Posts by David@home

21) Message boards : Number crunching : Rosetta keeps preempting (Message 15011) Posted 29 Apr 2006 by David@home Post: CPU is a P4 2.5Ghz before the days of HT or dual cores :-( I gave up on Rosetta for awhile as the lack of checkpointing seemed to be wasting CPU when you rebooted etc. Saw the news on the new client so I allowed new work and this is the log: Added colors to help ID events. After third go it seems to have settled down. Although why it downloaded so much work is a concern, rosetta only has a resource allocation of 10% and downloaded enough work as if it had 100% allocation for the connect to network every setting. I would expect Rosetta to have only downloaded its allocation so this can only add complexity to the alogrithm the schduler has to work out. 29/04/2006 13:59:42\|\|request_reschedule_cpus: project op 29/04/2006 13:59:44\|rosetta@home\|Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi 29/04/2006 13:59:44\|rosetta@home\|Reason: To fetch work 29/04/2006 13:59:44\|rosetta@home\|Requesting 172800 seconds of new work 29/04/2006 13:59:49\|rosetta@home\|Scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi succeeded 29/04/2006 13:59:52\|rosetta@home\|Started download of rosetta_5.07_windows_intelx86.exe 29/04/2006 13:59:52\|rosetta@home\|Started download of jump_templates_v2.dat.gz 29/04/2006 13:59:57\|rosetta@home\|Finished download of jump_templates_v2.dat.gz 29/04/2006 13:59:57\|rosetta@home\|Throughput 135793 bytes/sec 29/04/2006 13:59:57\|rosetta@home\|Started download of 1di2_.psipred_ss2.gz 29/04/2006 13:59:59\|rosetta@home\|Finished download of 1di2_.psipred_ss2.gz 29/04/2006 13:59:59\|rosetta@home\|Throughput 651 bytes/sec 29/04/2006 13:59:59\|rosetta@home\|Started download of frags400.txt 29/04/2006 14:00:00\|rosetta@home\|Finished download of frags400.txt 29/04/2006 14:00:00\|rosetta@home\|Throughput 2073 bytes/sec 29/04/2006 14:00:00\|rosetta@home\|Started download of 1di2.pdb.gz 29/04/2006 14:00:02\|rosetta@home\|Finished download of 1di2.pdb.gz 29/04/2006 14:00:02\|rosetta@home\|Throughput 8956 bytes/sec 29/04/2006 14:00:02\|rosetta@home\|Started download of 1di2_.fasta 29/04/2006 14:00:04\|rosetta@home\|Finished download of 1di2_.fasta 29/04/2006 14:00:04\|rosetta@home\|Throughput 72 bytes/sec 29/04/2006 14:00:04\|rosetta@home\|Started download of aa1di2_09_05.400_v1_3.gz 29/04/2006 14:00:36\|rosetta@home\|Finished download of rosetta_5.07_windows_intelx86.exe 29/04/2006 14:00:36\|rosetta@home\|Throughput 171096 bytes/sec 29/04/2006 14:00:36\|rosetta@home\|Started download of aa1di2_03_05.400_v1_3.gz 29/04/2006 14:00:43\|rosetta@home\|Finished download of aa1di2_09_05.400_v1_3.gz 29/04/2006 14:00:43\|rosetta@home\|Throughput 83310 bytes/sec 29/04/2006 14:00:43\|rosetta@home\|Started download of 1mkyA.psipred_ss2.gz 29/04/2006 14:00:44\|rosetta@home\|Finished download of 1mkyA.psipred_ss2.gz 29/04/2006 14:00:44\|rosetta@home\|Throughput 923 bytes/sec 29/04/2006 14:00:44\|rosetta@home\|Started download of 1mky.pdb.gz 29/04/2006 14:00:45\|rosetta@home\|Finished download of 1mky.pdb.gz 29/04/2006 14:00:45\|rosetta@home\|Throughput 13889 bytes/sec 29/04/2006 14:00:45\|rosetta@home\|Started download of aa1mkyA03_05.400_v1_3.gz 29/04/2006 14:00:47\|rosetta@home\|Finished download of aa1di2_03_05.400_v1_3.gz 29/04/2006 14:00:47\|rosetta@home\|Throughput 111137 