Posts by stewjack

1) Message boards : Number crunching : Is there any way to force a higher priority on Rosetta? (Message 66849)
Posted 11 Jul 2010 by stewjack
Post:

@ stewjack, only the latest Pentium 4 and the new Intel chips
with the nehalem architecture (i7 and i5) have hyper threading.


Thanks Chilean


2) Message boards : Number crunching : Is there any way to force a higher priority on Rosetta? (Message 66847)
Posted 11 Jul 2010 by stewjack
Post:
Slightly off topic, but my laptop has Intel Core Duo type CPU.

BOINC gives the processor features as fpu vme de pse tsc msr pae mce
cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr
sse sse2 ss htt tm pni ssse3 cx16 sse4_1 syscall nx lm tm2 pbe.

Does htt refer to Hyper-Threading Technology?

Jack
3) Message boards : Rosetta@home Science : podcast about X-ray crystallography (Message 66711)
Posted 30 Jun 2010 by stewjack
Post:
When people talk about "known" protein structures they are probably talking about protein structures determined by X-ray crystallography. Apparently,
determining protein structures by X-ray crystallography is not easy, fast or cheap. IMO: That is one reason why people would like to compute the structures.

June 25th, 2010
Futures in Biotech 62: X-Ray Crystallography
(30 MB audio file)
http://www.podtrac.com/pts/redirect.mp3/twit.cachefly.net/fib0062.mp3

Our guest today is a Professor in the Department of Molecular Biology and Biochemistry at the University of California, Irvine's School of Biological sciences. Dr. McPherson is the author of six books and 300 papers or reviews. He is widely considered the nation's foremost authority in the field of macromolecular crystallography. For over a decade he has served as principal instructor of the Cold Spring Harbor Laboratory course in macromolecular X-Ray crystallography.

A live unedited video version of the podcast,

(175 MB MP4 file)
http://www.podtrac.com/pts/redirect.mp4/twit.cachefly.net/odtv/0618-fib62.mp4


4) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58177)
Posted 26 Dec 2008 by stewjack
Post:

The runtimes look very reasonable though! I'm afraid making a single decoy shorter than 3-4 hours is not always possible


That would make sense. Normally my WU run time is set to 4 hours.


- what kind of machine was this on ?


Compaq Presario 6029
AMD Athalon XP 2100 (1.7 GHZ)
Windows XP Home ( BOINC v 6.2.19 )
RAM: 768 MB
VIDEO CARD: Radeon 9250 128MB
Dial-up: USRobotics Controller Modem
5) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58166)
Posted 24 Dec 2008 by stewjack
Post:
Hi.

I have this task at the moment running, it's odd. This morning when i restarted

the ... task cc_nonideal_1_8_nocst4_hb_t303__IGNORE_THE_REST_1FEZA_6_6019_17_0 using minirosetta version 147
pete.


I have had that happen three times during the last 4 or 5 days. I didn't report it because technically
such actions are not prohibited. The tasks complete and grant credit.
However; I have set my tasks length to 2 hours for now,
and these task run well over that time.

NOTE: I have checkpoint logging turned on!

ALL TIMES APPROX.

4 hours with no ckeckpoints after 40 min
cc_nonideal_3_5_nocst4_hb_t374__IGNORE_THE_REST_2FCKA_10_5832_14_0

3.5 hours with no checkpoints after 35 min
cc2_1_8_mammoth_mix_cen_cst_hb_t332__IGNORE_THE_REST_1V2XA_7_5888_15_0

3 hours with no checkpoints after 50 min
cc_nonideal_0_6_nocst4_hb_t313__IGNORE_THE_REST_1GOJA_10_5910_16_0

NOTE: On the last WU I noticed that when I restarted the task,
well into the no checkpointing period -
checkpointing restarted for a short period of time!



6) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58050)
Posted 20 Dec 2008 by stewjack
Post:
"graphic viewer" hangs with this task
cs_noe_fullw_nolin_homo_bench_cs_noe_abrelax_cs_mth1598_olange_5607_11086_0


I had the same thing happen with this similar WU.

cs_noe_fullw_nolin_homo_bench_cs_noe_abrelax_cs_nsp1_olange_5608_14752_0

Note: I didn't have time to mess with this one - so I just aborted it.
7) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 57946)
Posted 16 Dec 2008 by stewjack
Post:

I'm having the same (graphics) problem, but in XP 32-bit, in one of the hosts after the installation of mini 1.47


Same problem here. Also with XP 32bit. I guess that makes it three (edit now 4 ) of us.

The WU seems to be unaffected. The WU has only been processing for abut 15 minutes, but it is check-pointing regularly.
8) Message boards : Number crunching : Minirosetta v1.45 bug thread (Message 57712)
Posted 8 Dec 2008 by stewjack
Post:
This WU was crunched under v.1.45 and exited with an error.

========
Task ID 212609043
Name: loopbuild_reference_hombench_loopbuild_t327__IGNORE_THE_REST_1XMAA_2_5453_3_0

Workunit 193817482

http://boinc.bakerlab.org/rosetta/result.php?resultid=212609043

==== stderr out ======
<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007FA87A read attempt to address 0x000002E8


<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007FA87A read attempt to address 0x000002E8

Jack
9) Message boards : Rosetta@home Science : Rosetta@home Active WorkUnit(s) Log update ? (Message 50732)
Posted 16 Jan 2008 by stewjack
Post:

CF work units are also new!
10) Message boards : Number crunching : Problems with version 5.90/5.91 (Message 50012)
Posted 24 Dec 2007 by stewjack
Post:

My best guess is that the new wus ... are requiring more memory than you/I/MOST(by most, I mean I think the vast majority of hosts connected to rosetta have 512K or less, although that percentage will lessen over time) of the "normal" crunchers out there, and they don't have any other work queued up for us to participate on. So in effect they're saying "we don't need you at the moment, please come back when we do". ....Atleast that's my guess.


Now that you mention it, I think that I remember this problem being discussed on this board.

I'm OK for 2 or 3 days at my normal Rosetta 50% duty cycle.

Thanks for the reply -
Jack
11) Message boards : Number crunching : Problems with version 5.90/5.91 (Message 50009)
Posted 24 Dec 2007 by stewjack
Post:
Joachim in message #4999 mentioned a problem similar to mine.


I have a single core CPU, and I have just started getting those limited memory errors when attempting to request new work from Rosetta.

---------

12/24/2007 12:07:28 PM|rosetta@home|Message from server: No work sent
12/24/2007 12:07:28 PM|rosetta@home|Message from server: Your preferences limit memory usage to 691 MB, and 763 MB is needed

--------

For whatever it is worth my total system memory is 768 MB

Jack


12) Message boards : Rosetta@home Science : Wacky Science Podcast talks about Protein Folding on Computers (Message 47182)
Posted 29 Sep 2007 by stewjack
Post:
This science podcast from Berkley can often be both funny and informative, but IMO this particular show had a bad day. However, it does contain a segment that tries to talk about protein folding with computers. They mention Folding@HOME, but not Rosetta.

I decided that some people might like to keep track of the media's presentation of computer folding. At least nobody can claim I oversold the show!

The show is about an hour long and the folding segment runs from 25:00 min to 31:00.

This Week in Science - September 18, 2007

Jack
13) Message boards : Number crunching : Problems with Rosetta version 5.80 (Message 46371)
Posted 16 Sep 2007 by stewjack
Post:
I had to abort this one due to 'waiting for memory'. All the others have worked without a problem.

http://boinc.bakerlab.org/rosetta/result.php?resultid=105692089


Evan,
I have had your single 'waiting for memory' problem out of 3 Capri WU's
I run a single core CPU with 512 memory.

My WU is very similar to yours.
http://boinc.bakerlab.org/rosetta/result.php?resultid=105635179


Jack

14) Message boards : Number crunching : How to get a million credits? (Message 44901)
Posted 12 Aug 2007 by stewjack
Post:


don't forget to set aside some of the retirement funds for the electric company or your private alternative energy source.


