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Thread: Easy Ubuntu Clustering

  1. #21
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    Re: Easy Ubuntu Clustering

    rereading previous posts it seems I overlooked this argument I've failed to notice since I thought we're talking headless compute nodes.
    Quote Originally Posted by ajt View Post
    ....
    but Sarge and Etch were crude on the Desktop compared to Ubuntu 6.06...
    ....
    So just out of curiosity.
    Tony are you really implying an X server / client in the SSI nodes ? Aside from the unnecessary cost this would cause major problems as all GPU's should be of the same brand. Considering you'd only install the client X libraries on the nodes and use a remote X > XDMCP ( the machine which renders the image on screen / has display is the X server ) then still it's nearly impossible since kerrighed doesn't support LVS ( common cluster IP address ) that the X client could use to communicate with a standalone X server > could be handy for a multiseat system .
    I have some experience with OpenGL clusters, and that is a completely different topic in all aspects ( would be nice though ).....
    In any case, the easiest way to implement a GUI is a web-based one tied to a job scheduler.

    Quote Originally Posted by tinkertim View Post
    .
    ...
    However, the jump to 2.6.29 would make it much easier.
    in all aspects ... kerrighed being part of the kernel instead of a module, changes things drastically....

    Quote Originally Posted by tinkertim View Post
    .
    For a long time many people used the word 'commercial' to refer to non-free software which now causes a lot of confusion and mistrust.

    Kerrighed has a very good, very honest and very transparent business model. Use / share / modify the software any way you like .. if you get stuck, paid support and development is available.

    You will always have those who are a little over-sensitive to this kind of arrangement. For instance, someone might ask for help to implement thread migration and get a reply that they'll be better off hiring Kerlabs (which they would be). Then, the person will start screaming 'baitware' or worse.
    I feel I need to clarify my statement on this.
    The amount of money involved to develop thread migration ( the estimate I got from Kerlabs ) is considerable ( for a person ) and enough to buy myself a nice house.....
    Knowing that its very hard to turn OSS into something commercial / proprietary, one could only try to commercialize a web-based front-end / scheduler....

    Quote Originally Posted by tinkertim View Post
    I don't know if you'd be able to find a MOTU that would be interested in keeping up with Kerrighed, but surely nothing is preventing someone from making it available via PPA.
    I doubt an ubuntu MOTU will be interested/has time so yes PPA is a valid option...

    Jan
    democracy : 2 wolves and a sheep voting on "what's for dinner"
    i am self-employed, and my views reflect the electrical charges held between many simultaneously firing synapses... or is that synapsi?
    http://3d.uk.to

  2. #22
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by kvk View Post
    This is wonderful information- thanks for posting it. I've been interested for a while now in constructing a small cluster (8-16 nodes) for running ecological models, but both my hardware abilities and programming need a bit more development. This will be great stuff to read through!
    Hello, kvk.

    I'm a biologist, turned bioinformatician, and there are lots of people just like me and you building our own DIY Beowulf clusters

    The real essence of this thread is to try and make it as 'easy' as possible for Ubuntu users to build this type of Beowulf cluster. I'm sure you already know that it can be quite a steep learning curve if you've never done anything like this before. However, there is nothing magic or particularly difficult about putting the hardware together. To give you a flavour of this approach, there is a chemical modeling cluster called 'COBALT' (Computers On Benches All Linked Together):

    http://www.cobalt.chem.ucalgary.ca/

    We do some of this type of quantum chemistry modeling under Ubuntu

    The Kerrighed links I posted recently give examples of setting up DHCP and PXE booting of cluster nodes. I'm using this to PXE boot eight of our compute nodes to experiment with Kerrighed. Anyway, thanks for joining the discussion.

    Bye,

    Tony.

  3. #23
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by altonbr View Post
    Here's an amazing article on how to turn Xboxs into a Beofwulf cluster. Looks inherently more simple than I thought.

    http://www.anandtech.com/linux/showdoc.aspx?i=2271&p=8
    Hello, altonbr.

    Connecting the boxes together is easy - Getting them to do something useful is the tricky bit

    Actually, I'm quite interested in clustering PS3's...

    Not this one:

    http://www.engadget.com/2007/08/11/s...arhawk-mayhem/

    More like this:

    http://gravity.phy.umassd.edu/ps3.html

    Bye,

    Tony.

  4. #24
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by djamu View Post
    [...]
    But let's not get into any kind of flaming, IMO I really think ubuntu is a great desktop distro..., just my personal opinion..
    Hello, Jan.

    Good to know you like Ubuntu

    Quote Originally Posted by djamu View Post
    [...]
    isn't PMI a rebranded OpenMOSIX ?
    It's a continuation of the project to port openMosix to the 2.6 kernel.

