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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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  • Generic DRM (Distributed resource management) wrapper

    - by Pavel Bernshtam
    I need to write a software, which launches DRM jobs in a customer environment and monitors those jobs status. It should work with various customer environments and DRMs - like LSF, Sun Grid and others. Can you recommend some 3rd party library, which hides DRM differences from me and has API like "launch job", "get list of jobs", "get job status" etc. ? Both Java and native libraries are good for me.

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  • Accurate least-squares fit algorithm needed

    - by ggkmath
    I've experimented with the two ways of implementing a least-squares fit (LSF) algorithm shown here. The first code is simply the textbook approach, as described by Wolfram's page on LSF. The second code re-arranges the equation to minimize machine errors. Both codes produce similar results for my data. I compared these results with Matlab's p=polyfit(x,y,1) function, using correlation coefficients to measure the "goodness" of fit and compare each of the 3 routines. I observed that while all 3 methods produced good results, at least for my data, Matlab's routine had the best fit (the other 2 routines had similar results to each other). Matlab's p=polyfit(x,y,1) function uses a Vandermonde matrix, V (n x 2 matrix) and QR factorization to solve the least-squares problem. In Matlab code, it looks like: V = [x1,1; x2,1; x3,1; ... xn,1] % this line is pseudo-code [Q,R] = qr(V,0); p = R\(Q'*y); % performs same as p = V\y I'm not a mathematician, so I don't understand why it would be more accurate. Although the difference is slight, in my case I need to obtain the slope from the LSF and multiply it by a large number, so any improvement in accuracy shows up in my results. For reasons I can't get into, I cannot use Matlab's routine in my work. So, I'm wondering if anyone has a more accurate equation-based approach recommendation I could use that is an improvement over the above two approaches, in terms of rounding errors/machine accuracy/etc. Any comments appreciated! thanks in advance.

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  • Custom array sort in perl

    - by ABach
    I have a perl array of to-do tasks that looks like this: @todos = ( "1 (A) Complete online final @evm4700 t:2010-06-02", "3 Write thank-you t:2010-06-10", "4 (B) Clean t:2010-05-30", "5 Donate to LSF t:2010-06-02", "6 (A) t:2010-05-30 Pick up dry cleaning", "2 (C) Call Chris Johnson t:2010-06-01" ); That first number is the task's ID. If a task has ([A-Z]) next to, that defines the task's priority. What I want to do is sort the tasks array in a way that places the prioritized items first (and in order): @todos = ( "1 (A) Complete online final @evm4700 t:2010-06-02", "6 (A) t:2010-05-30 Pick up dry cleaning", "4 (B) Clean t:2010-05-30", "2 (C) Call Chris Johnson t:2010-06-01" "3 Write thank-you t:2010-06-10", "5 Donate to LSF t:2010-06-02", ); I cannot use a regular sort() because of those IDs next to the tasks, so I'm assuming that some sort of customized sorting subroutine is needed. However, my knowledge of how to do this efficiently in perl is minimal. Thanks, all.

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  • 1D Function into 2D Function Interpolation

    - by Drazick
    Hello. I have a 1D function which I want to interpolate into 2D function. I know the function should have "Polar Symmetry". Hence I use the following code (Matlab Syntax): Assuming the 1D function is LSF of the length 15. [x, y] = meshgrid([-7:7]); r = sqrt(x.^2 + y.^2); PSF = interp1([-7:7], LSF, r(:)); % Sometimes using 'spline' option, same results. PSF = reshape(PSF, [7, 7]); I have few problems: 1. Got some overshoot at the edges (As there some Extrapolation). 2. Can't enforce some assumptions (Monotonic, Non Negative). Is there a better Interpolation method for those circumstances? I couldn't find "Lanczos" based interpolation I can use the same way as interp1 (For a certain vector of points, in "imresize" you can only set the length). Is there such function anywhere? Has anyone encountered a function which allows enforcing some assumptions (Monotonically Decreasing, Non Negative, etc..). Thanks.

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  • CodePlex Daily Summary for Sunday, November 28, 2010

    CodePlex Daily Summary for Sunday, November 28, 2010Popular ReleasesMDownloader: MDownloader-0.15.25.7002: Fixed updater Fixed FileServe Fixed LetItBitNotepad.NET: Notepad.NET 0.7 Preview 1: Whats New?* Optimized Code Generation: Which means it will run significantly faster. * Preview of Syntax Highlighting: Only VB.NET highlighting is supported, C# and Ruby will come in Preview 2. * Improved Editing Updates (when the line number, etc updates) to be more graceful. * Recent Documents works! * Images can be inserted but they're extremely large. Known Bugs* The Update Process hangs: This is a bug apparently spawning since 0.5. It will be fixed in Preview 2. Until then, perform a fr...Flickr Schedulr: Schedulr v2.2.3984: This is v2.2 of Flickr Schedulr, a Windows desktop application that automatically uploads pictures and videos to Flickr based on a schedule (e.g. to post a new picture every day at a certain time). What's new in this release? Videos are now supported as well. The application can now automatically add pictures to the queue when it starts up, from specific monitored folders. Sets and Groups can now be displayed as text only (without icons) to speed up the application. Fixed issue that ta...Cropper: 1.9.4: Mostly fixes for issues with a few feature requests. Fixed Issues 2730 & 3638 & 14467 11044 11447 11448 11449 14665 Implemented Features 6123 11581PFC: PFC for PB 11.5: This is just a migration from the 11.0 code. No changes have been made yet (and they are needed) for it to work properly with 11.5.PDF Rider: PDF Rider 0.5: This release does not add any new feature for pdf manipulation, but enables automatic updates checking, so it is reccomended to install it in order to stay updated with next releases. Prerequisites * Microsoft Windows Operating Systems (XP - Vista - 7) * Microsoft .NET Framework 3.5 runtime * A PDF rendering software (i.e. Adobe Reader) that can be opened inside Internet Explorer. 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What's NewThis release adds a feature for aggregating the overall metrics in a folder full of NodeXL workbooks, adds geographical coordinates to the Twitter import features, and fixes a memory-related bug. See the Complete NodeXL Release History for details. Please Note: There is a new option in the setup program to install for "Just Me" or "Everyone." Most people...VFPX: FoxBarcode v.0.11: FoxBarcode v.0.11 - Released 2010.11.22 FoxBarcode is a 100% Visual FoxPro class that provides a tool for generating images with different bar code symbologies to be used in VFP forms and reports, or exported to other applications. Its use and distribution is free for all Visual FoxPro Community. Whats is new? 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It is designed to support out-of-the-box features: * interface-driven Xml serialization * class-driven Xml serialization * runtime serializationVoXign: - Proposer une formation introductive à la langue des signes, en e-Learning. - autonomie de gestion de l’emploi du temps, du rythme - apprentissage d’un lexique de « première nécessité » - introduction à la culture sourde et approche des spécificités linguistiques de la LSF Weyland: A .NET metaprogramming framework.

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