Posts by senatoralex85

1) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59959)
Posted 4 Mar 2009 by senatoralex85
Post:
Once in awhile, I get a Microsoft Visual C++ Runtime Library Error? It is for minirosetta_1.54_windows_intelx86.exe. The error message reads \"This application has requested the runtime to terminate it in an unusual way. Please contact the applications support team for more information.\"

Received it for this workunit. http://boinc.bakerlab.org/rosetta/result.php?resultid=232499308

Currently Using XP service pack 2 with Boinc version 5.10.45
2) Message boards : Number crunching : Report long-running models here (Message 58186)
Posted 27 Dec 2008 by senatoralex85
Post:
My Preferences are set to 4 hours per workunit. This workunit lasted 12 hours.

Task ID 217245063
Name cc2_1_8_mammoth_mix_fa_cst_hb_t313__IGNORE_THE_REST_1BG2A_7_6180_31_0
Workunit 197983062
Created 27 Dec 2008 3:47:57 UTC
Sent 27 Dec 2008 4:19:00 UTC
Received 27 Dec 2008 19:09:47 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x0)
Computer ID 792930
Report deadline 6 Jan 2009 4:19:00 UTC
CPU time 43297.02
stderr out <core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 21600
======================================================
DONE :: 1 starting structures 43296 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

</stderr_txt>
]]>


Validate state Valid
Claimed credit 118.702972598747
Granted credit 59.6309170544315
application version 1.47
3) Message boards : Number crunching : Problems with web site (Message 57412)
Posted 1 Dec 2008 by senatoralex85
Post:
I\'m not sure my problem relates to your upgrade, however, in the last 24 hours all my completed task stay in \'Uploading\' status. Just wondering if anyone else is having the same problem.



Yes, although I have only one task that\'s completed since they started switching to the new fileserver. I assume that although they\'ve transferred enough files to the new fileserver to be able to send out at least some new workunits, they haven\'t transferred some of the files needed to be able to be able to let everyone upload their results. The Technical News says it will take a few more days to finish transferring all the files from the old fileserver to the new one, so do you have enough free disk space available to store your results for that long, and have you made sure BOINC is allowed to use that much of it?



I got loads of disk space, so it doesn\'t matter, other than a cluttered boinc manager task screen and a ton of comm messages.


I can\'t upload anything either. This has been happening since 11-33-08. Below are the first messages seen with error. Uploads before this time succeedded.



11/30/2008 9:38:19 AM|rosetta@home|Sending scheduler request: To fetch work. Requesting 12 seconds of work, reporting 1 completed tasks
11/30/2008 9:38:41 AM||Project communication failed: attempting access to reference site
11/30/2008 9:38:43 AM||Access to reference site succeeded - project servers may be temporarily down.
4) Message boards : Rosetta@home Science : My visit to Baker Lab (Message 56677)
Posted 3 Nov 2008 by senatoralex85
Post:
Wow! Glad to see you were not only impressed with the Baker Lab, but you show the interest to further biology as well as science in general. Your write-up was fantastic for not having much of a background in Biology.

I am in the exact opposite postion you are in. I majored in Biology, but after college I found my first job in the computer field. It has been a year since I graduated and have not gone back to biology. I would like to work part-time somewhere in the sciences, but don\'t know a lab that will hire me part-time. :(

Anyways, its awesome to see the lab open up to its crunchers and equally amazing is your open mind to new fields. Society needs more people like yourself. Keep it up!
5) Message boards : Rosetta@home Science : Discussion on Stories from CASP8 (Message 56488)
Posted 27 Oct 2008 by senatoralex85
Post:


We have to be careful about the comparisons being made with POEM targets at this point. They did better than the mean, but we don\'t exactly know the other competitors and how they compete. More importantly, those results only offer some insight on TWO targets. We also don\'t know much about the dificulty level of the targets poem posted to crunch.

