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Thread: New information regarding D20L

  1. #1
    Peaches Moogie's Avatar
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    New information regarding D20L

    Here's a nice write up submitted by Chinasaur.
    ============================================

    D2OL (Distributed Drug Optimization lab) - http://www.d2ol.com/

    New and improved and now at version 2.0

    From the D2OL website

    "The Drug Design and Optimization Lab (D2OL) works to discover drug candidates against Anthrax, Smallpox, Ebola and SARS and other potentially devastating infectious diseases.

    The (D2OL) software is downloaded to your personal computer and given drug candidates to evaluate. Once your computer receives tasks to execute, it begins a candidate evaluation process similar to finding the right key to fit into a lock. Distributed computing technology enables the process of sending hundreds of thousands of possible keys to all computing devices participating in the network. This site manages the results generated and returned to the network once you connect again to the internet. As a user, no intervention is required and the software executes as long as it is turned on, even when disconnected from the Internet."

    What does this mean? Very simply, the program takes a protein from something like Ebola, SARS, Anthrax and attempts to match (through modeling) drug candidates against receptor sites on the protein. The software ranks how well each "candidate" "docks" to the protein and assigns it a rank. The software records how well the candiate docks to the protein and that is the information reported back to the server...among other things.

    Features include:

    • Ability to download up to 2000 WU's to ensure plenty of work for your no-netted/sneakernetted/bandwidth challenged crunchers.
    • Cache your work units (up to 2000) to send later
    • Modem friendly.
    • The client software allows you to force a WU upload at any time without stopping the client.
    • SMP is supported through the standard "two sep directory w/ different names" methodology.
    • Supported OS's
      Windows 98/2000/NT/ME/XP
      Mac OS X
      Solaris
      Linux


    Installation:

    The client is drop dead gorgeous and simple to use (it is a bit confusing at first until you understand what all the icons are for). it comes in two flavors, with and without a JVM (Java Virtual Machine), depending on whether or not your computer already has one installed/running. If you are an existing D2OL user, version 2.0 has an upgrade install option that most people report good success rates using when updating the client. If you are a new user, the New Install option is for you.

    The best way to install is to download the client (try downloading the version with the JVM first) and attempt to install. If you already have a JVM running (and you should know if you do), then the install will error out and you simply download the non-JVM package and install it. I haven't installed the Windows client, but the Linux version downloads "installDDOL.bin" (same name for both JVM/non-JVM client) and installs with "sh ./installDDOL.bin". Installing the non-JVM version where the JVM version is required will generate an install error. The reverse applies for installing the JVM version. Once downloaded and installed, the client will start after the installation routine quits.

    • Note - Knoppix does not require the JVM version to run but the other Linux distro's I've tried (Debian, Mandrake) require the JVM version.


    D2OL generates a unique ID # called a Node # for each install. D2OL will ask for your email addy during start-up. After entering your email addy, the program will begin Initializing itself, downloading 50 WU's (default #) and begin to work. At this time I recommend going to the D2OL site and registering.

    Registration requires that you specify your email address, select a username and password. After validating that information, you will be asked for the node# you just installed and then it will setup an account. An interesting sidenote is that when installing subsequent installs/nodes, D2OL does NOT automatically add them to your email address/account. The user needs to log back into their account homepage and ADD them to their account, even though they are tagged to the email addy at install. This is an extra step to get your clients adding WU's to your account, but it also adds the flexibility to delete nodes that are lost through disk crashes, bad installs, etc. At any rate, be aware of it. If after installing numerous clients you don't find your numbers climbing as fast as expected, you probably need to log in and add your nodes to your account.

    Client Operation

    GUI - Normal operation is to display the GUI along with all possible information shown. There are many toggles that can be thrown to disable the display of information as well as animations (a notorious CPU hog anywhere). The main display window, the Agent, can be minimized, hidden or stopped without affecting the D2OL engine itself.

    Command Line - Running from the command line is possible/supported. The client has numerous switches that can be set to control the amount of GUI shown or to turn off the GUI completely. CLI mode is reported to make no difference to production vs minimized GUI mode.

    Three negatives associated with this client

    1. Installation location is hardcoded into the working files of the client itself. IE - you install Node #12345 at /home/user, the location is hard coded into files so that the client will only startup in located in /home/user directory. If you installed under, say Knoppix for instance, in /mnt/hda4/user and then tried to copy the folder to /home/fred then the client will not run. This makes sneakernetting problematic for Linux. I'm not sure about Windows moves as I don't have the client installed under Win.

    2. The node # is also hard coded. This makes for interesting problems. Say you wish to wipe out a RH 8 install and put Libranet 2.8 on the same box and want to keep your same node number. In most DC projects, you simply enter your email or user ID and off you go,; not so in D2OL. You will need to copy the node.prp file (for safety's sake I always copy the entire directory) to a safe disk, install your new distro, install the D2OL client (which will generate a new node #), let it finish initializing, quit the client and then copy your old node.prp file over the new node.prp file. Convoluted yes, but at least you can keep your node # tied to a specific machine. Additionally, it is wise to reuse your node #'s as NOT reusing will leave you with multiple "dead" non-productive node #'s. The node.prp file does not just contain your node #. It is a derived file (hashed/encrypted/encoded) containing your node # and email addy so you simply cannot type in it without destroying it.

