Any ideas for a Beowulf Bigadv cluster?

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Any ideas for a Beowulf Bigadv cluster?

Postby thatsmychin » Fri Apr 15, 2011 6:55 am

From what I've read, it seems that bigadv is not really working now on the linux client. Even if I'm uninformed it doesn't matter...I'm looking at future builds. I'm slightly informed on how a beowulf cluster could work, but I'm wondering if anyone has any input on running bigadv on a something like that. Before anyone tells me to man up and buy an i7 975, I already have two idle AM3 mobos with RAM and PSU's, but no CPU's. So I'm wondering what I could do with 3 or 4 Athlon II X4's on some kind of a cluster...which I don't know much about. Is it possible? What fun to add a client to the mix as funds allow! I'd assume that 12+ cores would be able to kick out some bigadv WU's...just hoping that someone has some input for me.
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby gwildperson » Fri Apr 15, 2011 7:12 am

Support for cluster computing has never been part of the client that FAH distributes. Search this forum and you'll find that question has been asked and answered many times.
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby thatsmychin » Fri Apr 15, 2011 6:36 pm

The question has been asked once...maybe twice and never answered. This is why I asked that no one flat out tell me to just purchase a single system. Search the forum before you shut down a thread/discourage others from weighing in.

*Turns to the more reasonable and tactful members of the forum* From what I understand a beowulf setup acts more like a single system and not a cluster of workstations which is why it seems plausible. Those of use with higher end hardware laying around might be able to get a piece of that bigadv pie without breaking my meager bank account (or my marriage).
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby Grandpa_01 » Fri Apr 15, 2011 7:26 pm

Hi thatsmychin

The question has been answered before but the answer is a little foggy in this old brain. I will try to answer this to the best of my ability which is not that great. FAH does not work very well with Clusters due to the communication lanes between computers 2 or more computers cannot communicate with themselves anywhere near as fast as cores on a single chip can and FAH has to use these slow lanes to communicate with the different CPU's by the time FAH send's instructions to one CPU, the previous instruction given to another CPU on another machine has already been completed and is waiting to notify FAH what the results were so it can assign the next step. In all allot of time is spent on waiting to transfer information therefore allot of wasted CPU cycles. I hope this answers your question that is the best I can remember. Perhaps someone else can explain it better.
Image
2 - SM H8QGi-F AMD 6xxx=112 cores @ 3.2 & 3.9Ghz
5 - SM X9QRI-f+ Intel 4650 = 320 cores @ 3.15Ghz
2 - I7 980X 4.4Ghz 2-GTX680
1 - 2700k 4.4Ghz GTX680
Total = 464 cores folding
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby bruce » Fri Apr 15, 2011 7:54 pm

Grandpa_01 has an excellent memory.

WUs are large blocks of computation which only need to be synchronized rarely. They can be assigned as uniprocessor assignments to each of the nodes in a cluster as independent machines or to individual donor's machines. Each WU contains an entire protein. If you were assigned half of a protein (as in the case of -smp on a duo) you cannot process more than one step of that half-protein without knowing what changed in the other half of the protein during the same timestep. Breaking up a protein into fractional parts as in SMP assignments is severely limited by the need to constantly interchange a lot of data but it does allow for cooperative processing at the expense of a huge amount of data interchange.

Clusters work well as a single system when portions of a single process consist of relatively large computation blocks that need relatively rare synchronization. When working on a fraction of a single protein from a single SMP assignment, FAH has relatively small computation blocks that need constant synchronization. In a cluster, network latency is a huge impediment to getting anything done on SMP assignments. Latency in the interchange of data between cores is manageable but shows up when something like the GPU client delays a single thread.

For that reason, there is no FAH client that is designed to run on clusters. FAH, itself is a massive cluster, and each of us represents one or a few nodes, but you can't subdivide the work designed for a single node.
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby thatsmychin » Fri Apr 15, 2011 8:52 pm

Thanks for taking the time to explain it. I'll admit I didn't exactly know what's going on under the hood of these WU's. I'll go ahead and eat crow, but in my defense I read every discussion on these forums relating to beowulf clusters. However, it looked like there is a defunct fah community forum that was linked to a lot. I'm assuming a majority of the beowulf discussion took place there.
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby bruce » Fri Apr 15, 2011 9:03 pm

Probably.

For those who have been around FAH for long enough, the two forums fuse in eveybody's memory -- and the life of the defunct forum represented more than half of that fused memory.
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Re: Any ideas for a Beowulf Bigadv cluster?

Postby MtM » Fri Apr 15, 2011 11:13 pm

Don't forget the wiki still holds allot of information -> http://fahwiki.net/index.php/Alternative_FAH_Platforms
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