Posts by Rabinovitch

1) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 80390) Posted 18 Jul 2016 by Rabinovitch Post: Hi all! Sorry if this is not a right thread to post it, but... Will this article be useful in rosetta's calculations methods? http://www.pnas.org/content/early/2016/07/12/1603929113.abstract
2) Message boards : Number crunching : Mini Rosetta 3.45 (Message 75347) Posted 11 Apr 2013 by Rabinovitch Post: Hi all! I found that there appears tasks with "Validate error" on both my Linux and Windows PCs. I have described this problem already, but I thought that it is present only at my Linux machine. Example WU from Win7 box: http://boinc.bakerlab.org/rosetta/result.php?resultid=573733678 From Linux: http://boinc.bakerlab.org/rosetta/result.php?resultid=573992857 Is there any way to fix it? 'Cause I just worrying for (as they say here) science done by my PCs (so as consumed electricity) and going to waste...
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 75304) Posted 1 Apr 2013 by Rabinovitch Post: Hi all! Consider please my problem described in adjacent thread.
4) Message boards : Number crunching : Client errors (Message 75302) Posted 1 Apr 2013 by Rabinovitch Post: Hi all! There appears a validate error periodically (about 30% of total WUs quantity) on this PC. Examples: http://boinc.bakerlab.org/rosetta/workunit.php?wuid=519386705 http://boinc.bakerlab.org/rosetta/workunit.php?wuid=519386349 The last one has been crunched in together with this WU which was validated normally. What can the matter be? For now I set target time to 4 hr, just to loose as few CPU time as possible in case of "Validate error" will appear again...
5) Message boards : Number crunching : Minirosetta 3.14 (Message 70704) Posted 10 Jul 2011 by Rabinovitch Post: Hi all! I have just installed new "inkarnation" of Kubuntu 10.10 amd64, BOINC and x32-libs proposed by boinc.berkeley.edu. All my CPU tasks (rosetta, ralph and QMC) are exiting with "Compute error" after several hours of processing. Rosetta's application says different things, for example: Task 435109856 <core_client_version>6.10.58</core_client_version> <![CDATA[ <message> process got signal 11 </message> <stderr_txt> [2011- 7- 9 18:58: 0:] :: BOINC:: Initializing ... ok. [2011- 7- 9 18:58: 0:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing broker options ... Registered extra options. Initializing core... Initializing options.... ok Options::initialize() Options::adding_options() Options::initialize() Check specs. Options::initialize() End reached Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev42272.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/ECH19_looprem_verif_long404.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 86400 FILE_LOCK::unlock(): close failed.: Bad file descriptor [2011- 7- 9 19:27:26:] :: BOINC:: Initializing ... ok. [2011- 7- 9 19:27:26:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing broker options ... Registered extra options. Initializing core... Initializing options.... ok Options::initialize() Options::adding_options() Options::initialize() Check specs. Options::initialize() End reached Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev42272.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/ECH19_looprem_verif_long404.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 86400 </stderr_txt> ]]> Task 435105624 <core_client_version>6.10.58</core_client_version> <![CDATA[ <message> Input file minirosetta_database_rev42272.zip missing or invalid: -120 </message> ]]> For QMC tasks there is always "process got signal 11" message. What can the matter be? Einstein's CUDA WUs are working good enough.
6) Message boards : Number crunching : minirosetta 2.17 (Message 70588) Posted 19 Jun 2011 by Rabinovitch Post: It's all OK now with new version (3.14). Seems that it was just a bug.
7) Message boards : Number crunching : minirosetta 2.17 (Message 70560) Posted 16 Jun 2011 by Rabinovitch Post: Please someone tell why this application create 4 (!) processes (under Linux) with memory consumption same as one process under Windows? Thus it needs 4 times more RAM space under Linux to process the WU comparing to Windows! It's very prodigally and I want to solve this bug ('cause it can't be a legal option by design).
8) Message boards : Number crunching : minirosetta 2.17 (Message 68374) Posted 4 Nov 2010 by Rabinovitch Post: Two times on both PC and notebook (both under Kubuntu 10.xx amd 64) WUs became very "heavy" (more than 1000 MB in the RAM). Ain't it a bug? I have suspended both of them now.
9) Message boards : Number crunching : Crunching with GPU? (Message 67952) Posted 4 Oct 2010 by Rabinovitch Post: Then why do other molecular dynamics projects run on GPU? Yep, Gpugrid.net for main example.
10) Message boards : Number crunching : minirosetta 2.05 (Message 65095) Posted 25 Jan 2010 by Rabinovitch Post: New app working well. And it seems that now the WU need less RAM (about 100 MB per WU). Is it true? If it is, then may be this is a step to rosetta's GPU client? :-) Well, now I see two WUs are being processed, and one is consupting about 510 MB of RAM, and another - 480. I like such a heavy WUs, give me more please! :-)
11) Message boards : Number crunching : minirosetta 2.05 (Message 64974) Posted 14 Jan 2010 by Rabinovitch Post: New app working well. And it seems that now the WU need less RAM (about 100 MB per WU). Is it true? If it is, then may be this is a step to rosetta's GPU client? :-)
12) Message boards : Number crunching : Discussion on increasing the default run time (Message 64973) Posted 14 Jan 2010 by Rabinovitch Post: We are planning to increase the default run time from 3 hours to 6 hours and the minimum from 1 to 3 hours to reduce the load on our servers. Nice idea. And what about increasing maximum crunching time? I am ready crunch even several days if it necessary, or crunch untill all models will be processed. What about checkbox like "Work till the end"? :-)
13) Message boards : Number crunching : Extreme RAM usage (Message 64433) Posted 11 Dec 2009 by Rabinovitch Post: Yep. And now I never observe how the system crying of memory insufficience... :-) It's very important while my home PC is crunching memory-consumpting WUs (of Rosetta, ibercivis and EDGeS projects) in 24/7 mode.