With that said, I would like to see a comparison (Rosetta vs. POEM) once the results are reported. Have been busy at work so have not had the time to read the stories. Will hopefully have a follow-up soon.
6) Message boards : Number crunching : Anyone know how the Phenom 9600 is as a cruncher? (Message 53493)
Posted 1 Jun 2008 by senatoralex85
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).
7) Message boards : Cafe Rosetta : Asking For Your Help (Message 53091)
Posted 16 May 2008 by senatoralex85
Post:
They got my vote!

Keep crunching for Rosetta!
8) Message boards : Number crunching : Increase TFLOPS during CASP 8 by utilizing RALPH (Message 53044)
Posted 13 May 2008 by senatoralex85
Post:
Suggestion for increasing TFLOPS during CASP

Is this concept being done today?

If not, it might be beneficial to the project to put a FEW CASP work units through RALPH for those who only run RALPH exclusively and not Rosetta . Maximize those machines over on that project.

It would also help for those running multiple projects other than rosetta and ralph. Example: I am running RALPH, Rosetta, Einstein and Seti and share my resources evenly amongst all 4 projects. Giving RALPH CASP workunits would double the production of the user example above......

9) Message boards : Number crunching : minirosetta v1.19 bug thread (Message 53025)
Posted 12 May 2008 by senatoralex85
Post:
Bitspit, is that the root cause of the \"no heartbeat from client in 31 secs\" msgs?? Do you have a link to the trac item for this?

Not sure if there\'s a trac for this, but waiting for DNS-lookup is definitely one of the reasons for \"no heartbeat\". If not mis-remembers, I\'ve seen this problem on win2k, there one time internet-connection went down it was spitting-out \"no heartbeat\" all the time, while another running win2003 just continued crunching even didn\'t manage doing DNS-lookup...

Not sure, but during very heavy disk-usage it\'s likely also possible to get a \"no heartbeat\".

And, atleast in my experience, each and every time any of the dvd-players makes a nasty noise before spitting-out \"read-error\", I\'m getting a \"no heartbeat\" in BOINC...



David Baker has gotten this error on his own laptop.

See here

http://boinc.bakerlab.org/rosetta/result.php?resultid=161624205

stderr out <core_client_version>5.4.9</core_client_version>
<stderr_txt>
No heartbeat from core client for 30 sec - exiting
No heartbeat from core client for 30 sec - exiting
FILE_LOCK::unlock(): close failed.: Bad file descriptor
No heartbeat from core client for 30 sec - exiting
No heartbeat from core client for 30 sec - exiting
No heartbeat from core client for 30 sec - exiting
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 131.476 cpu seconds
This process generated 0 decoys from 0 attempts

**Edit** Added Error Log results!
10) Message boards : Number crunching : No credit for work units (Message 52891)
Posted 7 May 2008 by senatoralex85
Post:
I have about 50 computers all running Rosetta@home and was making great progress until recently. My computers are finishing tasks and uploading them but I never seem to get any credit. Any thoughts? Do you need me to provide you with some specific info? Let me know, as I want to get back on track with Rosetta ASAP.


Also, my personal computer at home is a Q6600 and it\'s taking over 24 hours to complete tasks. What gives?


I am not an expert by any means but will do my best to help you. I took a look at the computers and it looks like the majority of the workunits that you did not receive credit for are either still in progress or have missed their deadline. Have you checked the internet connection to those computers that have not reported any results? Update the project from the computers that have not received credit for completed workunits. Then take a look at the messages tab. If you receive an error message, please post it here. Maybe I missed something but your home computer has not reported any results.

