Posts by XeNO

1) Message boards : Number crunching : Improvements to Rosetta@home based on user feedback (Message 16624) Posted 19 May 2006 by XeNO Post: Rosetta 5.16: (1) We're continuing our efforts to reduce memory usage by typical workunits by rosetta@home. You can expect an even further reduction in memory footprint in our next update. (2) We're testing a new science mode which uses the sequence and structural information from homologous proteins in an early phase of the simulation, but then returns to the target protein sequence in the final refinement phase. This mode appears to have a larger memory footprint than typical workunits, so we will only send out these jobs to computers that have >1Gb RAM. (3) Also, we're trying a new feature where at the end of a simulation, Rosetta compares its fold to the predictions made by a dozen other algorithms. (Those predictions are sent to the clients in a compressed format.) Seeing consensus between different algorithms is usually a good sign that a prediction is right. Is that Greater than or Equal to 1GB of RAM, or just Greater? When my Computer is not in use I have no problems with Rosetta taking a hog's share of resources.
2) Message boards : Rosetta@home Science : Where are amino acids built? (Message 15549) Posted 5 May 2006 by XeNO Post: Twenty amino acids are encoded by the standard genetic code, but what builds them and where? tRNA transfers amino acid to ribosome, but where does it get it from? tRNA carries a message from the cell nucleus (where DNA is stored) to the Ribosome where it is then run through like a computer program to construct an amino acid chain that becomes a protein.
3) Message boards : Rosetta@home Science : Would a PPU client be possible, down the road? (Message 15548) Posted 5 May 2006 by XeNO Post: I asked if the card can do the types of general purpose calculations R@H uses (single precision floats as stated in another thread), and if so, how much faster can it do them than a modern cpu. If you can give the same commands to the ppu that you can to a cpu, then it shouldn't be a hard port. If it's more specialized, like a gpu, then it may not be worth the trouble. While it would be great if it worked and a percentage of users bought cards, it would still be a small percentage of work. I pictured these being used by the Rosetta folks in house. These cards are pci, so you could potentially put 4 or 5 into a machine. If each card is 10x faster than the cpu, all of a sudden you have the equivalent of 50 cpu's where before you may have only been able to fit 10 in the rack. For a group that's out of rack space, this could help them out. -E Although my knowledge of hardware architecture is limited, I do have to ask, if all those cards are running on the same PCI bus, are they not limited by the measly 133MB/s data transfer rate of the PCI bus? Considering the average computer gets at least 6.4 (theoretical) GB/s between memory and processor, thats seems like it would fall down pretty fast.
4) Message boards : Number crunching : 64-Bit Rosetta? (Message 15242) Posted 2 May 2006 by XeNO Post: Are there any plans for a version of Rosetta that will take advantage of the huge performance benefit in using 64-bit processing? I can only think that good things would come of the project, especially since your AMD users would get the full bang for their buck if they're running a 64-bit OS.
5) Message boards : Number crunching : Plodding Workunit... (Message 14769) Posted 27 Apr 2006 by XeNO Post: HB_BARCODE_30_1ctf__351_22101_3 Has run now for 24 hours and 31 minutes, says only 4.14% completed, and 26 hours left. Is this a bug, or just a really fantastically huge workunit?
6) Message boards : Number crunching : Problems with ATI GPU/catalyst driver (Message 14633) Posted 26 Apr 2006 by XeNO Post: There has been fixes to the screensaver in the newer boinc dev versions. There have always been issues reported with some ATI cards, although I don't remember the specific nature of the errors. What I remember is that users were recommended by other users was to either upgrade driver versions or stop using the screensaver. I don't know if your card has the issue, since I can't remember what the issues were. Wouldn't hurt to make sure you have the latest video driver and update to the latest developmental version of boinc. The 5.01 update made it better. It still makes the VPU fail, however, it doesn't freeze the whole system in the process. Takes 2-5 minutes, random but never longer than 5 min (when I had set it to go blank.) 1min works fine again.
7) Message boards : Number crunching : Problems with ATI GPU/catalyst driver (Message 14456) Posted 23 Apr 2006 by XeNO Post: Problem came back now with a vengeance... maybe 10 seconds until VPU crash now. Were you talking about Rosetta 5.01 or Catalyst?
8) Message boards : Number crunching : Problems with ATI GPU/catalyst driver (Message 14180) Posted 20 Apr 2006 by XeNO Post: Temp fix: I switched so the screensaver goes to blank screen after 1 minute instead of 5 minutes. Problem has not resurfaced.
9) Message boards : Number crunching : Problems with ATI GPU/catalyst driver (Message 14018) Posted 18 Apr 2006 by XeNO Post: Recently updated to version 6.4--04/12/06 release. After about 3minutes, the screensaver causes the GPU to fail, resulting in a card crash and an error report sent to ATI. This issue did not exist with previous driver, but thought I'd let the board know to troubleshoot if it's not something else.