Posts by Rabinovitch

1) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 80390)
Posted 18 Jul 2016 by Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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 Profile 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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