In your BOINC preferences, how often do you have the project communicate with the rosetta servers?
11) Message boards : Rosetta@home Science : CASP 8 (Message 52867)
Posted 5 May 2008 by senatoralex85
Post:
The last CASP this project went through, there was much more fanfare and many more announcements leading up to the event. How come I don\'t see this now?
12) Message boards : Rosetta@home Science : CASP 8 (Message 52840)
Posted 3 May 2008 by senatoralex85
Post:
Does the project have any plans to decrease the report deadlines of workunits at the start of CASP?
13) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39421)
Posted 15 Apr 2007 by senatoralex85
Post:
Boinc is not downloading from Rosetta. I have disabled my firewall, restarted my computer but the usual suspects are not fixing the problem. Here is a copy of my log below. I know it is a problem with Rosetta because malariacontrol downloaded without a problem.

4/15/2007 1:00:31 PM||Starting BOINC client version 4.45 for windows_intelx86
4/15/2007 1:00:31 PM||Data directory: F:\\Program Files\\BOINC
4/15/2007 1:02:00 PM|rosetta@home|Temporarily failed download of rosetta_5.59_windows_intelx86.exe: -106
4/15/2007 1:02:00 PM|rosetta@home|Temporarily failed download of hom001_m2hd_.fasta.gz: -106
4/15/2007 1:02:00 PM|rosetta@home|Started download of hom001_m2hd_.psipred_ss2.gz
4/15/2007 1:02:00 PM|rosetta@home|Started download of boinc_hom001_aam2hd_03_05.200_v1_3.gz
4/15/2007 1:02:02 PM|malariacontrol.net beta|Scheduler request to http://www.malariacontrol.net/malariacontrol_cgi/cgi succeeded
4/15/2007 1:02:03 PM|malariacontrol.net beta|Deferring communication with project for 9 seconds
4/15/2007 1:02:03 PM|malariacontrol.net beta|Started download of malariacontrol_5.45_windows_intelx86
4/15/2007 1:02:03 PM|malariacontrol.net beta|Started download of wu_21_35_36864_0_1064057379
4/15/2007 1:02:05 PM|malariacontrol.net beta|Finished download of wu_21_35_36864_0_1064057379
4/15/2007 1:02:05 PM|malariacontrol.net beta|Throughput 25733 bytes/sec
4/15/2007 1:02:05 PM|malariacontrol.net beta|Started download of densities.csv
4/15/2007 1:02:10 PM|malariacontrol.net beta|Finished download of densities.csv
4/15/2007 1:02:10 PM|malariacontrol.net beta|Throughput 9174 bytes/sec
14) Message boards : Rosetta@home Science : Can computional biology play an important role ? (Message 31803)
Posted 29 Nov 2006 by senatoralex85
Post:
\"What I wonder is: with that range of variation, how much variation occurs in ourselves compared to our parents and siblings?\"


This is an interesting question that I have been asking myself for a long time too. I assume that you are talking about variation at the genotypic level. It is a difficult question for me to even begin to try to answer for several reasons. First, I am not sure how to quantify the answer. Second, we have things (e.g. viruses) over time that have intercalated into our DNA and changed it over long periods of time which would then beg the question what base standard would we use to determine if an area in the DNA is mutated? Another question I ask myself is at what point in our life do we analyze our DNA for mutations? There are some \"good\" mutations (our immune system is one of many) as well as bad mutations (cancer is one of many). Also, we inheret our mitochondria differently than the rest of our DNA which makes comparison to our siblings even harder. There are many other questions as well. This is dangerous to say in science, but I do not think it is possible to get a COMPLETE answer to the question you mentioned. However, if one believes in intelligent design, then this question does not even need to be answered because only the \"omniscient creator\" knows.


What do you think?
15) Message boards : Number crunching : New credit system now being tested at RALPH@home (Message 22214)
Posted 10 Aug 2006 by senatoralex85
Post:
Hmm, this thread is getting way off topic. May I ask that we focus on the new credit system as best we can so that when the Baker lab reads this post they can better address our concerns.

Thanks mmciastro for your information. Keep us posted on what gooes on RALPH as I do not have time to keep up with it and like periodic updates!

