Posts by j2satx

1) Message boards : Number crunching : Minirosetta 1.90 and 1.91 (Message 62721) Posted 2 Aug 2009 by j2satx Post: Thanks! There was a change in that flag and I missed it. That work unit is disabled. I got a few errors on lr5_combine_mods_run01_rlbn WUs. http://boinc.bakerlab.org/rosetta/result.php?resultid=269713462 http://boinc.bakerlab.org/rosetta/result.php?resultid=269758962 http://boinc.bakerlab.org/rosetta/result.php?resultid=269787057 http://boinc.bakerlab.org/rosetta/result.php?resultid=269811876 They end after about 10 seconds with the error: Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544 BOINC:: Error reading and gzipping output datafile: default.out Is this one of the WUs tested on Ralph?
2) Message boards : Number crunching : Chaos in Rosetta@Home??? (Message 62704) Posted 1 Aug 2009 by j2satx Post: Hi, David. First of all I should like to thank you for your explanations. I appreciate it. As this has been discused before in other threads, it should be a good idea transmit this information to all the volunteers; perhaps in the main page of R@H. Not everybody goes into the forums and not evereybody will read this thread, I suppose. I do not understand the science behind this project; I only work as an IT professional not related with protein folding. But let me give you a couple of advices (without understand your "business"!): - Never, never perform a change in the software/hardware just before a weekend. If something fails, nobody could attend and fix it. - You must to build a Pre-Production environment to test the changes. As I said, I dont understand your environment/software and so on. I give you this advices with a total humility but I think that someone of your team should take some actions. The price with these errors is high if you want to maintain thousands of volunteers working for you. Thanks again. They have ralph@home to test on, but they don't use it.
3) Message boards : Number crunching : Resource Share Obsolete? (Message 60758) Posted 20 Apr 2009 by j2satx Post: @Mikey One of the mind model problems in the BOINC universe is that sometimes concepts get muddled and no one notices. Specifically there is a blurring of the point of work fetch and resource scheduling. At the moment I am most specifically addressing work fetch only because I think that the scheduling of the work on the processors should be rather more in line with deadline order with attention paid to most other priorities only to the degree that I would be more restrictive of some current policies. To these points I would abandon processing of tasks only if there was the certainty of deadline miss if we didn't and that we would to the extent possible never run more than one task at a time from a project on a specific resource class. In other words if I have 4 CPUs and tasks from 10 projects I would never run two tasks from any one project unless I was in deadline jeopardy. Fundamentally, if you correctly control the gateway, the population on hand is the one that you want. At the current time we are doing neither well ... @Nothing But Idle Time I posted here because Einstein and SaH are both having significant difficulties with their servers, firstly, and secondly, SaH has grown increasingly hostile to, ahem, pagan ideas ... But, not that it matters, I have also posted this on the Dev mailing lists but in that most people don't read those I decided to post here for the nonce and collect some comments. If you are managing to control your workload with the resources as you have them, wouldn't it work to merely have the option to also limit the number of WUs by project, so you would only have the exact number of WUs you want in the work queue?
4) Message boards : Number crunching : LHC@home gives BOINC a bad name (Message 59431) Posted 7 Feb 2009 by j2satx Post: The discussion is importyant to Rosetta and all BOINC projects because LHC@ home needlessly wastes CPU time that would other wise go to other projects. If the CPU time is wasted, why do you think it would go to other projects? Good point. It would go to other projects if and only if the machine is attached to other projects. If the computer is not attached to other projects as well as LHC@home then of course the waste is almost a non-issue. I peeked at over 100 user profiles at LHC@home and all of them were attached to other projects. I am not saying that proves 100% are attached to other projects. I am saying it appears that for most users the cycles wasted by LHC@home would go to other projects. It just seems to be a more compelling argument for LHC, since if the CPU time is wasted, it is LHC's loss.
5) Message boards : Number crunching : LHC@home gives BOINC a bad name (Message 59427) Posted 7 Feb 2009 by j2satx Post: The discussion is importyant to Rosetta and all BOINC projects because LHC@ home needlessly wastes CPU time that would other wise go to other projects. If the CPU time is wasted, why do you think it would go to other projects?