bytes/sec 29/04/2006 14:00:47\|rosetta@home\|Started download of aa1mkyA09_05.400_v1_3.gz 29/04/2006 14:00:48\|\|request_reschedule_cpus: files downloaded 29/04/2006 14:00:48\|SETI@home\|Pausing result 05mr99ab.17601.3778.529820.1.137_0 (left in memory) 29/04/2006 14:00:48\|rosetta@home\|Starting result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 using rosetta version 507 29/04/2006 14:01:01\|rosetta@home\|Finished download of aa1mkyA03_05.400_v1_3.gz 29/04/2006 14:01:01\|rosetta@home\|Throughput 101046 bytes/sec 29/04/2006 14:01:01\|rosetta@home\|Started download of 1mkyA.fasta 29/04/2006 14:01:03\|rosetta@home\|Finished download of 1mkyA.fasta 29/04/2006 14:01:03\|rosetta@home\|Throughput 90 bytes/sec 29/04/2006 14:01:03\|rosetta@home\|Started download of 1b72_.psipred_ss2.gz 29/04/2006 14:01:04\|rosetta@home\|Finished download of 1b72_.psipred_ss2.gz 29/04/2006 14:01:04\|rosetta@home\|Throughput 880 bytes/sec 29/04/2006 14:01:04\|rosetta@home\|Started download of aa1b72_09_05.400_v1_3.gz 29/04/2006 14:01:16\|\|request_reschedule_cpus: project op 29/04/2006 14:01:16\|SETI@home\|Resuming result 05mr99ab.17601.3778.529820.1.137_0 using setiathome version 411 29/04/2006 14:01:16\|rosetta@home\|Pausing result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 (left in memory) 29/04/2006 14:01:18\|rosetta@home\|Finished download of aa1b72_09_05.400_v1_3.gz 29/04/2006 14:01:18\|rosetta@home\|Throughput 149884 bytes/sec 29/04/2006 14:01:18\|rosetta@home\|Started download of 1b72.pdb.gz 29/04/2006 14:01:19\|rosetta@home\|Finished download of aa1mkyA09_05.400_v1_3.gz 29/04/2006 14:01:19\|rosetta@home\|Throughput 124865 bytes/sec 29/04/2006 14:01:19\|rosetta@home\|Finished download of 1b72.pdb.gz 29/04/2006 14:01:19\|rosetta@home\|Throughput 25462 bytes/sec 29/04/2006 14:01:19\|rosetta@home\|Started download of 1b72_.fasta 29/04/2006 14:01:19\|rosetta@home\|Started download of aa1b72_03_05.400_v1_3.gz 29/04/2006 14:01:20\|\|request_reschedule_cpus: files downloaded 29/04/2006 14:01:22\|rosetta@home\|Finished download of 1b72_.fasta 29/04/2006 14:01:22\|rosetta@home\|Throughput 188 bytes/sec 29/04/2006 14:01:22\|rosetta@home\|Started download of aa1dtj_09_05.400_v1_3.gz 29/04/2006 14:01:26\|rosetta@home\|Finished download of aa1b72_03_05.400_v1_3.gz 29/04/2006 14:01:26\|rosetta@home\|Throughput 195509 bytes/sec 29/04/2006 14:01:26\|rosetta@home\|Started download of 1dtj.pdb.gz 29/04/2006 14:01:27\|\|request_reschedule_cpus: files downloaded 29/04/2006 14:01:27\|rosetta@home\|Finished download of 1dtj.pdb.gz 29/04/2006 14:01:27\|rosetta@home\|Throughput 12664 bytes/sec 29/04/2006 14:01:27\|rosetta@home\|Started download of aa1dtj_03_05.400_v1_3.gz 29/04/2006 14:01:38\|rosetta@home\|Finished download of aa1dtj_03_05.400_v1_3.gz 29/04/2006 14:01:38\|rosetta@home\|Throughput 127723 bytes/sec 29/04/2006 14:01:38\|rosetta@home\|Started download of 1dtj_.fasta 29/04/2006 14:01:40\|rosetta@home\|Finished download of 1dtj_.fasta 29/04/2006 14:01:40\|rosetta@home\|Throughput 84 bytes/sec 29/04/2006 14:01:40\|rosetta@home\|Started download of 1dtj_.psipred_ss2.gz 29/04/2006 14:01:41\|rosetta@home\|Finished download of 1dtj_.psipred_ss2.gz 29/04/2006 14:01:41\|rosetta@home\|Throughput 996 bytes/sec 29/04/2006 14:01:41\|rosetta@home\|Started download of aa2tif_03_05.400_v1_3.gz 29/04/2006 14:01:49\|rosetta@home\|Finished