would think. I want to plot: g <- qplot(reg, coef, facets=.~y, data = r.together) + coord_flip() But when I try to display the plot, I get: > print(g) Error in names(df) <- output : 'names' attribute [2] must be the same length as the vector [1] What's strange is that qplot(reg, coef, colour=y, data = r.together) + coord_flip() plots as you would expect.

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• DNSMASQ configuration

  - by sean

  I am using DNSmasq, OpenDNS and DYNDNS. DYNDNS is for my FTP site, and I am using OPEN DNS to filter porn from my kids itouch/ipad. However, I would like a few computers to have the capability to bypass openDNS, and pass through to a fast DNS server like google or similar. I would also like to fowrard all traffice from DYNDNS to my FTP server. Any ideas? This is what I have thus far.. strict-order dhcp-mac=filter,00:25:64:DB:A8:8A dhcp-option=net:filter,6,8.8.8.8,8.8.4.4 Its not working thus far, can someone help me accomplish what I want to do?

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• Server Security

  - by mahatmanich

  I want to run my own root server (directly accessible from the web without a hardware firewall) with debian lenny, apache2, php5, mysql, postfix MTA, sftp (based on ssh) and maybe dns server. What measures/software would you recomend, and why, to secure this server down and minimalize the attack vector? Webapplications aside ... This is what I have so far: iptables (for gen. packet filtering) fail2ban (brute force attack defense) ssh (chang default, port disable root access) modsecurity - is really clumsy and a pain (any alternative here?) ?Sudo why should I use it? what is the advantage to normal user handling thinking about greensql for mysql www.greensql.net is tripwire worth looking at? snort? What am I missing? What is hot and what is not? Best practices? I like "KISS" - Keep it simple secure, I know it would be nice! Thanks in advance ...

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• Faster two way Boomark/History Sync for Firefox?

  - by geocoo

  I need a fast automatic two-way bookmark & history sync. Firefox sync seems too slow because I might bookmark/visit a URL then within a few mins put desktop to sleep and leave the house; if it hasn't synced, then I don't have a way of getting it on my laptop (or vice versa). My home upload is only around 200kbps so maybe that's why FF sync seems slow? (I mean it's minutes, not seconds slow). I have read there are a few ways like xmarks/delicious/google but I don't want clutter like extra toolbars or have to visit a site to get bookmarks, they should be as native in the Firefox bookmarks bar as possible, organised in the folders/tags. I know someone must have experimented/know more about this. Thanks.

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• creating a 3d plane using Frank Luna's technique

  - by numerical25

  I am creating a 3d plane that lays on the x and z axis. and has hills that extend on the y axis. bulk of the code looks like this float PeaksAndValleys::getHeight(float x, float z)const { return 0.3f*( z*sinf(0.1f*x) + x*cosf(0.1f*z) ); } void PeaksAndValleys::init(ID3D10Device* device, DWORD m, DWORD n, float dx) { md3dDevice = device; mNumRows = m; mNumCols = n; mNumVertices = m*n; mNumFaces = (m-1)*(n-1)*2; // Create the geometry and fill the vertex buffer. std::vector<Vertex> vertices(mNumVertices); float halfWidth = (n-1)*dx*0.5f; float halfDepth = (m-1)*dx*0.5f; for(DWORD i = 0; i < m; ++i) { float z = halfDepth - i*dx; for(DWORD j = 0; j < n; ++j) { float x = -halfWidth + j*dx; // Graph of this function looks like a mountain range. float y = getHeight(x,z); vertices[i*n+j].pos = D3DXVECTOR3(x, y, z); // Color the vertex based on its height. if( y < -10.0f ) vertices[i*n+j].color = BEACH_SAND; else if( y < 5.0f ) vertices[i*n+j].color = LIGHT_YELLOW_GREEN; else if( y < 12.0f ) vertices[i*n+j].color = DARK_YELLOW_GREEN; else if( y < 20.0f ) vertices[i*n+j].color = DARKBROWN; else vertices[i*n+j].color = WHITE; } } D3D10_BUFFER_DESC vbd; vbd.Usage = D3D10_USAGE_IMMUTABLE; vbd.ByteWidth = sizeof(Vertex) * mNumVertices; vbd.BindFlags = D3D10_BIND_VERTEX_BUFFER; vbd.CPUAccessFlags = 0; vbd.MiscFlags = 0; D3D10_SUBRESOURCE_DATA vinitData; vinitData.pSysMem = &vertices[0]; HR(md3dDevice->CreateBuffer(&vbd, &vinitData, &mVB)); // Create the index buffer. The index buffer is fixed, so we only // need to create and set once. std::vector<DWORD> indices(mNumFaces*3); // 3 indices per face // Iterate over each quad and compute indices. int k = 0; for(DWORD i = 0; i < m-1; ++i) { for(DWORD j = 0; j < n-1; ++j) { indices[k] = i*n+j; indices[k+1] = i*n+j+1; indices[k+2] = (i+1)*n+j; indices[k+3] = (i+1)*n+j; indices[k+4] = i*n+j+1; indices[k+5] = (i+1)*n+j+1; k += 6; // next quad } } D3D10_BUFFER_DESC ibd; ibd.Usage = D3D10_USAGE_IMMUTABLE; ibd.ByteWidth = sizeof(DWORD) * mNumFaces*3; ibd.BindFlags = D3D10_BIND_INDEX_BUFFER; ibd.CPUAccessFlags = 0; ibd.MiscFlags = 0; D3D10_SUBRESOURCE_DATA iinitData; iinitData.pSysMem = &indices[0]; HR(md3dDevice->CreateBuffer(&ibd, &iinitData, &mIB)); } My question pretains to the cosf and sinf. I am formiluar with trigonometry and I understand sin, cosine, and tangent. but I am not formiluar with cosf and sinf and what they do. From looking at this example. they have alot to do with finding a y value.

