Posts by BennyRop

41) Message boards : Rosetta@home Science : RFC (request for commemts) (Message 34626)
Posted 13 Jan 2007 by BennyRop
Post:
Derek: One of the difficulties we had at FAD (Find-A-Drug) was finding labs that would test out the results we came up with. For CF, we'd need knowledge about CF that would benefit from something like the HIV vaccine therapy that the Baker Labs is working on - or information about which receptors to block so CF symptoms are stopped.

Once there's something to work with, then Rosetta can be used - either here, at World Community Grid (which is using an older version of Rosetta for at least one of the projects they're running) or a new Boinc project - perhaps CF only.

After years spent on DC projects, I'm still waiting for something we've worked on to make it onto the market as a cure/treatment. It takes time; and perhaps the current work by Bakerlabs on HIV vaccines will be the first DC medical project to make it out into the real world and encourage more DC medical breakthroughs.
42) Message boards : Rosetta@home Science : How can we bring more users to the Rosetta project? (Message 34625)
Posted 13 Jan 2007 by BennyRop
Post:
It's been a few years since I was studying Communications Electronics the in the Seattle area - but I've had a trip to the KIMO studios downtown. For on air t.v. time, perhaps contacting the local television stations - and point out what we're doing, our CASP7 results, the Gates foundation investment in Rosetta for HIV research, and discussion about our progress with creating a vaccine for HIV. If it can get reported on locally, then there's a better chance that folks like CNN will broadcast a story on Rosetta. (For a writeup on CNN, perhaps contacting the medical/technology folks will spark interest, as well.)

And if it's too technical for the likes of KIMO - perhaps we could get in touch with Bill Nye, the Science Guy; offer to not camp out in front of his office chanting, "High Fiving White Guys!" (From a Seattle comedy program he was associated with for years.) for a week, and see if he's interested in doing a segment on Rosetta@Home.

43) Message boards : Number crunching : How much has your RAC Dropped Since 12/6/06 (Message 34134)
Posted 4 Jan 2007 by BennyRop
Post:
My RAC has dropped since Dec 14th since the program has stopped running from time to time, and has not been generating 86,400 seconds of work a day (or 604,800 seconds of work a week).

Stevea gives the impression that he's still producing the same number of seconds of work a day - just getting less credit for it.

So there's multiple causes for the lower RAC of those of us seeing lower RAC.

And while this probably isn't Stevea's problem - getting infected with spyware/worms/virii that were being spammed the last month would also slow systems down. Or installing a cpu hog of an antivirus app like Norton's.

It takes a bit of work to prove and identify the source of the problem. My system uses windows automatic update to download new updates - but I believe my problems showed up with 5.4.3.





44) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 34124)
Posted 4 Jan 2007 by BennyRop
Post:
a little more info:

