Posts by staffann

1) Message boards : Number crunching : Getting WU's (Message 64837)
Posted 6 Jan 2010 by Profile staffann
Their reasoning was that it takes time to post, time needed to fix things. Would you rather get a note saying 'we are down' or the project up and running was their thinking. They said 'you KNOW we are down'!

They must have had bad luck when doing their thinking. Taking a couple of minutes to inform the users is a very small investment to reduce a very large cost in terms of time invested by the users. And if the project comes up 3 minutes later because of giving information then it is well worth it. It isn't only what is the best for the project - it is as much showing that you care about the crunchers who contribute.

When it comes to companies like ISPs their information when they have technical problems tells alot about how/if they care about their customers. This is not a commercial company and christmas/new year is a natural explanation but still the same goes here.
2) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58146)
Posted 23 Dec 2008 by Profile staffann
I had one WU crash on me today. Running on a WinXPSP3 Athlon X2 3800+ with 1Gb RAM. Link to task details.

Name 1nkuA_BOINC_MPZN_vanilla_abrelax_5901_16326_0
Workunit 197297715
Created 23 Dec 2008 8:53:31 UTC
Sent 23 Dec 2008 9:33:56 UTC
Received 23 Dec 2008 22:08:04 UTC
Server state Over
Outcome Client error
Client state Compute error
Exit status -1073741819 (0xc0000005)
Computer ID 625945
Report deadline 2 Jan 2009 9:33:56 UTC
CPU time 4928.609
stderr out

- exit code -1073741819 (0xc0000005)
3) Message boards : Number crunching : Minirosetta v1.28 bug thread (Message 53630)
Posted 11 Jun 2008 by Profile staffann
I just had a minirosetta workunit fail on me. When I took a look at my computer I had a firewall (Zonelarm) popup saying that minirosetta 1.28 wanted to communicate with the internet and asked me whether to allow it. I don't know if it failed because it had to wait too long to communicate or if it tried to communicate because it failed...

Anyway, here is the info:

2008-06-11 18:06:47|rosetta@home|Starting d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1
2008-06-11 18:06:47|rosetta@home|Starting task d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1 using minirosetta version 128
2008-06-11 18:07:41|rosetta@home|Deferring communication for 1 min 0 sec
2008-06-11 18:07:41|rosetta@home|Reason: Unrecoverable error for result d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1 ( - exit code -1073741819 (0xc0000005))
2008-06-11 18:07:44|rosetta@home|Computation for task d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1 finished
2008-06-11 18:07:44|rosetta@home|Output file d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1_0 for task d110a_BOINC_CASP8_ABRELAX_main_t405_IGNORE_THE_REST-S25-10-S3-9--d110a-_3740_1264_1 absent
2008-06-11 18:07:44|rosetta@home|Starting FRA_t411_CASP8_1QXN_3_IGNORE_THE_RESTt411_3_aamodel1.template_0003_3713_8105_0
4) Message boards : Rosetta@home Science : Rosetta vs POEM (Message 53314)
Posted 24 May 2008 by Profile staffann
Thank you for the answer. I did find the expanation strange. Do you at rosetta know enough about POEM in order to be able to explain the difference between it and rosetta?
5) Message boards : Rosetta@home Science : Rosetta vs POEM (Message 53106)
Posted 17 May 2008 by Profile staffann
I am trying to understand the difference between the Rosetta and the POEM@home projects. In the POEM forum, I found a post that explains it like this:

As a quick first answer: Protein simulation is presently dominated by two approaches.