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• Placement coordinates of bitmapData in AS3

  - by TheDarkIn1978

  i've programatically created a vector graphic (rect), repositioned the graphic, and set up an MOUSE_MOVE eventListener to trace color information of the graphic using getPixel(). however, the bitmapData is placed at 0,0 of the stage and i don't know how to move it so that it matches the graphic's location. var coloredSquare:Sprite = new GradientRect(200, 200, 0xFFFFFF, 0x000000, 0xFF0000, 0xFFFF00); coloredSquare.x = 100; addChild(coloredSquare); var coloredSquareBitmap:BitmapData = new BitmapData(coloredSquare.width, coloredSquare.height, true, 0); coloredSquareBitmap.draw(coloredSquare); coloredSquare.addEventListener(MouseEvent.MOUSE_MOVE, readColor); function readColor(evt:Event):void { var pixelValue:uint = coloredSquare.getPixel(mouseX, mouseY); trace(pixelValue.toString(16)); }

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• LVM2 vs MDADM performance

  - by archer

  I've used MDADM + LVM2 on many boxes for quite a while. MDADM was serving for both RAID0 and RAID1 arrays, while LVM2 where used for logical volumes on top of MDADM. Recently I've found that LVM2 could be used w/o MDADM (thus minus one layer, as the result - less overhead) for both mirroring and stripping. However, some guys claims that READ PERFORMANCE on LVM2 for mirrored array is not that fast as for LVM2 (linear) on top of MDADM (RAID1) as LVM2 does not read from 2+ devices at a time, but use 2nd and higher devices in case of 1st device failure. MDADM reads from 2 devices at a time (even in mirrored mode). Who could confirm that?

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• Our wi-fi at work is ridiculously slow, will adding more range extenders improve it?

  - by john

  At work, we have two wireless networks (e.g., Work1 Work2); the Work2 is used downstairs and Work1 is used upstairs. However, both are notoriously slow. The connection is better when we are wired in, but unfortunately due to our building being very old and our company growing very fast, most employees are not seated near the walls where the ethernet cables are. I had Cox, our ISP, run a bandwidth utilization test and it doesn't seem like we are capping out on upstream/downstream, which leads me to believe that it's strictly an issue with the wireless networks (which were implemented before I got there). The wireless networks are both Apple Airport Extremes. Is there anything I can do to improve the situation for everyone? Speeds are extremely slow, and sometimes drops out.