It would be cheaper for some of these "crunchers" to pay for control of one supercomputer processor. I got into DC because it used slightly LESS resources (disregarding my personal time) than one supercomputer processor used. That is only true when your computer would be "on" anyway.

I wonder what will happen with BOINC on server farms using quad cores. I am not an IT professional, but I have heard that, in some - if not all cases, the individual cores shut down when not in use. Even the CPU fans stop!

Jack


15) Message boards : Number crunching : How to get a million credits? (Message 44879)
Posted 10 Aug 2007 by stewjack
Post:
William Ostie said:
I don't understand how some people reach credits in the millions, when it took me 5 months to reach 18,000


If I ever joined a team it would be called - The only one or two computers and we always turn them OFF at night TEAM.

Edit and stats banner added

Jack


16) Message boards : Number crunching : How to get a million credits? (Message 44865)
Posted 10 Aug 2007 by stewjack
Post:
William Ostie said:
I don't understand how some people reach credits in the millions, when it took me 5 months to reach 18,000


If I ever joined a team it would be called - The only one or two computers and we always turn them of at night TEAM.


17) Message boards : Number crunching : Report Rosetta screensaver problems here (Message 34928)
Posted 17 Jan 2007 by stewjack
Post:
I will add what may be another symptom.

Note: I was busy at the time and was primarily interested in resolving the issue fast. This is what I believed occurred.-

1. graphics froze.

2. BOINC manager showed work unit still updating CPU time.

3. I didn't notice (As I have noticed on other occasions.) the application escaping from the control of ThreadMaster, but I wasn't really paying attention to that.

4. I opened task manager and surprise, surprise, my WU was listed twice as an application that wasn't responding! I don't believe it should be recognized as an application. Maybe I was mistaken, and what I really noticed was the graphic application listed twice?

5. I ended one of the non responding tasks, and lost the WU.

Jack


18) Message boards : Number crunching : Report Rosetta screensaver problems here (Message 33980)
Posted 3 Jan 2007 by stewjack
Post:
I have also been experiencing similar graphic/WU problems with the last two Rosetta versions. Since plenty of other people were reporting on the problem, I decided that I would wait until I was confident about the pattern and maybe had something new to add.

My Pattern ( 5 incidents )
1. Graphics activated ( I don't run in screen saver mode. )

2. Graphics window "freezes." Nothing updates and the graphics window cannot be closed. Task manager offers to close non-responding application.

3.a ( 2 incidents )
Using task manager to close application shuts BOINC down, but causes a WU error.
( I don't have the error codes. )

3.b ( 3 incidents )
Going to BOINC manager and suspending Rosetta, then exiting BOINC manager, shuts everything down and the original WU can be restarted at the last checkpoint.

NEW?? I only paid attention to this this with the last two incidents.
I run ThreadMaster, and I noticed that the WU with the frozen graphics had escaped ThreadMasters control. I don't think that it's priority had changed, but it was definitely running at 100%, versus the 70% threshhold it was supposed to run at.

Jack


19) Message boards : Number crunching : Is XP Hibernation Function a Long-Setpoint Solution? (Message 30567)
Posted 3 Nov 2006 by stewjack
Post:
Thank you for all your help, but I have made my decision. I plan to stop monitoring this thread.

I think that I understand my own situation best. Just a few points.

I have a Compaq and can not use any of the XP disk recovery options. The computer was well worth the price because, it had been stored in a closet for three years and was given to me for free. I still had to download SP1 and SP2 over my dial-up connection! I don't want to think about reinstalling my OS.

Once again, Thanks for all your help.

Jack
20) Message boards : Number crunching : Is XP Hibernation Function a Long-Setpoint Solution? (Message 30527)
Posted 2 Nov 2006 by stewjack
Post:
As the individual who started this thread I would just like to say that you have scared me off hibernation completly.

My problem may have become less serious with the Rosetta 5.36 application. I have just started working on a series sf FRA work units with save points every 3 min!

I can live with occasional work units with hour-or-longer setpoint intervals.


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