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MPI Program suddenly slows to a crawl
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odeSolver
Tux's lil' helper
Tux's lil' helper


Joined: 11 Jul 2010
Posts: 84
Location: NJ, USA

PostPosted: Sun Oct 13, 2013 2:51 am    Post subject: MPI Program suddenly slows to a crawl Reply with quote

Hi. I managed to write a Gentoo Linux MPI program in C which was chugging along nicely. I have a BASH file which is submitting executions. Each execution was running along nicely, spitting out 100,000 line data files in about 7 minutes each. Suddenly, during one of the jobs, it seemed to stop. Closer investigation reveals that it is now generating about 100 lines of data every minute - that's quite the slowdown. What can cause this? Where do I begin looking to get this running again?

Note that we do not have a job scheduler (or whatever they're called) - and there is no option to install one.

Edit: Oh, and I checked that there is still enough disk space (see http://forums.gentoo.org/viewtopic.php?p=7338412) - there's plenty.
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Depserately needs help learning Gentoo Linux in order to use a 32-node cluster for my master's thesis in mathematics.
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Akkara
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Joined: 28 Mar 2006
Posts: 5173
Location: &akkara

PostPosted: Sun Oct 13, 2013 3:16 am    Post subject: Reply with quote

Is it processing very small numbers (decaying exponentials, convergence to zero type of stuff)?

On some processors, the hardware floating-point doesn't handle "denormal numbers", so when one is encountered, it traps out to the OS for emulation. If many numbers are denormal, this would slow things down a lot.

(Denormals are different from 0 but smaller than the minimum exponent can represent. "Small" means less than (in magnitude) 2^-1022 for double; 2^-125 for float.)

A remedy for the slow-denormals problem - if less precise small-magnitude calculations are acceptable - is to turn on the flush-to-zero option in the floating point control word. I don't recall offhand how. Post back if you think this is the problem you're having; or search for it.
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odeSolver
Tux's lil' helper
Tux's lil' helper


Joined: 11 Jul 2010
Posts: 84
Location: NJ, USA

PostPosted: Sun Oct 13, 2013 3:28 am    Post subject: Reply with quote

I don't think that's the problem. The program is solving a second order ODE with values that fluctuate between -1 and 1.

I think it could be a load problem. I suspect, some other student - besides me, that is - is not spending his (or her) Saturday night out chasing girls (or guys - or whatever they prefer). And this despite the nice weather here. Who the heck spends their Saturday night programming (when I have a thesis to work on)?

I found the top command and see that someone has 16 jobs sitting above mine on one of the processors! :(
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