    Quote Originally Posted by djamu View Post
    [...]
    True, but since OpenSSI lacks the funding of the XtreemOS consortium ... chances are little it will emerge again..
    http://www.xtreemos.eu/overview/plon...43452/partners
    [...]
    In my (now obsolete) 'biobuntu' blue-print, you will see that I'm also interested in XtreemOS as well as Kerrighed:

    https://blueprints.launchpad.net/ubuntu/+spec/biobuntu

    Quote Originally Posted by djamu View Post
    [...]
    [...]
    But I'm a little afraid the title of the thread is not well chosen > I'll elaborate .. quite a lot of people reading this have will have a hard time grasping the type of cluster were discussing. To me it's obvious were talking (headless) HPC clustering...
    In other words this thread is prone to pollution as soon as people start suggesting for example RHEL or SAN failover mechanisms as an alternative...
    I disagree - I've got more than 26 years experience of 'parallel' computing but I obtained most of my computing (and image analysis) experience working as a biologist. I now work as a bioinformatician.

    There are lots of people like me working in bioinformatics: A common thread in discussions like this is that it is MUCH more difficult to grasp the scientific questions being asked than it is to build a Beowulf. The technology is a means to an end. The draconian 'lock-down' policies of some highly centralised IT departments lack the flexibility to allow R&D approaches to be used by scientists who often know more about the technology than people trained in provision of IT for the 'enterprise'.

    BTW, That's not a criticism of people providing IT for the 'enterprise'. it's an observation, borne of my own experience, that IT for science and IT provided for the 'enterprise' have completely different objectives. My intention in starting a thread in this forum is to try to draw together opinions and help from other people with similar objectives to my own. I agree that it's important to keep the topic clear: It is how we make it 'easy' to cluster Ubuntu systems in order to use the aggregate resources of many computers to solve one problem. This is the essence of Beowulf:

    http://www.beowulf.org/

    Bye,

    Tony.

  5. #25
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by kloplop321 View Post
    I would simply be interested in using 3 old computers running as a cluster to slightly speed things up and add some elbow room.
    Hello, kloplop321.

    I think that using a few old computers to learn about Beowulf clusters is fine, but at the end of the day they are still old computers and there is an overhead involved in communication between the compute nodes in a cluster. The first rule of 'parallel' computing is to determine what can be done independently by the nodes: That's where you gain an advantage.

    Quote Originally Posted by kloplop321 View Post
    I have tried some live CD's but my old laptop's LAN card isn't supported(odd), and I would need to run a fan control program on one of the computers because it's fan control is not automatic from the bios(I find that stupid)
    the last one is a pentium MMX machine.
    Maybe this would be a good time to learn how to compile the Linux kernel?

    It's not that difficult the second time you do it, but the first time takes a bit longer

    Check the Kerrighed links I posted earlier in this thread for more info.

    Thanks for joining in.

    Bye,

    Tony.

  6. #26
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by altonbr View Post
    It's already in there
    Hello, altonbr.

    Why not add things like this to the Wiki:

    https://wiki.ubuntu.com/EasyUbuntuClustering

    Bye,

    Tony.

  7. #27
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by djamu View Post
    Hello, Jan.

    The BIG difference is using SIMD/MIMD instead of Von Neumann Arhitecture:

    http://en.wikipedia.org/wiki/Von_Neumann_architecture

    SIMD (Single Instruction Multiple Data) is fast, but extremely limited. I used a 9216 SIMD processor array for image analysis some time ago (CLIP4R). There is a brief summary of this type of processor here if anyone is interested:

    http://homepages.inf.ed.ac.uk/rbf/CV...ERATOS/iii.htm

    However, we concluded that the advantages of using 'exotic' processor architectures like this does not outweigh the difficulty of programming them, or the 'corner-turning' problem of actually getting images into the SIMD processor array. Our CLIP4R was a very interesting machine, but its CPU boards ended up being made into wall clocks. Sad, but well worth the lessons learned. The host controller for the CLIP4R was a pdp11/34, so you can tell how long about this was (1986). I replaced the pdp11 with a Vax 750, which had less than 1MIP integer performance (a MIP is defined as an integer perfomance of one million VAX780 instructions per second).

    Enough nostalgia for now - This has little to do with Ubuntu clustering, but might rectify some misunderstandings about what 'parallel' computing involves. What we are talking about in the Easy Ubuntu Clustering blue-print, and this thread, is using a collection of Von Neumann architecture processors in different computers as if they were one large SMP (Symmetric Multi-Processing) computer. This is the SSI (Single System Image) approach to parallel computing used by openMosix, openSSI and Kerrighed. It's also the approach taken by Donald Becker, who invented the Beowulf cluster at NASA and commercialised it:

    http://www.scyld.com/home.html

    [Scyld, was Beowulf's companion in the Beowulf poem]

    http://en.wikipedia.org/wiki/Beowulf

    Bye,

    Tony.