-------

2006-12-14 12:36:37 [rosetta@home] Reason: To report completed tasks
2006-12-14 12:36:37 [rosetta@home] Reporting 1 tasks
2006-12-14 12:36:43 [rosetta@home] Scheduler request succeeded
2006-12-14 16:14:05 [rosetta@home] Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
2006-12-14 16:14:05 [rosetta@home] Reason: To fetch work
2006-12-14 16:14:05 [rosetta@home] Requesting 8640 seconds of new work
2006-12-14 16:14:10 [rosetta@home] Scheduler request succeeded
2006-12-14 16:14:12 [rosetta@home] Started download of file hom001_s014_.fasta.gz
2006-12-14 16:14:12 [rosetta@home] Started download of file hom001_s014_.psipred_ss2.gz
2006-12-14 16:14:15 [rosetta@home] Finished download of file hom001_s014_.fasta.gz
2006-12-14 16:14:15 [rosetta@home] Throughput 61 bytes/sec
2006-12-14 16:14:15 [rosetta@home] Started download of file boinc_hom001_aas014_03_05.200_v1_3.gz
2006-12-14 16:14:16 [rosetta@home] Finished download of file hom001_s014_.psipred_ss2.gz
2006-12-14 16:14:16 [rosetta@home] Throughput 426 bytes/sec
2006-12-14 16:14:16 [rosetta@home] Started download of file boinc_hom001_aas014_09_05.200_v1_3.gz
2006-12-14 16:14:35 [rosetta@home] Finished download of file boinc_hom001_aas014_09_05.200_v1_3.gz
2006-12-14 16:14:35 [rosetta@home] Throughput 11669 bytes/sec
2006-12-14 16:14:35 [rosetta@home] Started download of file mapback_hom017_S_00002_0010496_0.pdb.gz
2006-12-14 16:14:43 [rosetta@home] Finished download of file boinc_hom001_aas014_03_05.200_v1_3.gz
2006-12-14 16:14:43 [rosetta@home] Throughput 29957 bytes/sec
2006-12-14 16:14:43 [rosetta@home] Finished download of file mapback_hom017_S_00002_0010496_0.pdb.gz
2006-12-14 16:14:43 [rosetta@home] Throughput 1002 bytes/sec
2006-12-14 16:14:43 [rosetta@home] Started download of file mapback_hom017_S_00002_0010496_0.loopfile.gz
2006-12-14 16:14:43 [rosetta@home] Started download of file mapback_hom017_S_00002_0010496_0.obligate_loopfile.gz
2006-12-14 16:14:46 [rosetta@home] Finished download of file mapback_hom017_S_00002_0010496_0.loopfile.gz
2006-12-14 16:14:46 [rosetta@home] Throughput 63 bytes/sec
2006-12-14 16:14:46 [rosetta@home] Finished download of file mapback_hom017_S_00002_0010496_0.obligate_loopfile.gz
2006-12-14 16:14:46 [rosetta@home] Throughput 47 bytes/sec
2006-12-14 16:14:47 [---] Rescheduling CPU: files downloaded
2006-12-15 14:27:05 [---] Suspending computation - running CPU benchmarks
2006-12-15 14:27:05 [rosetta@home] Pausing task s018__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom014_S_00018_0003425_0_1446_49_0 (left in memory)
2006-12-15 14:27:05 [---] Suspending network activity - running CPU benchmarks
2006-12-15 14:27:08 [---] Running CPU benchmarks
2006-12-15 14:28:06 [---] Benchmark results:
2006-12-15 14:28:06 [---] Number of CPUs: 1
2006-12-15 14:28:06 [---] 1898 floating point MIPS (Whetstone) per CPU
2006-12-15 14:28:06 [---] 3506 integer MIPS (Dhrystone) per CPU
2006-12-15 14:28:06 [---] Finished CPU benchmarks
2006-12-15 14:28:08 [---] Resuming computation
2006-12-15 14:28:08 [---] Rescheduling CPU: Resuming computation
2006-12-15 14:28:08 [---] Resuming network activity
2006-12-15 14:28:08 [rosetta@home] Resuming task s018__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom014_S_00018_0003425_0_1446_49_0 using rosetta version 543
2006-12-17 12:00:37 [rosetta@home] Aborting task s018__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom014_S_00018_0003425_0_1446_49_0: exceeded CPU time limit 263980.263158
2006-12-17 12:00:37 [rosetta@home] Unrecoverable error for result s018__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom014_S_00018_0003425_0_1446_49_0 (Maximum CPU time exceeded)
2006-12-17 12:00:37 [rosetta@home] Deferring scheduler requests for 1 minutes and 0 seconds
2006-12-17 12:00:43 [---] Rescheduling CPU: application exited
2006-12-17 12:00:43 [rosetta@home] Computation for task s018__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom014_S_00018_0003425_0_1446_49_0 finished
2006-12-17 12:00:43 [rosetta@home] Starting task s014__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom017_S_00002_0010496_0_1447_26_0 using rosetta version 543
2006-12-17 14:24:41 [rosetta@home] Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
2006-12-17 14:24:41 [rosetta@home] Reason: To report completed tasks
2006-12-17 14:24:41 [rosetta@home] Reporting 1 tasks
2006-12-17 14:24:46 [rosetta@home] Scheduler request succeeded
2006-12-17 15:43:52 [rosetta@home] Task s014__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom017_S_00002_0010496_0_1447_26_0 exited with zero status but no 'finished' file
2006-12-17 15:43:52 [rosetta@home] If this happens repeatedly you may need to reset the project.
2006-12-17 15:43:52 [---] Rescheduling CPU: application exited
2006-12-17 15:43:52 [rosetta@home] Restarting task s014__BOINC_LOOP_RELAX_IGNORE_THE_REST_hom001__IGNORE_THE_REST_mapback_hom017_S_00002_0010496_0_1447_26_0 using rosetta version 543
------
evidently twiddling it's thumbs until the reboot on the 17th.