download of aa1dtj_09_05.400_v1_3.gz 29/04/2006 14:01:49\|rosetta@home\|Throughput 130439 bytes/sec 29/04/2006 14:01:49\|rosetta@home\|Finished download of aa2tif_03_05.400_v1_3.gz 29/04/2006 14:01:49\|rosetta@home\|Throughput 146385 bytes/sec 29/04/2006 14:01:49\|rosetta@home\|Started download of 2tif.pdb.gz 29/04/2006 14:01:49\|rosetta@home\|Started download of aa2tif_09_05.400_v1_3.gz 29/04/2006 14:01:50\|\|request_reschedule_cpus: files downloaded 29/04/2006 14:01:51\|rosetta@home\|Finished download of 2tif.pdb.gz 29/04/2006 14:01:51\|rosetta@home\|Throughput 9284 bytes/sec 29/04/2006 14:01:51\|rosetta@home\|Started download of 2tif_.fasta 29/04/2006 14:01:52\|rosetta@home\|Finished download of 2tif_.fasta 29/04/2006 14:01:52\|rosetta@home\|Throughput 78 bytes/sec 29/04/2006 14:01:52\|rosetta@home\|Started download of 2tif_.psipred_ss2.gz 29/04/2006 14:01:53\|rosetta@home\|Finished download of 2tif_.psipred_ss2.gz 29/04/2006 14:01:53\|rosetta@home\|Throughput 664 bytes/sec 29/04/2006 14:02:01\|rosetta@home\|Finished download of aa2tif_09_05.400_v1_3.gz 29/04/2006 14:02:01\|rosetta@home\|Throughput 242493 bytes/sec 29/04/2006 14:02:02\|\|request_reschedule_cpus: files downloaded 29/04/2006 14:53:12\|\|request_reschedule_cpus: process exited 29/04/2006 14:53:12\|SETI@home\|Computation for result 05mr99ab.17601.3778.529820.1.137_0 finished 29/04/2006 14:53:12\|rosetta@home\|Resuming result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 using rosetta version 507 29/04/2006 14:53:14\|SETI@home\|Started upload of 05mr99ab.17601.3778.529820.1.137_0_0 29/04/2006 14:53:24\|SETI@home\|Finished upload of 05mr99ab.17601.3778.529820.1.137_0_0 29/04/2006 14:53:24\|SETI@home\|Throughput 2763 bytes/sec 29/04/2006 15:02:01\|\|request_reschedule_cpus: project op 29/04/2006 15:02:02\|rosetta@home\|Pausing result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 (left in memory) 29/04/2006 15:02:02\|SETI@home\|Starting result 05mr99ab.17601.4162.997154.1.52_1 using setiathome version 411 29/04/2006 15:02:03\|SETI@home\|Sending scheduler request to http://setiboinc.ssl.berkeley.edu/sah_cgi/cgi 29/04/2006 15:02:03\|SETI@home\|Reason: Requested by user 29/04/2006 15:02:03\|SETI@home\|Reporting 1 results 29/04/2006 15:02:08\|SETI@home\|Scheduler request to http://setiboinc.ssl.berkeley.edu/sah_cgi/cgi succeeded 29/04/2006 16:02:02\|rosetta@home\|Resuming result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 using rosetta version 507 29/04/2006 16:02:02\|SETI@home\|Pausing result 05mr99ab.17601.4162.997154.1.52_1 (left in memory) 29/04/2006 17:02:02\|rosetta@home\|Pausing result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 (left in memory) 29/04/2006 17:02:02\|SETI@home\|Resuming result 05mr99ab.17601.4162.997154.1.52_1 using setiathome version 411
22) Message boards : Number crunching : Rosetta keeps preempting (Message 15005) Posted 29 Apr 2006 by David@home Post: OK, previous to this it downloaded new Rosetta work and ran the WU for 1 min before prempting, than it ran Rosetta for approx 7 mins as below. I am not sure of the checkpoint interval for the new Rosetta so wondered if any useful work was being done in these brief spells of CPU time. I thought the switch time was used so a project would get one hour and not a fraction of an hour. Maybe the scheduler needs to settle down after getting new Rosetta work.