  8. #28
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by meatpan View Post
    The scope of EasyUbuntuClustering is very wide, which might be why the discussions on this thread have been so broad.

    Is it realistic for an 'easy' clustering solution to cater to inexperienced developers, offer portable environments via VM's, provide automated load-balancing, and still maintain high QoS?

    These are great goals to shoot for, but IMO you will likely have more success if you just pick one or two of the major features.
    Hello, meatpan.

    I found the previous discussions dispersed over several different forums difficult to follow, and repeating many of the same questions. Yes, the discussion so far has been quite broad but, as we realise what people are actually interested in, I think the discussion will become more focussed.

    Quote Originally Posted by meatpan View Post
    I can't comment much on the process migration (automated load balancing), since it's been more than 4 years since I've used OpenMosix. These features typically require savvy system admins, and configuration problems can be difficult to diagnose.
    Not really - I run a 90-node openMosix system and I'm a biologist

    Quote Originally Posted by meatpan View Post
    Automated deployment of VM's on a cluster or grid (not going to get into a definition war here. I'm referring to a grid as a federated assembly of heterogeneous clusters) is a hot topic that industry giants such as VMware (EMC), IBM, Microsoft, and Amazon are investigating. There are numerous technical subtleties relating this topic, and a logical solution might be to create a specific flavor of debian or ubuntu server that is adapted to hosting the popular VM's. This is especially relevant considering the CISC vendors have product roadmap plans that address common VM bottlenecks.
    Hmm... 'cloudy' today?

    The BIG problem with VM's is that they are designed to be using for HAC (High Availablility Computing) not HPC (High Performance Computing). It's not HPC to virtualise instances of e.g. Ubuntu then merge them again into a 'virtual' SSI. It's a way of making your IT provisioning resilient and platform-independant. Nothing wrong with that, if you're an ISP...

    Quote Originally Posted by meatpan View Post
    I admire your efforts to approach this complicated technical issue, and my only suggestion is to consider narrowing your scope a bit.
    Thanks - The technical aspects are really not that difficult, but the advantage of packaging up Kerrighed for Ubuntu would make it a lot easier!

    Bye,

    Tony.

  9. #29
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by tinkertim View Post
    Its not just a question of building, its how the kernel is built (i.e. using the Debian / Ubuntu patching and build system). The current Kerrighed 2.6.20 kernel (the way its patched and built) would make this problematic.

    However, the jump to 2.6.29 would make it much easier.
    Hello, tinkertim.

    I'm a bit confused by what you say about patching: The 'patch' program is the same under Debian and Ubuntu, and the Kerrighed patches are relative to the 'vanilla' kernel sources for 2.6.20. The kernel Makefile includes a 'deb-pkg' target, which has nothing to do with the Debian or Ubuntu patches to their kernels. I built and installed Kerrighed kernel debs under Ubuntu 6.06 using only the 2.6.20 sources and kerrighed patches.

    Quote Originally Posted by tinkertim View Post
    I remain subscribed to the OpenSSI lists. Once in a while you'll see a flurry of activity, then radio silence for a few months. I'm still a big fan of the project, I think it will continue to advance for years to come. Its one of those projects where you need a solid block of time to actually do anything useful, so I'd imagine the devs devote what they can to it.
    I've followed openSSI developmenmts for years, and I tried quite hard to get openSSI running, to use as a replacement for openMosix, but gave up in the end.

    Quote Originally Posted by tinkertim View Post
    [...]
    I don't know if you'd be able to find a MOTU that would be interested in keeping up with Kerrighed, but surely nothing is preventing someone from making it available via PPA.
    OK, I'll take that as you volunteering to help me do it

    Bye,

    Tony.

  10. #30
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    Re: Easy Ubuntu Clustering

    Quote Originally Posted by crazy___cow View Post
    In the next month I'll try to setup a small cluster (using kerrighed or mosix) to research purpose (http://afni.nimh.nih.gov/afni). I have two dell poweredge 2900 monster (2cpu x 4 core) and several "old" dual CPU Xeon 3Ghz. The first idea is to use ubuntu hardy with a custom kernel (2.6.20 for kerrighed or 2.6.28 for mosix (it's free for researchers)). I think that it'will be a tricky job patching the kernel (with 64 bit support and all the modules to load onto pe2900 and others pcs)...but I'll try to do it, because ubuntu/debian is the most easy and powerful distro to use, configure and administrate.
    Hello, crazy___cow.

    Be very careful how you interpret "free for researchers" - I looked into this too, and the deal is you are given one 'free' snapshot of MOSIX2 kernel patches plus binaries of the MOSIX2 utilities. The snapshot is the current release, which is good, but you have to pay $1,000 per year to get updates and you don't get any sources other than the kernel patches. It depends what your objectives are. MOSIX2 looks very good, but it's not FLOSS. That might not matter to everyone, but it matters to me.

    Bye,

    Tony.

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