------

2006-12-29 14:47:20 [rosetta@home] Reporting 1 tasks
2006-12-29 14:47:25 [rosetta@home] Scheduler request succeeded
2006-12-30 10:09:20 [rosetta@home] Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
2006-12-30 10:09:20 [rosetta@home] Reason: To fetch work
2006-12-30 10:09:20 [rosetta@home] Requesting 175 seconds of new work
2006-12-30 10:09:25 [rosetta@home] Scheduler request succeeded
2006-12-30 10:09:27 [---] Rescheduling CPU: files downloaded
2006-12-30 12:37:24 [---] Rescheduling CPU: application exited
2006-12-30 12:37:24 [rosetta@home] Computation for task 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_4638_1 finished
2006-12-30 12:37:25 [rosetta@home] Starting task 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_8433_0 using rosetta version 543
2006-12-30 12:37:26 [rosetta@home] Started upload of file 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_4638_1_0
2006-12-30 12:37:51 [rosetta@home] Finished upload of file 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_4638_1_0
2006-12-30 12:37:51 [rosetta@home] Throughput 39040 bytes/sec
2006-12-30 14:30:11 [---] Suspending computation - running CPU benchmarks
2006-12-30 14:30:11 [rosetta@home] Pausing task 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_8433_0 (left in memory)
2006-12-30 14:30:11 [---] Suspending network activity - running CPU benchmarks
2006-12-30 14:30:14 [---] Running CPU benchmarks
2006-12-30 14:31:13 [---] Benchmark results:
2006-12-30 14:31:13 [---] Number of CPUs: 1
2006-12-30 14:31:13 [---] 1888 floating point MIPS (Whetstone) per CPU
2006-12-30 14:31:13 [---] 3480 integer MIPS (Dhrystone) per CPU
2006-12-30 14:31:13 [---] Finished CPU benchmarks
2006-12-30 14:31:15 [---] Resuming computation
2006-12-30 14:31:15 [---] Rescheduling CPU: Resuming computation
2006-12-30 14:31:15 [---] Resuming network activity
2006-12-30 14:31:15 [rosetta@home] Resuming task 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_8433_0 using rosetta version 543
2006-12-30 15:01:55 [rosetta@home] Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
2006-12-30 15:01:55 [rosetta@home] Reason: To report completed tasks
2006-12-30 15:01:55 [rosetta@home] Reporting 1 tasks
2006-12-30 15:02:00 [rosetta@home] Scheduler request succeeded
2007-01-02 19:31:32 [---] Suspending work fetch because computer is overcommitted.
2007-01-02 20:31:29 [---] Using earliest-deadline-first scheduling because computer is overcommitted.
2007-01-04 13:18:39 [---] Exit requested by user
2007-01-04 13:18:45 [---] Rescheduling CPU: exit_tasks

To pause/resume tasks hit CTRL-C, to exit hit CTRL-BREAK

StartServiceCtrlDispatcher being called.
This may take several seconds. Please wait.
2007-01-04 13:20:58 [---] Starting BOINC client version 5.4.9 for windows_intelx86
2007-01-04 13:20:58 [---] libcurl/7.15.3 OpenSSL/0.9.8a zlib/1.2.3
2007-01-04 13:20:58 [---] Executing as a daemon
2007-01-04 13:20:58 [---] Data directory: C:Program FilesBOINC
2007-01-04 13:20:58 [---] BOINC is running as a service and as a non-system user.
2007-01-04 13:20:58 [---] No application graphics will be available.
2007-01-04 13:20:59 [---] Processor: 1 AuthenticAMD AMD Athlon(tm) 64 Processor 3000+
2007-01-04 13:20:59 [---] Memory: 1023.48 MB physical, 1.65 GB virtual
2007-01-04 13:20:59 [---] Disk: 29.29 GB total, 7.25 GB free
2007-01-04 13:20:59 [rosetta@home] URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 121218; location: home; project prefs: default
2007-01-04 13:20:59 [ralph@home] URL: http://ralph.bakerlab.org/; Computer ID: 2698; location: home; project prefs: default
2007-01-04 13:20:59 [---] General prefs: from rosetta@home (last modified 2006-05-11 00:15:56)
2007-01-04 13:20:59 [---] General prefs: no separate prefs for home; using your defaults
2007-01-04 13:21:02 [---] Local control only allowed
2007-01-04 13:21:02 [---] Listening on port 31416
2007-01-04 13:21:02 [rosetta@home] Resuming task 1mmm_1_NMRREF_1_1mmm_1_id_model_12IGNORE_THE_REST_idl_1470_8433_0 using rosetta version 543
2007-01-04 13:21:22 [---] Using earliest-deadline-first scheduling because computer is overcommitted.
2007-01-04 13:21:22 [---] Suspending work fetch because computer is overcommitted.
-----
Boincmgr is claiming that the task is 64.85% done. But never finishes..