6) Message boards : Number crunching : Anyone know how the Phenom 9600 is as a cruncher? (Message 53510) Posted 1 Jun 2008 by j2satx Post: AMD PHENOM X4 9500 Quad core processor vs. an Intel Core 2 Quad Q6600 processor. Do both these computers have the same crunching power or is one better to crunch with (in general)? Both have 4 gig of ram and are around 700 dollars (intel processor is running 850.00 at Frys). Do the Q6600. At default settings Q6600 out performs X4 9600, so will beat X4 9500. Q6600 easily beats my X4 9600 Black Editions (both OC'd 5-10%)
7) Message boards : Number crunching : Dual vs quad core -- performance's proportionality (Message 52544) Posted 17 Apr 2008 by j2satx Post: If it will only be a cruncher, a slower quad would crunch more WUs, but if you are going to use the computer for other purposes, you may want a dual-core with a higher clock.
8) Message boards : Number crunching : Dual vs quad core -- performance's proportionality (Message 52517) Posted 16 Apr 2008 by j2satx Post: Ok, now I know many things, thank you! One last doubt: with a quad core, 2 Gb of memory in dual channel, will be enough or it requests 4 Gb (but only 3 avaliable due to Win XP restriction)? Rosetta currently uses around 180MB per thread, so you can expect up to 800MB for the four cores with the current client. That leaves you 1.2GB for whatever you do - so it depends what you do on your PC. If it's just email, web, light office apps etc then 2GB will be plenty. If you're doing something memory intensive then i'd recommend a bit more. 4GB is probably overkill, but there isn't much middle-ground - you won't save much by going for 3x1GB or 2GB + 1GB, so maybe just go for 4GB if you've got the cash. HTH Danny If you use 31Gb or 21G + 1G, you will lose the dual-channel memory function. True, but how much difference does it make? It might have more effect on Rosetta than other apps - it wouldn't suprise me - but Tomshardware showed that with modern CPUs dual channel makes very little difference. You could test your machine. Put two 1Gs in single-channel and benchmark, then put the same two 1Gs in dual-channel and benchmark. If the difference isn't significant to you, then no issue.
9) Message boards : Number crunching : Dual vs quad core -- performance's proportionality (Message 52503) Posted 16 Apr 2008 by j2satx Post: Ok, now I know many things, thank you! One last doubt: with a quad core, 2 Gb of memory in dual channel, will be enough or it requests 4 Gb (but only 3 avaliable due to Win XP restriction)? Rosetta currently uses around 180MB per thread, so you can expect up to 800MB for the four cores with the current client. That leaves you 1.2GB for whatever you do - so it depends what you do on your PC. If it's just email, web, light office apps etc then 2GB will be plenty. If you're doing something memory intensive then i'd recommend a bit more. 4GB is probably overkill, but there isn't much middle-ground - you won't save much by going for 3x1GB or 2GB + 1GB, so maybe just go for 4GB if you've got the cash. HTH Danny If you use 31Gb or 21G + 1G, you will lose the dual-channel memory function.
10) Message boards : Number crunching : various systems and credit (Message 52375) Posted 10 Apr 2008 by j2satx Post: How much does that cool'n'quiet take out of your cpu speed? I have a 64 2800+ runing win xp sp 2. It typically drops the CPU to 1GHz on my puters.
11) Message boards : Number crunching : various systems and credit (Message 52374) Posted 10 Apr 2008 by j2satx Post: How much does that cool'n'quiet take out of your cpu speed? I have a 64 2800+ runing win xp sp 2. It typically drops the CPU to 1GHz on my puters.
12) Message boards : Number crunching : various systems and credit (Message 52334) Posted 8 Apr 2008 by j2satx Post: Hello AmusingFool, A few weeks ago I installed Ubuntu as a dual-boot, next to my Windows XP. Boinc on Linux was (at first) crunching much less credits than XP. After checking out some other threads (eg http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3593) I realized my AMD 3000+ didn't run its normal 1.8 G Hz but slowed down to 1 G Hz because the low priority R@h appication didn't urge Linux to go faster. Now My single core machine crunches more credit running Ubuntu than XP (in the same period of time). Well, this is of course one point of view, this might be different on a multi-core machine. Have a nice day, Path7. Make sure "Cool n Quiet" is disabled in BIOS and try the Linux again.
13) Message boards : Number crunching : Benchmark Rosetta - the sesults are incredible (Message 52068) Posted 21 Mar 2008 by j2satx Post: If people think such an opportunity to perform a benchmark like this would be useful, please let me know your comments, and express your interest in this thread. I'm interested....wouldn't you have to run the same WU multiple times to get DCF trained? I'd like to see about ten in a package.