14) Message boards : Number crunching : Extreme RAM usage (Message 64419) Posted 9 Dec 2009 by Rabinovitch Post: I like watching the 4GB of RAM I paid for getting used for something useful :) Use Vista or Win7 then, they automatically use or release ram as it needs it or other programs need it. Since I have no money now for bying additional RAM for such a gluttonous OS like Windows 7 I have changed it to Ubuntu 9.10 x64. And I am pretty satisfied now - 2 rosetta's WUs, a couple of user's applications - and we have about 60% of 2 Gb busy. On Windows in the same conditions memory occupation was about 80-85%. btw, now I also can work normally with OS during CUDA WUs processing, without freezes or smth... :-)
15) Message boards : Rosetta@home Science : CHARMM in rosetta@home (Message 64168) Posted 24 Nov 2009 by Rabinovitch Post: Greetings! Could you please inform wether CHARMM will be used in this project at least in beta-applications, or should I help to improve it participating in Docking@Home project? Thanx in advance!
16) Message boards : Number crunching : Minirosetta v1.40 bug thread (Message 56964) Posted 15 Nov 2008 by Rabinovitch Post: Aenozer wuan: http://boinc.bakerlab.org/rosetta/result.php?resultid=207358562
17) Message boards : Number crunching : Minirosetta v1.40 bug thread (Message 56944) Posted 15 Nov 2008 by Rabinovitch Post: 15.11.2008 8:23:48\|rosetta@home\|Computation for task 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0 finished 15.11.2008 8:23:48\|rosetta@home\|Output file 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0_0 for task 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0 absent http://boinc.bakerlab.org/rosetta/result.php?resultid=207358562
18) Message boards : Number crunching : Rosetta Mini with new score terms bug thread (Message 56624) Posted 2 Nov 2008 by Rabinovitch Post: Once again: 02.11.2008 15:42:03\|rosetta@home\|Starting 2chf__BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--2chf_-_4662_4628_1 02.11.2008 15:42:11\|rosetta@home\|Starting task 2chf__BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--2chf_-_4662_4628_1 using minirosetta_split_terms version 102 02.11.2008 15:46:21\|rosetta@home\|Computation for task 2chf__BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--2chf_-_4662_4628_1 finished 02.11.2008 15:46:21\|rosetta@home\|Output file 2chf__BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--2chf_-_4662_4628_1_0 for task 2chf__BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--2chf_-_4662_4628_1 absent BOINC manager version: 02.11.2008 10:16:24\|\|Starting BOINC client version 6.3.19 for windows_x86_64
19) Message boards : Number crunching : Minirosetta v1.39 bug thread (Message 56623) Posted 2 Nov 2008 by Rabinovitch Post: 3 fresh WUs, v1.39, computation error after 14-40 minutes. 02.11.2008 15:21:00\|rosetta@home\|Computation for task abinitio_nohomfrag_70_A_1jfvA_4466_83424_0 finished 02.11.2008 15:21:00\|rosetta@home\|Output file abinitio_nohomfrag_70_A_1jfvA_4466_83424_0_0 for task abinitio_nohomfrag_70_A_1jfvA_4466_83424_0 absent 02.11.2008 15:21:00\|rosetta@home\|Starting abinitio_nohomfrag_70_A_2uzrA_4466_83276_0 02.11.2008 15:21:00\|rosetta@home\|Starting task abinitio_nohomfrag_70_A_2uzrA_4466_83276_0 using minirosetta version 139 02.11.2008 15:25:41\|rosetta@home\|Computation for task abinitio_nohomfrag_70_A_2uzrA_4466_83276_0 finished 02.11.2008 15:25:41\|rosetta@home\|Output file abinitio_nohomfrag_70_A_2uzrA_4466_83276_0_0 for task abinitio_nohomfrag_70_A_2uzrA_4466_83276_0 absent 02.11.2008 15:25:41\|rosetta@home\|Starting abinitio_nohomfrag_70_A_1unpA_4466_83485_1 02.11.2008 15:25:41\|rosetta@home\|Starting task abinitio_nohomfrag_70_A_1unpA_4466_83485_1 using minirosetta version 139 02.11.2008 15:42:03\|rosetta@home\|Computation for task abinitio_nohomfrag_70_A_1unpA_4466_83485_1 finished 02.11.2008 15:42:03\|rosetta@home\|Output file abinitio_nohomfrag_70_A_1unpA_4466_83485_1_0 for task abinitio_nohomfrag_70_A_1unpA_4466_83485_1 absent
20) Message boards : Number crunching : Rosetta Mini with new score terms bug thread (Message 56619) Posted 2 Nov 2008 by Rabinovitch Post: Rabinovitch, Looking at the result you iedntified, I noticed that the BOINC version you are using is Version 6.3.19. According to the BOINC site, Version 6.3.19 is not a production version, and is to be used "only for testing." It would be a good idea to use a production version such as Version 6.2.19. Then, an error, if it appears, will be viewed as more legitimate. Thanks for crunching Rosetta! Well, I suppose that most of us are not using a develompenst versions of BOINS Manager. But they meet a bugs anyway... By the way, I'm using it only for crunching PS3GRID WUs.

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