1) You learn/copy from nature (ROSETTA@HOME is a good example). Given a new sequence, one tries to copy structural fragments of known proteins and assembles them to good structures. Pros: Works for big proteins, gives excellent structures for high sequence similarity. Cons: Does not work, when there is no sequence similarity (new folds), does not work when there is no experimental data (transmembrane proteins, to which 40% of all known drugs bind), no kinetics

2) You simulate the folding process as it occurs in nature (Folding@Home) with a biophysical model. This is done with molecular dynamics (MD), an essentially sequential method with a time resolution of 10E-15 s/step. For a folding process in millisecond range you need A LOT of steps. Pros: full dynamics info, folding times, high accuracy structures, Cons: works only for small proteins, specific questions

POEM tries to interpolate between these two worlds. It uses an atomistic model for the protein free energy, i.e. is can work for new folds and applications in nanobiotechnology, where there is no experimental data. In contrast to MD, it exploits Anfinsons thermodynamic hypothesis (Nobel Prize in Chemistry 1972) that proteins in their biologically active state have a minimal free energy. The simulation process is thus replaced by an optimization process that is thousands of times faster than MD. Pros: Can do at least medium size proteins, gets the folding landscape, works for "new folds", Cons: still limited to proteins < 100 amino acids, no real kinetics (yet).

With POEM@HOME we will try to make progress on these two cons. Specifically we hope to make progress for

* "new fold" proteins with low sequence similarity to existing proteins
* proteins in nonphysiological environments (we just got a grant to develop implants, which are more biocompatible)
* understanding the folding process of more complex proteins that cannot be studied with direct kinetic simulation
* protein-protein interactions, where the partners change their conformation upon docking (biological signal process)
* refinement of model structures for transmembrane proteins

Is this a correct explanation, especially regarding Rosetta? The statement that Rosetta doesn't work for new folds surprised me a bit.
6) Message boards : Number crunching : minirosetta v1.15 bug thread (Message 52834)
Posted 2 May 2008 by Profile staffann
First posted in the "problems with minirosetta 1.+" thread but realised that this is probably a better place:

I just had a minirosetta 1.15 fail right after I had hit the graphics button. My computer runs WinXPSP2 on an Athlon 64 X2 3800+ and has a NVidia graphics card. AV is Avast.

2008-05-02 13:42:02|World Community Grid|Sending scheduler request: To report completed tasks
2008-05-02 13:42:02|World Community Grid|Reporting 1 tasks
2008-05-02 13:42:07|World Community Grid|Scheduler RPC succeeded [server version 601]
2008-05-02 13:42:07|World Community Grid|Deferring communication for 1 min 1 sec
2008-05-02 13:42:07|World Community Grid|Reason: requested by project
2008-05-02 13:45:11|rosetta@home|Deferring communication for 1 min 0 sec
2008-05-02 13:45:11|rosetta@home|Reason: Unrecoverable error for result 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1who_-_3092_1911_0 ( - exit code -1073741819 (0xc0000005))
2008-05-02 13:45:11|rosetta@home|Computation for task 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1who_-_3092_1911_0 finished
2008-05-02 13:45:11|rosetta@home|Output file 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1who_-_3092_1911_0_0 for task 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1who_-_3092_1911_0 absent
2008-05-02 13:45:11|World Community Grid|Resuming task faah4030_NSC119913_chem3D_B_xmd05230_02_1 using faah version 603

Computer & BOINC data:
2008-05-02 09:56:38||Starting BOINC client version 5.10.20 for windows_intelx86
2008-05-02 09:56:38||log flags: task, file_xfer, sched_ops
2008-05-02 09:56:38||Libraries: libcurl/7.16.4 OpenSSL/0.9.8e zlib/1.2.3
2008-05-02 09:56:38||Data directory: C:ProgramBOINC
2008-05-02 09:56:38|SETI@home|Found app_info.xml; using anonymous platform
2008-05-02 09:56:38||Processor: 2 AuthenticAMD AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ [x86 Family 15 Model 43 Stepping 1]
2008-05-02 09:56:38||Processor features: fpu tsc pae nx sse sse2 3dnow mmx
2008-05-02 09:56:38||OS: Microsoft Windows XP: Professional Edition, Service Pack 2, (05.01.2600.00)
2008-05-02 09:56:38||Memory: 1023.23 MB physical, 3.40 GB virtual
2008-05-02 09:56:38||Disk: 76.32 GB total, 5.24 GB free
2008-05-02 09:56:38||Local time is UTC +1 hours
7) Message boards : Number crunching : Problems with minirosetta version 1.+ (Message 52833)
Posted 2 May 2008 by Profile staffann
Moved the post to the "minirosetta v1.15 bug thread"

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