It had registered 15 hrs of work since it started on the 30th.. although it has been on 24/7.
45) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 34044)
Posted 3 Jan 2007 by BennyRop
Post:
Running 5.43 - and noticing days where nothing has been uploaded. This hasn't uploaded anything since Dec 30 according to the logs; and there's no mention of communication problems while trying to upload data.

i.e. 5.43 seems to have halted working for a day or days at a time since Dec 14th on this system.



46) Message boards : Number crunching : How much has your RAC Dropped Since 12/6/06 (Message 34037)
Posted 3 Jan 2007 by BennyRop
Post:
Checking my machine, I see that I've got several days of the client not producing anything starting on Dec 14. And it last uploaded data on dec 30, and hasn't turned anything in since. So it seems to be that I'm getting the communication disconnect problems that Feet1st was talking about. I've got my system setup with a 24hr setting; and am not sure what's causing the system to regain communication - since the system was last rebooted on the 24th. i.e. if it restarts communication when it decides the system is overcommitted - or something else, because I haven't been checking it regularly.



47) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 32831)
Posted 18 Dec 2006 by BennyRop
Post:
This is impressive praise.. that Rosetta is ready for predicting native configurations against the labor intensive techniques currently used. What was different between the predictions where we were in the middle of the pack on the predictions and the ones where we were at the head of the pack?

Here's looking forward to further improvements - that will hopefully reduce the workload and get more of our results closer to the neighborhood of the winning results.
48) Message boards : Number crunching : Discuss Rosetta Application Errors and Fixes (all Vers) (Message 32829)
Posted 17 Dec 2006 by BennyRop
Post:
What's listed on the Projects and Tasks tabs of the Boinc manager screens under Status?

49) Message boards : Number crunching : BOINC isn't helpful to science? (Message 32554)
Posted 13 Dec 2006 by BennyRop
Post:
The tip is a plastic tube with a tiny hole- and with enough pressure becomes a jet that shoots the insulin under the skin. No needles involved.

http://www.medijector.com/?gclid=CNDVs6-ljokCFR0OYAodDHbq6Q
It's about 8 inches long and has a 1 inch diameter.

It's a bummer that changes in the medical field take so long; but it hopefully keeps the pills my dad was taking to boost insulin production when he first came down with diabetes from making it out into the wild. (They were pulled after they'd caused the deaths of a handful of diabetics.)
50) Message boards : Number crunching : BOINC isn't helpful to science? (Message 32475)
Posted 11 Dec 2006 by BennyRop
Post:
Matt:

Find out what your friend considers a medical practical result. If it's a "cure" or a new treatment for various diseases.. we won't see it any time soon.

When talking to a pharmacist about my hatred for syringe injections of insulin, he told me about the fact they were coming out with a sniffable insulin. It was around 10 years later that sniffable insulin became available to normal people - not just the test subjects used in the studies. Granted.. I will continue using a medijector (shoots a jet of insulin under the skin) before sniffing insulin - but once a DC project comes up with promising results - the testing process and FDA allowing it to be used on non-test subjects takes forever..

51) Message boards : Number crunching : Does overclocking adversley affect rosetta? (Message 32305)
Posted 9 Dec 2006 by BennyRop
Post:
I've had multiple bad experiences with long term overclocking - one using a overclocking board that was recommended by a forum I haven't associated with in years. Ram tested out fine.. temps were cooler than the overclockers.. but my ibm/hitachi HDs didn't like the 5% overclock on the via chipset being used. It managed to corrupt windows so it needed a reinstall to boot up. :) Which was followed by a similar experience on a via chipset Athlon 64 motherboard.

The 5% improvement for 2 weeks to a month wasn't worth it in those cases - after which both systems ran years with no problems at stock speeds. (The joy of proving an incompatibility.. :) And while I know lots of people who have had good experiences OCing.. (I'm probably the only member of TRBCF that runs stock speeds..) - I also know some that would brag about their video redraw rates - and disappear after 20 minutes in Desert Combat matches due to video corruption. And then be gone for 30 minutes getting everything cooled down and set back to stock speeds.

So there are a number of folks that are just not cut out to run above stock speeds. More power to those who are able to OC error free, though. :)

52) Message boards : Number crunching : AMD 64x2 dual core computer not showing two CPU's (Message 32303)
Posted 8 Dec 2006 by BennyRop
Post:
Switching Hals to get Windows 2k and XP to use the new cpu has been discussed on The Rebel's Haven Computer Forum - as well as many other tech forums. Sometimes, you're able to reinstall windows over itself, and it updates your HAL, sometimes you have to update the HAL yourself.