    3. Macintosh users take note - SMP does work on OS X, but due to "hard coded install locations", the fix is involved as the user must edit multiple files in the first install directory.

    Once you have setup your node(s), joining Tream Free-DC is also easy. Your user account homepage contains links to joining teams so it's easy to get your WU's tagged against Free-DC immediately. The client has no functionality to join a Team itself so visiting your homepage is a must.

    The D2OL website is a genuine joy to use and glean information from. There is a multi-page section devoted to understanding the client (take advantage of it as it teaches you a lot) (http://www.d2ol.com/software_support.html) and how to customize it for your preferences. For maximum effect, run with animations turned off, minimal information shown and run minimized. Additionally, it contains large amounts of data on the science of the project itself, a fleshed out FAQ, details on the Pathogens and Drugs being studied and an overall realtime Statistics page to view the total project info. D2OL has it's own supported Forum (active participation from project developers as well) with plenty of users available to answer questions.

    The stats are complete, updated constantly and pretty much realtime (MacNN also tracks D2OL here - http://teamstats.macnn.com/d2ol/stat...TID=24&page=s3). Stats by Team and by Member with Overall, Weekly and Daily production make charting progress a snap.

    Stats were not reset when v2.0 was released in September of 2003 so the leader field is pretty much set. The usual suspects are crunching this project with Anandtech, Dutch Power Cows, hardCOREware, Ars Frozen Yogurt and BIOHazard teams taking the top five positions. Team Free-DC is currently at #20 overall but produces at the #13 spot on the dailies.

    As usual, AMD rules the roost here. My machines performance is as follows:

    iMac G3 233Mhz - 9 WU/day - OS X 10.2.8
    G3 Mac @ 800Mhz - 34 WU/day - OS X 10.2.8
    Dual XP1800 (1.53Ghz) - 60+~ WU/day - Libranet 2.7 (Debian) and Knoppix
    XP2400 (2.0Ghz) - 80 WU/day - Knoppix

    Performance is, of course, dependent on use of the computer. I cache 3 days worth of WU's per machine ... just in case. Linux distro flavor seems to be irrelevant to production. D2OL likes a large L2 cache, larger the better.


    Interesting bits of minutae
    • The program switches between two programs (GridWin.exe and DockWin.exe) while running. "Nice"ing of a running process will be lost when the other program starts up.
    • GridWin.exe and DockWin.exe retain the .exe extension under *nix as well.
    • The program defaults to sending results every six hours from last update time.


    Summary:

    All in all, this client is a genuine pleasure to use. The client itself is very stable, contains lots of "winky-blinkies" to play with, gives maximum client control to the user and offers plenty of stats for the "gotta check every ten minutes" set. I did not use the previous versions of D2OL, but from what I've read, this client is a quantum leap ahead of previous generations in all aspects.





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  2. #2
    Fixer of Broken Things FoBoT's Avatar
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    mmm, i'll have to try it out, i'll put that 1.6Ghz P4 at home onto it
    Use the right tool for the right job!

  3. #3
    Target Butt IronBits's Avatar
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    Edited the Rank panel to show only d2ol
    renamed /sengent to /d2ol
    edited /d2ol/index.shtml
    edited /includes/navigation.html
    renamed /includes/nav-sengent.html to nav-d2ol.html
    same project, different name.

  4. #4
    Downsized Chinasaur's Avatar
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    Thanks to Moogie and IronBits. Would you mind pasting this in the D2OL section as well please?

    you da peeps
    Last edited by Chinasaur; 10-11-2003 at 12:25 AM.
    Agent Smith was right!: "I hate this place. This zoo. This prison. This reality, whatever you want to call it, I can't stand it any longer. It's the smell! If there is such a thing. I feel saturated by it. I can taste your stink and every time I do, I fear that I've somehow been infected by it."

  5. #5
    Target Butt IronBits's Avatar
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    Done. Thanks for the write up Chinasaur!

  6. #6
    Fixer of Broken Things FoBoT's Avatar
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    i downloaded the full/with JVM support windows version and installed to W2K3 Server this morning, no problems at all

    set the cache to 90 and let it go, no problems so far

    p.s. did they add a way to remove old nodes yet? i don't really have 10 nodes, some of those are very old and they certainly don't exist anymore
    Use the right tool for the right job!

  7. #7
    Target Butt IronBits's Avatar
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    Originally posted by FoBoT
    p.s. did they add a way to remove old nodes yet? i don't really have 10 nodes, some of those are very old and they certainly don't exist anymore
    That would be nice! So many projects, so few boxen

  8. #8
    Peaches Moogie's Avatar
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    You're welcome. Glad to help.





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  9. #9
    Downsized Chinasaur's Avatar
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    FoBoT,

    Log into your homepage and you can delete them from a browser based node management system.