Jose, I would suggest talking with the Rosetta @ home staff about your statistical tool. I would agree with you that most of the users on the boards here (including myself) do not have the necessary tools to perform some of the statistical analysis that you seem to be eluding to. I have a hard enough time applying standard deviation. Its a great idea and if the staff is willing to work with you on it, I think it would be an asset to this project.

What does everyone else think about using statistics to catch dishonest crunchers? If so, do you have any suggestions on a system so that honest people do not get upset when they are mislabled as dishonest?
16) Message boards : Number crunching : New credit system now being tested at RALPH@home (Message 22176)
Posted 10 Aug 2006 by senatoralex85
Post:
After carefully reading this thread I have come to a few conclusions that many of you seem to elude too.

1. People have a lot of time and money invested in this project and to zero out the credits would leave many people disenchanted. What I feel would really hurt this project is NEGATIVE publicity. Please remember that Dr. Baker and many other researchers have dedicated a lot of time to this project and to lose people over credits and not science would be foolish. I have done research with my professor and know the pain and glory that comes with research.

2. The staff here at Rosetta have the cruncher\'s best interest in mind from what I have observed thus far. I am sure the Rosetta staff have looked and the mistakes of Seti and will definitely make the necessary adjustments to prevent a reoccurrence.

****Sorry if I am off topic. I felt these points were important to mention****

My Suggestions:

I would have to agree with Tralala that it would be best to give each workunit a fixed credit value so that optimized clients that attempt to artificially adjust the benchmarks are thwarted. Many of you as well as I am wondering what kind of values will be assinged to each workunit and how R@H will determine them.

I think they should base the credit on the number of flops needed to complete the workunit as was previously mentioned. I would suggest looking a past work submitted to get a benchmark idea of the amount of credit that should be issued (pun not intended).

As far as how to deal with the current credit accumulated, I feel the Rosetta staff should NOT issue a new set of credits and freeze the old ones like what was done with BOINC classic. I feel this way because everyone will still be on a level playing field. Creating a new credit category will just be more uneccessary work for the staff. Those with few credits (such as myself) probably will not be affected that much because we do not compete for credit on an individual basis and will never be on the leaderboard (nor do I care whether I am or not). Those with high credit scores are way ahead of people like me who only have one computer and will stay that way. The users that are cheating now will either slowly drop back or find another way to beat the system.

17) Message boards : Number crunching : FLOPS/$ (Message 22172)
Posted 10 Aug 2006 by senatoralex85
Post:
Thanks for your advice Benny. I do find that my computer boots up offly slow, but I guess it will be something I have to deal with . Adding another 256mb of RD ram would probably be in the $250 price range which is too much to handle. I do have a bit of patience with computers since my last one I had was 233 MHz P2 with 6 GB hard drive running Windows 95. Lets just say I count my blessings going from Windows 95 to windows XP. I have had this computer for 4 years now and I usally never buy a new computer until the one I have breaks. On my old one, it happened to be the monitor. They lose their value so fast......
18) Message boards : Rosetta@home Science : rosetta is a scam (Message 22170)
Posted 10 Aug 2006 by senatoralex85
Post:
What I find interesting is that this person has not responded to anyone in this thread. Oh well, you cannot please everyone.
19) Message boards : Number crunching : FLOPS/$ (Message 22155)
Posted 9 Aug 2006 by senatoralex85
Post:
I am running a P4 2.26 GHz pc with Xp (my computer is not hidden for those who want to see) and have 128mb of PC 800 RD ram. Does anyone have a rough estimate on how much performance I can gain by doubling the memory? How well does PC 800 RD ram compare to DDR2 memory chips? PC 800 ram is expensive relative to DDR2. I have constantly looked on the internet for a webstite that compares the two types of memory \"head to head\" but could not find any sources. Thanks in advance for your help!
20) Message boards : Rosetta@home Science : Better pill to swallow (Message 21523)
Posted 1 Aug 2006 by senatoralex85
Post:
Good explanation. I did not know that the ribosomes could do that. Thanks Christoph!


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