14) Message boards : Number crunching : Xeon processors produce less credits? (Message 51899) Posted 11 Mar 2008 by j2satx Post: I have to agree about HT. Distributed computing uses 100% of each core. So when you do HT to have each core do two WUs, then they are going to be competing for CPU memory cache. There's no magic thing where a program that uses 100% of the CPU will let you run two programs and use 200% of the CPU. A simplistic way to view HT and VM is that they add efficiency when non-intensive programs run on them. The big idea behind VM is if you have an office with 4 people on the internet and in word processors, you could run them all on one CPU instead of 4 CPUs. I thought the main idea behind VM, is to be able to run multiple OSs on the same hardware and at the same time.
15) Message boards : Number crunching : Best operating system for crunching (Message 51683) Posted 27 Feb 2008 by j2satx Post: Part of the challenge of having choices is that it's up to you to decide which is best for you and your situation. They've both shot my theory about memory contention out of the water and said Linux still makes a measurable difference. From here I can only tell you I believe they used RAC or credits (GRANTED) per hour of CPU time in their measurment. We don't care how well the machine runs the benchmark, we want to know how well it runs Rosetta, and so that's what they would have done. I don't know about you, but I can tell when the benchmarks are running because my cooling fan slows down because the load on my machine is so light. So it's obviously not as intense as doing real Rosetta crunching. To clarify what I'm saying: on my machines, Linux gets more credit per cpu time than Windows on a virtually identical machine. I do not know if that means it runs Rosetta (Ralph actually, as I don't run Rosetta) better than Windows, only that it gets more credit. On Ralph, I still run machines with both OSs regardless of which gets more credit for testing and comparison purposes.
16) Message boards : Number crunching : Best operating system for crunching (Message 51671) Posted 27 Feb 2008 by j2satx Post: Astro/ j2satx: How much memory on these machines? I can see that since Linux typically uses less memory then Windows, there might be a bigger difference on a machine that is basically memory constrained when running Windows. The machines I referenced are virtually identical: two are Intel E4500 with 2Gb RAM, one W2K and one Ubuntu; two are AMD 4400+ with 2Gb RAM, one W2K and one Ubuntu.
17) Message boards : Number crunching : Best operating system for crunching (Message 51658) Posted 26 Feb 2008 by j2satx Post: Be aware that credit granted on Rosetta is no longer dependant directly on your BOINC benchmarks. It is based on work completed. So taking a given machine and replacing Windows with Linux should not have any adverse impact on credit. Any variation should only be due to the relative overhead and memory contention with the operating system. So I would expect the two to be within about 5% of each other. That may be the intent, but my numbers show Linux does much better than Windows.
18) Message boards : Number crunching : Server Status (Message 51353) Posted 12 Feb 2008 by j2satx Post: Please show how many WUs were released in the last 24h so we can make the "Successes last 24h" meaningful.
19) Message boards : Number crunching : Problems with minirosetta version 1.+ (Message 51348) Posted 12 Feb 2008 by j2satx Post: j2satx, Did you download the 1.07 mini app symbols file into your ralph project directory? I see an access violation error from one of your computers but do not see any trace information. I downloaded 1.07 to all the computers I had attached to Ralph. However, now that you mention it........I added many more computers today after I noticed WUs were avail on Ralph and I forgot to download 1.07 to those new computers. I will do that in the next hour. Might not need it now........all the WUs on Ralph are gone already........!! I'll add some more, just let me know when it's best for you. thanks! edit: did this task have the symbols file? It hope it works as expected. I wonder if it needs to be in the slot directory? I don't think it does. http://ralph.bakerlab.org//result.php?resultid=746732 The computer that ran 746732 was one I added today without adding the 1.07. It's a dual-core AMD with Windows XP X64. 1.07 was added moments ago.
20) Message boards : Number crunching : Problems with minirosetta version 1.+ (Message 51347) Posted 12 Feb 2008 by j2satx Post: j2satx, Did you download the 1.07 mini app symbols file into your ralph project directory? I see an access violation error from one of your computers but do not see any trace information. I downloaded 1.07 to all the computers I had attached to Ralph. However, now that you mention it........I added many more computers today after I noticed WUs were avail on Ralph and I forgot to download 1.07 to those new computers. I will do that in the next hour. Might not need it now........all the WUs on Ralph are gone already........!! I'll add some more, just let me know when it's best for you. thanks! edit: did this task have the symbols file? It hope it works as expected. I wonder if it needs to be in the slot directory? I don't think it does. http://ralph.bakerlab.org//result.php?resultid=746732 I'll check on that result... I think I have 1.07 on all the Windows machines now. You can throw a few thousand WUs over the fence right now.

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