    Agent Smith was right!: "I hate this place. This zoo. This prison. This reality, whatever you want to call it, I can't stand it any longer. It's the smell! If there is such a thing. I feel saturated by it. I can taste your stink and every time I do, I fear that I've somehow been infected by it."

  10. #10
    Fixer of Broken Things FoBoT's Avatar
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    Originally posted by Chinasaur
    FoBoT,

    Log into your homepage and you can delete them from a browser based node management system.

    oh, now i see it, they added a column on the end [del] , ok, thanks

    D'oh!

    i got this message
    There was an error deleting 7363 from your member account.
    You cannot delete a node that already has statistics
    so, this isn't going to be much help to those of us that do installs on various pc's and then wipe out the install and reinstall later, we will still continue to pile up "nodes" over time
    Use the right tool for the right job!

  11. #11
    Downsized Chinasaur's Avatar
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    Yeah One of the big negatives of this project.

    I've got a copy of my node.prp files so I can switch machines, blow away directories but restore my node #

    Which is a sub-optimal answer but .....
    Agent Smith was right!: "I hate this place. This zoo. This prison. This reality, whatever you want to call it, I can't stand it any longer. It's the smell! If there is such a thing. I feel saturated by it. I can taste your stink and every time I do, I fear that I've somehow been infected by it."

  12. #12
    Fixer of Broken Things FoBoT's Avatar
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    it isn't a huge problem, just annoying, i see now that their stats are all based on unique nodes, so if they let you delete a node, it would remove the stats

    just an accounting thing
    Use the right tool for the right job!

  13. #13
    Fixer of Broken Things FoBoT's Avatar
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    i like the "status" - Manual Update feature of the client

    i checked it tonight and it had 6 "tasks" cached (why didn't it just send them?) , so i hit the manual update button and it uploaded them, the interface for the status is well done
    Use the right tool for the right job!

  14. #14
    Downsized Chinasaur's Avatar
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    FoBot,

    Normal upload is every six hours...the manual is nice feature..I tend to hit it every three or so to watch the stats
    Agent Smith was right!: "I hate this place. This zoo. This prison. This reality, whatever you want to call it, I can't stand it any longer. It's the smell! If there is such a thing. I feel saturated by it. I can taste your stink and every time I do, I fear that I've somehow been infected by it."

  15. #15
    Senior Member Rodzilla's Avatar
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    Can you change the upload time? Like every 30 min... or every 1hr?

  16. #16
    www.amdusers.com
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    Rodzilla,
    In Config.prp located in C:\Program Files\SengentD2OL\D2OL\res change HandshakeDelay=360 (6=hrs) to what ever number you want. Use Notepad to edit the file.

  17. #17
    Administrator PCZ's Avatar
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    Everytime I have changed the handshake delay from the default 6 hours it has changed itself back after communicating with the mothership.

  18. #18
    Senior Member Rodzilla's Avatar
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    Same here... It keeps changing back...

  19. #19
    www.amdusers.com
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    Um, me too. Looks like it needs a script. I wonder if Jeff Gilchrist could do something like he has D2OL Daddy to force it to IDLE priority?

  20. #20
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    Hiding the client window

    Just a tip. If you are using the client windows instead of the GUI one because it uses less memory then you can hide the windows client. How?

    The easiest method to run without a visible DOS Box is to use the Windows Task Scheduler to start the program at boot. The following instructions work in Win2K and WinXP. In Win2K you can start the Task Scheduler by looking in the Control Panel or by

    Start>Programs>Accessories>System Tools>Scheduled Tasks

    1. Click on "Add Scheduled Task" to start the wizard.
    2. Browse to the program "D2OL.exe".
    3. Select "When my computer starts".
    4. Fill in the user name and password for logging onto that computer.
    5. Check the box for "Open Special Properties," then click "Finish".
    6. Click the tab for "Settings".
    7. Uncheck the box for "Stop the task if it runs ...".
    8. Click "Apply" and "OK".

    The next time you boot the computer, the D2OL program will begin automatically and invisibly. If you need to stop the program, use the Task Manager to end D2OL.exe.
    Text updated to D2OL case. Only tested in another DC project and it works.

    Source

  21. #21
    Administrator Dyyryath's Avatar
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    Thanks, Moogie. This was just what I needed to get started with D2OL.
    "So utterly at variance is destiny with all the little plans of men." - H.G. Wells

  22. #22
    Speaking of D2OL Daddy - here's where to get it

    D2OLdaddy

    makes D2OL behave better

  23. #23
    Member rbutcher's Avatar
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    I saw the note about DockWin.exe & GridWin.exe regularly being relaunched with normal priority instead of lowest priority.
    For Linux I wrote a (crude) 1-line shell script to reset it to 19 :-

    renice 19 `ps -e | grep .*Win.exe | grep -o "[0-9]* p" | grep -o "[0-9\]*"`

    just create a 1-line textfile called e.g. switchpid.sh and make it executable.

    Create an entry in your cron file to execute this say every 5 minutes and forget about it.
    Crontab entry :-
    -0,5,10,15,20,25,30,35,40,45,50,55 * * * * /wherever/D2OL/switchpid.sh

    Any better way of achieving this I'd love to hear about...

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