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• Website pages very slow to load on first access

  - by Merianos Nikos

  I have a production web server that makes sites to be very slow when load for first time. After the first time all connections are normal and fast. In the following screen you can see the first test I have run for a random site in my server: and here you can see the result of the second time request: As you can see there is a big change in the second load of the same page. Here is the page load time graph: My problem is that I don't really know anything about Red Had Linux server, and also I don't know where can I start. Can somebody to help me ? I like to find out the solution for the long time "wait" in connection. I know that my question is very minimal, but you can always ask me to give you information about the server.

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• Connecting to VPN via Proxy

  - by Rodrigo

  Hi, My company's VPN server is located in Netherlands, from my current location this is a really crappy place in terms of connectivity, connection keeps dropping, it's slow and keeps being reset during high traffic times. I have a dedicated server over USA which is able to connect to VPN server without this issues, connection is stable and fast. My question is, how do I connect to this VPN using a proxy running on my dedicated server? I'm on Windows 7 using a VM on XP to connect to the VPN. Thanks.

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• High volume SVM (machine learning) system

  - by flyingcrab

  I working on a possible machine learning project that would be expected to do high speed computations for machine learning using SVM (support vector machines) and possibly some ANN. I'm resonably comfortable working on matlab with these, but primarly in small datasets, just for experimentation. I'm wondering if this matlab based approach will scale? or should i be looking into something else? C++ / gpu based computing? java wrapping of the matlab code and pushing it onto app engine? Incidentally, there seems to be a lot fo literature on GPUs, but not much on how useful they are on machine learning applications using matlab, & the cheapest CUDA enlabled GPU money can buy? is it even worth the trouble?

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• MySQL is killing the server IO.

  - by OneOfOne

  I manage a fairly large/busy vBulletin forums (~2-3k requests per second, running on gigenet cloud), the database is ~ 10 GB (~9 milion posts, ~60 queries per second), lately MySQL have been grinding the disk like there's no tomorrow according to iotop and slowing the site. The last idea I can think of is using replication, but I'm not sure how much that would help and worried about database sync. I'm out of ideas, any tips on how to improve the situation would be highly appreciated. Specs : Debian Lenny 64bit ~12Ghz (6 cores) CPU, 7520gb RAM, 160gb disk. Kernel : 2.6.32-4-amd64 mysqld Ver 5.1.54-0.dotdeb.0 for debian-linux-gnu on x86_64 ((Debian)) Other software: vBulletin 3.8.4 memcached 1.2.2 PHP 5.3.5-0.dotdeb.0 (fpm-fcgi) (built: Jan 7 2011 00:07:27) lighttpd/1.4.28 (ssl) - a light and fast webserver PHP and vBulletin are configured to use memcached. MySQL Settings : [mysqld] key_buffer = 128M max_allowed_packet = 16M thread_cache_size = 8 myisam-recover = BACKUP max_connections = 1024 query_cache_limit = 2M query_cache_size = 128M expire_logs_days = 10 max_binlog_size = 100M key_buffer_size = 128M join_buffer_size = 8M tmp_table_size = 16M max_heap_table_size = 16M table_cache = 96

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• How can I re-encode H.264 video with minimal quality loss?

  - by SofaKng

  I have a lot of MPEG-TS files (.TS container but H.264 video) and playback is fine except that when you skip forward/backward or fast forward it's very sluggish and gets pixelated, etc. I've been trying to do research and I'm guessing that they were encoding with very few reference blocks (ie. it's a capture from a DVB-S satellite stream). When I re-encode them with Handbrake (.MP4 container) they play very, very good and seeking in the video is instant, etc, etc. Is it possible to transcode/re-encode my MPEG-TS files with minimal quality loss? If so, what is my best bet? They are each about 2 Mbps (ie. 2 GB per hour) but I don't want to re-encode them if "minimal quality loss" requires 10+ GB per file. I'm hoping to keep the video are the same size. Can anybody give me any advice?

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• Replicate / SYNC / Copy thousands of files

  - by rihatum

  Windows 32BIT Box (Server OS) 4GB RAM a 800GB LUN Mapped to the above box as a local drive Around 700GB of text files (Yes text files and a few thousand word documents) nested in thousands of directories. I need to move this to a new storage and map another server to it. What would be the best way to go about it ? What I did was mapped the existing LUN to our new box and mapped a LUN from the New storage to the new box too, and tried copying (windows copy) but that wasn't good / fast enough considering the downtime. I am now looking for either a script which will do this or a utility (prefer opensource / free) to move this size of data at a good speed. 2 x 1GB Nics teamed ether channel 2GBPs Any suggestions or pointers would be off great help Thanks !