Win2k and WinXP deal with the issue differently; some of the options for Win2k didn't work at all on WinXP.
53) Message boards : Number crunching : Report Rosetta screensaver problems here (Message 32074)
Posted 4 Dec 2006 by BennyRop
Post:
For Win2k and WinXP:
Right click on the desktop and choose Properties. click on the Settings tab. Underneath the pic of the monitor, it'll read something like, "Display: Plug and Play monitor on nVidia Geoforce FX 5600XT"
In my case, the video card chipset is an nVidia FX 5600XT. That's the hardware side.

For driver info..
choose the advanced tab in the bottom right corner of the Settings tab.
The General tab should have the same hardware information you just made a note of. Click on the drivers tab. Provide the Provider, Date, and version..
in my case, Provider is nVidia; date is 11.03.2003; version is 5.3.0.3

I run Boinc & Rosetta as a service, so I don't have any problems with the screen saver. I.e. no screensaver.. :)

54) Message boards : Number crunching : Dual Core (Message 31918)
Posted 1 Dec 2006 by BennyRop
Post:
By this I mean how much faster will the new box crunch a related work unit. Addtionally, I have often wondered if it were possible to copy and paste an identicle WU and run it on two different machines to compare the different times. Is this even possible?

Each decoy evidently takes different amounts of time - on the same machine; so you need to run 24hours worth of a WU to generate enough decoys to make a decent comparison. Comparing the time to create decoys might not be a fast and accurate way to tell the difference.

Comparing a 2Ghz Athlon 64, a 3+ Ghz P4, and a ~2Ghz Core duo were about the same when dealing with a week's worth of uploaded data. (comparing ~186,000 secs of work between the 3). The Core 2 cpus were supposed to be even better - so your new lower clocked system will be at least 2 times faster than your higher clocked older system.
55) Message boards : Number crunching : CASP 7 Results are in! (Message 31747)
Posted 28 Nov 2006 by BennyRop
Post:
If you click on the Protein designation (T0384 for example) - it lists all the groups that submitted a result to test. There's perhaps another list on the CASP7 web page that identifies those groups/teams, so you can tell that "Baker" = Rosetta@Home - all of us, plus the team back in the computer labs.

Back when in CASP5, when crunching for Distributed Folding - the results we were getting were in the middle of the pack. Not great on some, lousy on others.. but always middle of the pack.

It's interesting to see that the Rosetta client seems similarly consistent - although near the top of the pack for most things. Is there an easy explanation for why it looks like we hit the middle of the pack for T0285 and T0287? i.e. do any of the recent changes to Rosetta@Home improve our results enough for that type of protein that we'd match or do better than the best score?
56) Message boards : Cafe Rosetta : BOINC, not so well reviewed (Message 31746)
Posted 28 Nov 2006 by BennyRop
Post:
I was directed to the Boinc forums when making comments and suggestions specifically about Boinc. And I got the impression that whomever is in charge of the message board software is a little overworked/too busy - and perhaps that hasn't changed.
57) Message boards : Number crunching : QX6700 or XEONs What should you choose for crunching (Message 31403)
Posted 19 Nov 2006 by BennyRop
Post:
It's nice to see some competition between Intel and AMD again to help spur innovation. Wonder what will be available from AMD when these chips eventually migrate down to the Dell home desktop machines.
58) Message boards : Cafe Rosetta : PS/3 hits the market (Message 31338)
Posted 18 Nov 2006 by BennyRop
Post:
People standing in long lines with $600 in their pockets or carrying around a $600 console seems to have been quite the attraction to thieves:
Dangers of buying a PS3 on the first day.

59) Message boards : Number crunching : GPUs - the Future Crunchers? (Message 31278)
Posted 17 Nov 2006 by BennyRop
Post:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=2435
is where more of the GPU conversation was being held.

With AMD/ATI releasing a programming interface for their cards geared to non graphics use - and nVidia doing something similar; it should be easier for the next set of DC gpu client programmers.

Looks like it'll be an interesting next few years.
60) Message boards : Rosetta@home Science : Number crunching using graphics processors (GPUs) (Message 30878)
Posted 10 Nov 2006 by BennyRop
Post:
But keep in mind the amount of time that F@H has been working on a GPU client (around 2 years) and the fact that we GPU beta testers are still running into truly annoying bugs with the GPU client after a month - and it's not a simple recompile of a client.

After another GPU generation or two is out, the current GPU chips should be easily affordable and mainstream. Others will have paved the way to making GPU clients work, and documented the major problems with the current device drivers. And I sure hope that by then, Rosetta will have a graphics programming guru on staff to give us a GPU client.


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