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Thread: Quick question - work unit expired

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    Quick question - work unit expired

    Hey guys,

    work unit has expired, how can I get a new one? It's just sitting still not doing anything. Using the SMP client. Also, how do I set it up to run automatically in the background, because at the min I have to run fah.exe every time and have a dos prompt window open in the task bar. Bit annoying.
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    Does he need a reason? Funkstar's Avatar
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    Re: Quick question - work unit expired

    There should be an option in the setup to install it as a serice. I've not had much luck with that in the past so just run it manually.

    The client should eventually decide to go fetch a new work unit. It does take a while for it to decide this.

    After a re-boot on thursday I forgot to re-start the client so the work unit had expired over the weekend. I just left it running while I sorted out some things in the flat and it had found a new one by the time I looked at it again.

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    Seething Cauldron of Hatred TheAnimus's Avatar
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    Re: Quick question - work unit expired

    SMP client can't run in as a service apparently.

    Its bizzare programming, launching child proccesses!? Threads, AppDomains, Proccesses, why the high isolation levels (and reduced intercommunication speed).

    I'm sure the maths going on is clever, but their not striking me as good developers.

    Anyway, i have that bug if i try to run two instances of the SMP client, from seperate folders, with different machine IDs too note.
    throw new ArgumentException (String, String, Exception)

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    Comfortably Numb directhex's Avatar
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    Re: Quick question - work unit expired

    Quote Originally Posted by TheAnimus View Post
    Its bizzare programming, launching child proccesses!? Threads, AppDomains, Proccesses, why the high isolation levels (and reduced intercommunication speed).
    it's MPI code, behaving the way MPI does on windows

    there's a reason talk of windows cluster edition receives giggles from the parallel compute community

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    Re: Quick question - work unit expired

    You could always delete the Work folder that should get you back to square 1 and it should ask for another unit.

    On a slightly different note if a work unit expires and it is almost finished it can carry on to the end and still submit, I had one a couple of weeks ago that expired at 96% but carried on, finished the unit and submitted successfully. Not sure if it carries on for a certain time after expiration; looks and says your at 90 odd % so decides to let you finish or perhaps it just keeps working until you close the window?

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    Re: Quick question - work unit expired

    Quote Originally Posted by directhex View Post
    it's MPI code, behaving the way MPI does on windows

    there's a reason talk of windows cluster edition receives giggles from the parallel compute community
    Pure Mpi.NET <-- from my quick reflector i can't see them using that. (its the MPI i'd use for a .Net app).

    Really didn't think that was the way it should behave.

    This is hardly a cluster, its 4 sodding threads. WCCS isn't what we're talking about here (which frankly, i don't see the point of).
    throw new ArgumentException (String, String, Exception)

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    Re: Quick question - work unit expired

    Deleted work folder, still saying unit deadline passed and nothing yet. Might leave it for the rest of the day. Cheers guys.
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    Re: Quick question - work unit expired

    If anyone knows a bit of windows stuff, would it be possible to make a .bat file, put it in the startup folder, that basically ran fah.exe but then hid it from the task bar?
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    Re: Quick question - work unit expired

    Quote Originally Posted by TheAnimus View Post
    This is hardly a cluster, its 4 sodding threads. WCCS isn't what we're talking about here (which frankly, i don't see the point of).
    4 sodding threads using a well respected, off the shelf, peer reviewed, journal-published molecular dynamics app. fah.exe is a wapper and queue manager, which handles downloading of work units, and invocations of mpirun. mpirun is most definitely what you'll find on a cluster.

    the options are:
    1) port GROMACS to a cross-platform threads mechanism such as pthreads or openmp. then try to have it accepted by the chemistry community as repeatably producing equivalent results
    2) statically compile GROMACS against a local-only MPI library, then just use clusteresque MPI threads

    if you want to port GROMACS to openmp, or write your own molecular dynamics code, and have the end result be accepted in the scientific community as worth using within, say, 5 years, be my guest

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    Re: Quick question - work unit expired

    Quote Originally Posted by directhex View Post
    4 sodding threads using a well respected, off the shelf, peer reviewed, journal-published molecular dynamics app. fah.exe is a wapper and queue manager, which handles downloading of work units, and invocations of mpirun. mpirun is most definitely what you'll find on a cluster.

    the options are:
    1) port GROMACS to a cross-platform threads mechanism such as pthreads or openmp. then try to have it accepted by the chemistry community as repeatably producing equivalent results
    2) statically compile GROMACS against a local-only MPI library, then just use clusteresque MPI threads

    if you want to port GROMACS to openmp, or write your own molecular dynamics code, and have the end result be accepted in the scientific community as worth using within, say, 5 years, be my guest
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    Re: Quick question - work unit expired

    Quote Originally Posted by Zak33 View Post
    TOTALLY LOST....TOTALLY!!

    there are, essentially, two ways to write a parallel app:

    • shared memory, where multiple threads of a single application all share one chunk of RAM
    • distributed memory, where different *processes* (i.e. separate copies of a .exe file) have their own local chunks of memory, and pass short messages to each other over some kind of network connection


    typically, shared memory apps are much easier to write, but when you're talking about serious research computation, you're talking MANY-way jobs (e.g. 32 or 64-way), and the cost of putting 64 proper cores in 1 box (and using shared memory) is a LOT higher than the cost of spreading the cores across lots of computers and writing a distributed memory app instead

    as a result, much as it's harder to do, MPI programming is MUCH more popular amongst the scientific community (as the kit to run it is roughly 3x cheaper)

    f@h's "smp" units are calculated by the "a1" core, which is essentially a pre-built copy of a real-world chemistry app called GROMACS. GROMACS is a *distributed memory only* app - it works by launching lots of copies of itself, and having those copies pass small messages to each other to collaborate. it's usually used on clusters. infact, i have a copy right here:
    334M /home/zuse/system/software/gromacs-3.3

    so, in order to use GROMACS as a code for performing calculations, the f@h team need to somehow make it work without a cluster. this is actually relatively easy: compile it as normal, but when you use the message passing app launcher (mpirun), rather than giving it a list of different machines to run on, tell it "this machine plz", multiple times. that way, when it invokes the parallel app (FahCore_a1.exe), rather than running 1 copy on 4 different nodes and having them talk over a network, it runs 4 copies locally and those local copies talk over the "virtual" network found in all operating systems

    the problems people experience with the smp client on windows are a direct result of the version of the message-passing library the developers use. essentially, it's a silly library that demands silly things (and i expect it's the microsoft library, MS-MPI, found on microsoft's windows-for-clusters)

    the alternative is to convert GROMACS to shared memory. this is, in many cases, like converting water into wine. even if it works, the scientific community (the *real* users of GROMACS and f@h) need to be convinced that this "port" actually produces the same science as the regular app. and experience says chemists are highly resistant to change. or, alternatively, write some new code from scratch - which carries even tougher "credibility" penalties

    perhaps a different MPI library on windows would make the app better behaved, perhaps not. but the complaint about the multiple processes is entirely missing the point about how parallel apps are written. and the problems with running the smp client don't exist on *nix, which is the real home of MPI applications

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    Seething Cauldron of Hatred TheAnimus's Avatar
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    Re: Quick question - work unit expired

    I think your missing my point.

    What percentage of computers that aren't mission critical (ie likely to be able to have a fah client running on them) run a POSIX unix system, and what run NT5 or later, heck what have .Net 2 already installed.

    Now given that potential for computer power, shouldn't effort be made to allow it too take advantage of that? Play well with it?

    Its simple to say, in massive custom clusters, a custom, heavily thinned down OS is best, things can be statically linked etc, which are bound to be faster, because theres no need for change.

    So, i can't complain about this because the scientific community wouldn't accept a different version happily. Great, because there are some luddites opposed to testing, lets make no progress. Even thou its ok to run it on a different platform?

    I don't see who's drawing this line, saying its Ok to run on x's OS, but not if you actually take advantage of it.

    So lets right off that hudge percentage of multiproccessor PCs that are already flooding the windows desktop market.

    Also did you even look at that MPI link i gave?
    throw new ArgumentException (String, String, Exception)

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    Re: Quick question - work unit expired

    Quote Originally Posted by TheAnimus View Post
    I think your missing my point.

    What percentage of computers that aren't mission critical (ie likely to be able to have a fah client running on them) run a POSIX unix system, and what run NT5 or later, heck what have .Net 2 already installed.

    Now given that potential for computer power, shouldn't effort be made to allow it too take advantage of that? Play well with it?

    Its simple to say, in massive custom clusters, a custom, heavily thinned down OS is best, things can be statically linked etc, which are bound to be faster, because theres no need for change.

    So, i can't complain about this because the scientific community wouldn't accept a different version happily. Great, because there are some luddites opposed to testing, lets make no progress. Even thou its ok to run it on a different platform?

    I don't see who's drawing this line, saying its Ok to run on x's OS, but not if you actually take advantage of it.

    So lets right off that hudge percentage of multiproccessor PCs that are already flooding the windows desktop market.

    Also did you even look at that MPI link i gave?
    i looked at the link, and thought "well, that's great, but GROMACS is very much unmanaged c"

    should f@h be easier to use on windows? yes. but just because lots of business desktops have windows on them, doesn't mean the people do this kind of research (and write these kinds of apps) really care. hell, GROMACS is cutting edge - it uses C, not F77. would a better mpi library fix the issues? probably, but it might be something as simple as licensing issues that forced a particular selection.

    if you're suggesting that a new, windows-only, win32threads molecular dynamics app should be written, then by all means - but it won't gain any traction from researchers who would be left without the means to test the app, nor produce reproducible scientific results that journals etc would trust.

    there are alternative volunteer computing projects, some of them even written using a managed layer, but f@h is molecular dynamics, which means using trusted molecular dynamics code to be of worth

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    Re: Quick question - work unit expired

    Quote Originally Posted by Dreaming View Post
    If anyone knows a bit of windows stuff, would it be possible to make a .bat file, put it in the startup folder, that basically ran fah.exe but then hid it from the task bar?
    the startup folder certainly yes. the hidden from the taskbar certainly yes. had a quick go tonight but wanted to find a descent freeware hide stuff from taskbar app rather than the shareware 30day then pay the good ones seem to be so ill leave that for another time.

    very doable though, and when you factor in FahMon that setup would do me
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    Re: Quick question - work unit expired

    Animus...I salute you for arguing with, or even understanding Hex

    Hex...you know too much

    I shall fold on XP and fight with it when it goes wrong again!

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    Re: Quick question - work unit expired

    Quote Originally Posted by Zak33 View Post
    Animus...I salute you for arguing with, or even understanding Hex

    Hex...you know too much

    I shall fold on XP and fight with it when it goes wrong again!
    That is a bit pessimistic we all know that F@H SMP doesn't like Windows but still we could live in hope of no problems rather than in the resignation that failure is an unavoidable outcome.

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