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• NX Client running on OS X 10.6.3 => NX Server Ubuntu 10.04: weird keymapping issue

  - by Mike D

  I have been using Ubuntu 9.10 at work after switching from vista. After being (expectedly) disappointed with performance over VNC (via VPN) when logging in from home, I came across the NOMACHINE suite. Last week, I upgraded from OS X 10.6.2 = 10.6.3 at home. After that, I also updated my NX Client at home to the latest version, as there were issues with recent changes in the OSX X11 setup that rendered the NX connection useless. At that point, everything worked fine. Fast forward, I upgraded from 9.10 = 10.04 on my work machine the next day, and after coming home and trying to log-in remotely, I noticed that the "s" and "m" keys, when pressed locally, acted as if the meta key was being pressed on the remote machine. That is, the "s" key opens in the Ubuntu login menu (the power icon), and the "m" key opens the messaging menu. I found some info on using xmodmap to remap keys, however, I can't even begin to fathom what keys I could remap to solve this issue. Any ideas?

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• Fragile XenServer won't create new VDIs anymore

  - by thoiz_vd

  I'm getting increasingly frustrated with XenServer. Currently I'm using 5.6FP1 and it seems to be very fragile. Canceling any VDI-related action almost guarantees trouble. This time I tried to create a new VM using a snapshot for a template, with the fast disk cloning option disabled. It would take much longer than I was able and willing to keep my XenCenter open, so I canceled it. That took ages too, so I had to decide to "Quit Anyway." Since, I seem unable to create any new VDI. New attempts at cloning halt with "The attempt to clone the VDI failed," and creating new VMs based on built-in templates hang at "Provisioning." I'm in need of some advice how to solve this. What I did so far is run a xe vdi-list, which returned nothing odd to me, but I'm no expert. I assume that an incomplete VDI is blocking my Storage Repository somehow, however, how to deal with that remains unclear.

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• internet access options in remote area? (read: no comcast,qwest, etc)

  - by freedrull

  Currently I am living in a fairly "remote" area, in the countryside, and cable internet access through the typical companies like comcast and qwest is just not available here. I've been trying to research other options for fast internet access. There are some small cable companies but they currently do not offer broadband access here. I thought about maybe buying a 3g phone with a data plan and doing some sort of tethering, or perhaps getting an android phone and using it as a wireless AP. This would of course depend on 3g being available here. The only other thing I can think of is some sort of satellite internet service, or doing something crazy like adapting wifi over am radio. Anyone have any ideas, at all, short of moving somewhere else?

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• Slow performance by PHP directory operations on virtual machine (Ubuntu libvirt)

  - by thonixx

  Some days ago I installed an Ubuntu server and two running virtual machines with libvirt. Everything works fine except one performance problem. Everytime when I call a PHP script with directory operations the operations are very slow and not performant. Here is an example: http://zother.white-tiger.ch/ And here you see an example without a directory operation and how fast it is: http://michaeltanner.ch/ It's all on the same virtual server. The virtual machine uses 6 cores (8 are available) and 7500 megabytes RAM (8 Gigabyte are available). The disk image format is qcow2. How can I improve the performance?

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• Does anyone know of a library in Java that can parse ESRI Shapefiles?

  - by KingNestor

  I'm interested in writing a visualization program for the road data in the 2009 Tiger/Line Shapefiles. I'd like to draw the line data to display all the roads for my county. The ESRI Shapefile or simply a shapefile is a popular geospatial vector data format for geographic information systems software. It is developed and regulated by ESRI as a (mostly) open specification for data interoperability among ESRI and other software products.1 A "shapefile" commonly refers to a collection of files with ".shp", ".shx", ".dbf", and other extensions on a common prefix name (e.g., "lakes.*"). The actual shapefile relates specifically to files with the ".shp" extension, however this file alone is incomplete for distribution, as the other supporting files are required. Does anyone know of existing libraries for parsing and reading in the line data for Shapefiles?

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