23) Message boards : Number crunching : Rosetta keeps preempting (Message 15001) Posted 29 Apr 2006 by David@home Post: Hi No sign of EDF messages. This is a sample: 29/04/2006 14:53:12\|\|request_reschedule_cpus: process exited 29/04/2006 14:53:12\|SETI@home\|Computation for result 05mr99ab.17601.3778.529820.1.137_0 finished 29/04/2006 14:53:12\|rosetta@home\|Resuming result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 using rosetta version 507 29/04/2006 14:53:14\|SETI@home\|Started upload of 05mr99ab.17601.3778.529820.1.137_0_0 29/04/2006 14:53:24\|SETI@home\|Finished upload of 05mr99ab.17601.3778.529820.1.137_0_0 29/04/2006 14:53:24\|SETI@home\|Throughput 2763 bytes/sec 29/04/2006 15:02:01\|\|request_reschedule_cpus: project op 29/04/2006 15:02:02\|rosetta@home\|Pausing result HBLR_1.0_1di2_ROT_TRIALS_TRIE_461_3976_0 (left in memory) 29/04/2006 15:02:02\|SETI@home\|Starting result 05mr99ab.17601.4162.997154.1.52_1 using setiathome version 411 What does that reschedule cpus project op message mean? Not sure why upload complete of a S@H WU caused a preempt of Rosetta.
24) Message boards : Number crunching : Rosetta keeps preempting (Message 14999) Posted 29 Apr 2006 by David@home Post: Rosetta keeps preempting after running for only a few minutes, e.g. 1 min, 7 min. Switch between applications every is set to 60 minutes, leave in memory is set on, other Rosetta specifics are as defaults. Running Boinc 5.2.13 on Windows XP Pro SP2 with Rosetta app 5.07. Only other project is S@H. Not sure why Rosetta is preempting so quickly. Any ideas? Will the new checkpoint mean the short time frame is valid work progress or is it just starting from the beginning each time? Many thanks
25) Message boards : Cafe Rosetta : Empire strikes back (Message 6163) Posted 13 Dec 2005 by David@home Post: No competition: The Empire Strikes Back is the best of the six: Hoth, Dagobah, Cloud city: the best + a great plot too. Although the pod racers in The Phantom Menace are pretty cool!
26) Message boards : Rosetta@home Science : I'm not getting any data (Message 6021) Posted 12 Dec 2005 by David@home Post: Try opening Boinc manager and then selecting the Rosetta project, then click on the update button. This will send a command to the Rosetta server and this may kick start the client into downloading. I have only recently connected and had to do this as the BOINC core deferred the initial communication with Rosetta for 4 minutes but after this time was up it never re-tired. A manual update as described above kicked the BOINC core into downloading. Worth a try.
27) Questions and Answers : Web site : Where to Download Rosetta@home ? (Message 1116) Posted 8 Oct 2005 by David@home Post: First you will need to create an account at rosetta@home. There is a link from the home page to this web page. http://boinc.bakerlab.org/rosetta/create_account_form.php On completing this you will be sent an email with the project URL and your account key. Then start BOINC manger on your PC, select the projects tab and click on the "Attach to new project button". Enter your details from the email click OK and it should automatically start downloading the client and data file to run Rosetta@home.
28) Questions and Answers : Web site : Rosetta email flagged as junk (Message 1095) Posted 8 Oct 2005 by David@home Post: I am using Outlook 2003 with SP2 and the latest junk filter update. For some reason the emails I have received from Rosetta@home are flagged as junk and the URL link disabled. (I was changing my email address and validation email was classified as junk!) Not sure what is triggering this. Not a big issue as I found the email in the junk folder but if anybody has problems getting email from this project it would be worth asking them to check their junk folder first. I also had to cut and paste the URL as the link was disabled by the anti-phishing feature in Outlook 2003 SP2.
29) Message boards : Cafe Rosetta : Welcome to Boinc Synergy Team (Message 1094) Posted 8 Oct 2005 by David@home Post: Looks like I will have to get around to fixing my laptop then I will have some spare CPU to donate to Rosetta@home. Will be crunching soon.

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